Query Fun_Sp_NP_594698.1 Command /cluster/toolkit/production/bioprogs/hhpred/hhsearch -cal -cpu 4 -v 1 -i /cluster/toolkit/production/tmp/production/94957/8548197.hhm -d /cluster/toolkit/production/databases/hhpred/new_dbs/pdb70_27Dec07/db/pdb.hhm /cluster/toolkit/production/databases/hhpred/new_dbs/scop70_1.72pre/db/scop.hhm /cluster/toolkit/production/databases/hhpred/new_dbs/scop70_1.71/db/scop.hhm /cluster/toolkit/production/databases/hhpred/new_dbs/pfamA_22.0/db/pfamA.hhm /cluster/toolkit/production/databases/hhpred/new_dbs/smart_18Apr07/db/smart.hhm /cluster/toolkit/production/databases/hhpred/new_dbs/panther_13Dec06/db/panther.hmm /cluster/toolkit/production/databases/hhpred/new_dbs/tigrfam_13Dec06/db/tigrfam.hmm /cluster/toolkit/production/databases/hhpred/new_dbs/pirsf_13Dec06/db/pirsf.hmm /cluster/toolkit/production/databases/hhpred/new_dbs/COG_18Apr07/db/COG.hhm /cluster/toolkit/production/databases/hhpred/new_dbs/KOG_18Apr07/db/KOG.hhm /cluster/toolkit/production/databases/hhpred/new_dbs/CATH_13Dec06/db/CATH.hmm /cluster/toolkit/production/databases/hhpred/new_dbs/supfam_13Dec06/db/supfam.hmm /cluster/toolkit/production/databases/hhpred/new_dbs/pfam_18Apr07/db//pfam.hhm /cluster/toolkit/production/databases/hhpred/new_dbs/cd_18Apr07/db/cd.hhm /cluster/toolkit/production/databases/hhpred/new_dbs/test56/db/test56.hhm /cluster/toolkit/production/databases/hhpred/new_dbs/test18/db/test18.hhm -o /cluster/toolkit/production/tmp/production/94957/8548197.hhr -p 20 -P 20 -Z 100 -B 100 -seq 1 -aliw 80 -local -ssm 2 -norealign -sc 1 No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam05783 DLIC Dynein light in 95.7 0.043 4.4E-07 35.7 4.4 84 168-254 237-320 (475) 2 PF05783 DLIC: Dynein light in 93.0 0.34 3.6E-06 29.9 4.0 84 168-254 255-338 (525) 3 PTHR12688 DYNEIN LIGHT INTERME 65.8 15 0.00015 19.5 2.8 84 168-254 154-237 (415) 4 KOG3905 Dynein light intermedi 64.7 24 0.00025 18.1 3.8 84 168-254 242-325 (473) 5 TIGR01513 NAPRTase_put putativ 24.7 2.3E+02 0.0024 11.9 3.3 66 267-332 257-332 (523) 6 cd04279 ZnMc_MMP_like_1 Zinc-d 24.4 1.2E+02 0.0013 13.7 1.9 21 154-174 105-126 (156) 7 d1l8ra_ a.6.1.4 (A:) Retinal d 21.9 1.8E+02 0.0019 12.5 2.4 22 16-37 4-25 (101) 8 d1l8ra_ a.6.1.4 (A:) Retinal d 21.9 1.8E+02 0.0019 12.5 2.4 22 16-37 4-25 (101) 9 1l8r_A Dachshund; winged-helix 19.7 2.2E+02 0.0023 12.1 2.4 22 16-37 4-25 (101) 10 KOG3066 Translin-associated pr 18.5 7.1E+02 0.0074 8.7 4.8 68 272-339 167-235 (271) No 1 >pfam05783 DLIC Dynein light intermediate chain (DLIC). This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo. Probab=95.71 E-value=0.043 Score=35.67 Aligned_columns=84 Identities=27% Q ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHEEHHHHHHHHCCCCCHHHHHHCCCEEECCCCHHHHHHH Q ss_conf 22345428999999998875157520267413776633300000012356414863101221122402426414568888 Q Fun_Sp_NP_5946 168 HTSVDNSQEFILQFLRTTLLSVPTSSIVSISADPTSWNNLNVLMKYNFMFQKFKPRDFHAQTIQSETMFIPPCWDTISKI 247 (340) Q Consensus 168 htsvdnsqefilqflrttllsvptssivsisadptswnnlnvlmkynfmfqkfkprdfhaqtiqsetmfippcwdtiski 247 (340) |.--|.--.||+||||+-+|+--.+-|-...-.+ .|+.+|.||-.----=-|-.-.|+.+.-+..|||.-||.-.|| T Consensus 237 ~~ykeE~fDfIqq~LR~~cLqYGAsLiYTS~ke~---kNldlLykYl~HrlYgfpf~~~a~VvekDaIfIPsGWDn~kKI 313 (475) T pfam05783 237 HDYRDEHFDFIQSHLRKFCLQYGAALIYTSVKET---KNIDLLYKYIVHRSYGFPFTTPALVVEKDAVFIPAGWDNEKKI 313 (475) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCEEEEECCCCC---CCHHHHHHHHHHHHHCCCCCCCCCEEEHHEEEECCCCCCHHHH T ss_conf 5664367999999999999870975898547764---2389999999988607654562200100003405888814556 Q ss_pred HHCCCHH Q ss_conf 6404112 Q Fun_Sp_NP_5946 248 QSVNHEF 254 (340) Q Consensus 248 qsvnhef 254 (340) .-....| T Consensus 314 ~Il~Enf 320 (475) T pfam05783 314 DILHENF 320 (475) T ss_pred HHHHCCC T ss_conf 7543365 No 2 >PF05783 DLIC: Dynein light intermediate chain (DLIC); InterPro: IPR008467 This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo .; GO: 0003774 motor activity Probab=93.00 E-value=0.34 Score=29.88 Aligned_columns=84 Identities=30% Q ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHEEHHHHHHHHCCCCCHHHHHHCCCEEECCCCHHHHHHH Q ss_conf 22345428999999998875157520267413776633300000012356414863101221122402426414568888 Q Fun_Sp_NP_5946 168 HTSVDNSQEFILQFLRTTLLSVPTSSIVSISADPTSWNNLNVLMKYNFMFQKFKPRDFHAQTIQSETMFIPPCWDTISKI 247 (340) Q Consensus 168 htsvdnsqefilqflrttllsvptssivsisadptswnnlnvlmkynfmfqkfkprdfhaqtiqsetmfippcwdtiski 247 (340) |.--|..-+||.|++|+-.|..-.+-|......+ .|+.+|.||-.----=-|-.-.|+.+.-+..|||.-||...|| T Consensus 255 ~d~kdE~fDfIqq~lR~fcL~yGAsLiYTSvKe~---kN~dllykYi~HrlYgf~f~~~a~vvekdavfiPaGwDn~kKI 331 (525) T PF05783_consen 255 HDYKDEHFDFIQQHLRRFCLQYGASLIYTSVKEE---KNIDLLYKYIVHRLYGFPFKTPAQVVEKDAVFIPAGWDNLKKI 331 (525) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCC---CCHHHHHHHHHHHHCCCCCCCCCEEEECCCEEECCCCCCHHHH T ss_conf 4752778999999999999760740467404552---1089999999887607755774303410001203676511333 Q ss_pred HHCCCHH Q ss_conf 6404112 Q Fun_Sp_NP_5946 248 QSVNHEF 254 (340) Q Consensus 248 qsvnhef 254 (340) +-....| T Consensus 332 ~Il~En~ 338 (525) T PF05783_consen 332 SILHENF 338 (525) T ss_pred HHHHHCC T ss_conf 4432033 No 3 >PTHR12688 DYNEIN LIGHT INTERMEDIATE CHAIN; InterPro: IPR008467 This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo .; GO: 0003774 motor activity. Probab=65.81 E-value=15 Score=19.51 Aligned_columns=84 Identities=26% Q ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHEEHHHHHHHHCCCCCHHHHHHCCCEEECCCCHHHHHHH Q ss_conf 22345428999999998875157520267413776633300000012356414863101221122402426414568888 Q Fun_Sp_NP_5946 168 HTSVDNSQEFILQFLRTTLLSVPTSSIVSISADPTSWNNLNVLMKYNFMFQKFKPRDFHAQTIQSETMFIPPCWDTISKI 247 (340) Q Consensus 168 htsvdnsqefilqflrttllsvptssivsisadptswnnlnvlmkynfmfqkfkprdfhaqtiqsetmfippcwdtiski 247 (340) |.--|..-.||.++||.-.|+...+-|..--... .|+..|.||-.----=-|-..-|.-+..+..|||+-||.-.|| T Consensus 154 ~dyrdehfDfiq~~lR~fcL~yga~L~ytsvke~---kN~dLlykYivh~~yGf~f~~~a~VvekdavfiPaGWD~~kKI 230 (415) T PTHR12688 154 HDYRDEHFDFIQSHLRKFCLQYGAALIYTSVKEE---KNIDLLYKYIVHKLYGFPFTIPALVVEKDAVFIPAGWDNEKKI 230 (415) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHCCCCCCCHHHEEEEEEEEECCCCCCHHHH T ss_conf 0312889999999999999984025311010013---3489999999888606543440111220004516898807788 Q ss_pred HHCCCHH Q ss_conf 6404112 Q Fun_Sp_NP_5946 248 QSVNHEF 254 (340) Q Consensus 248 qsvnhef 254 (340) .-....| T Consensus 231 ~il~enf 237 (415) T PTHR12688 231 GILHENF 237 (415) T ss_pred HHHHCCC T ss_conf 9876052 No 4 >KOG3905 Dynein light intermediate chain [Cell motility] Probab=64.74 E-value=24 Score=18.11 Aligned_columns=84 Identities=27% Q ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHEEHHHHHHHHCCCCCHHHHHHCCCEEECCCCHHHHHHH Q ss_conf 22345428999999998875157520267413776633300000012356414863101221122402426414568888 Q Fun_Sp_NP_5946 168 HTSVDNSQEFILQFLRTTLLSVPTSSIVSISADPTSWNNLNVLMKYNFMFQKFKPRDFHAQTIQSETMFIPPCWDTISKI 247 (340) Q Consensus 168 htsvdnsqefilqflrttllsvptssivsisadptswnnlnvlmkynfmfqkfkprdfhaqtiqsetmfippcwdtiski 247 (340) |.--|..-.||-+.+|.--|+.-++-|..-.... .|+.+|.||-.----=-|-.--|+.+..+..|||.-||.-.|| T Consensus 242 ~eyrDehfdfiq~~lRkFCLr~GaaLiyTSvKE~---KNidllyKYivhr~yG~~fttpAlVVEkdaVfIPAGWD~eKKI 318 (473) T KOG3905 242 HEYRDEHFDFIQSHLRKFCLRYGAALIYTSVKET---KNIDLLYKYIVHRSYGFPFTTPALVVEKDAVFIPAGWDNEKKI 318 (473) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCC---CCHHHHHHHHHHHHCCCCCCCHHHEEECCEEEECCCCCCCCHH T ss_conf 1001678999999999999860630255411124---5568888888876415531350012320314630466863002 Q ss_pred HHCCCHH Q ss_conf 6404112 Q Fun_Sp_NP_5946 248 QSVNHEF 254 (340) Q Consensus 248 qsvnhef 254 (340) .-....| T Consensus 319 ~Il~En~ 325 (473) T KOG3905 319 DILHENF 325 (473) T ss_pred HHHHCCC T ss_conf 2100035 No 5 >TIGR01513 NAPRTase_put putative nicotinate phosphoribosyltransferase; InterPro: IPR006405 A deep split separates two related families of proteins, one of which includes experimentally characterised examples of nicotinate phosphoribosyltransferase, the first enzyme of NAD salvage biosynthesis. This entry represents the other family. Members have a different (longer) spacing of several key motifs and have an additional C-terminal domain of up to 100 residues. One argument suggesting that this family represents the same enzyme is that no species has a member of both families. Another is that the gene encoding this protein is located near other NAD salvage biosynthesis genes in Nostoc and in at least four different Gram-positive bacteria. NAD and NADP are ubiquitous in life. Most members of this family are from Gram-positive bacteria. An additional set of mutually closely related archaeal sequences score between the trusted and noise cut-offs. . Probab=24.73 E-value=2.3e+02 Score=11.90 Aligned_columns=66 Identities=26% Q ss_pred HHHHH--HHHHHHHHHHHHHHHC-CCCCCCCCCCCCHHHHHHHHHHHHHH-------HHHHHHCCCCCCCHHHHHH Q ss_conf 64566--8898777730011100-13333556777605789999999745-------7763100134433567777 Q Fun_Sp_NP_5946 267 YDTLD--ISLLLGLFDKSISMLN-CHSSKISDGDIPYKSHQVFLQELQNK-------YSEIKTYSSNKLNKSSIKS 332 (340) Q Consensus 267 ydtld--islllglfdksismln-chsskisdgdipykshqvflqelqnk-------yseiktyssnklnkssiks 332 (340) ||||. +.-.+-++..-=.-.+ .-+-.|.-||+-|-|.++=-+==++- ..+.|-|-||.|...+|+. T Consensus 257 YDtL~SG~~nai~va~eLg~~~~~~~gVRiDSGDL~~LSk~~R~~LD~AGaqfqvPWL~~vkI~VSn~LDE~~I~~ 332 (523) T TIGR01513 257 YDTLRSGLPNAIAVAKELGEQGKEVVGVRIDSGDLAYLSKKVRKELDEAGAQFQVPWLEEVKIVVSNDLDENSIAA 332 (523) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEEEEEEECHHHHHHHHHHHHHHHHHHCHHCCCCCHHCCEEEEECCCCHHHHHH T ss_conf 6677678999999999975205505889961177999999999999861111158600375489967404789999 No 6 >cd04279 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin. Probab=24.43 E-value=1.2e+02 Score=13.68 Aligned_columns=21 Identities=43% Q ss_pred HHHHHHHHHHHHCC-CCCCCCH Q ss_conf 89999998877323-2234542 Q Fun_Sp_NP_5946 154 FTVVLKQLKHALGL-HTSVDNS 174 (340) Q Consensus 154 ftvvlkqlkhalgl-htsvdns 174 (340) |.|.+..+-||||| |.|...+ T Consensus 105 ~~vA~HElGHaLGL~Hss~~~~ 126 (156) T cd04279 105 QAIALHELGHALGLWHHSDRPE 126 (156) T ss_pred HHHHHHHHHHHHCCCCCCCCCC T ss_conf 8888987556532576777611 No 7 >d1l8ra_ a.6.1.4 (A:) Retinal determination protein Dachshund {Human (Homo sapiens)} SCOP: d1l8rb_ Probab=21.93 E-value=1.8e+02 Score=12.53 Aligned_columns=22 Identities=27% Q ss_pred CCCCCEEEECEEEEEEEEECCC Q ss_conf 0220211101046777520110 Q Fun_Sp_NP_5946 16 SNDCETVNFRGIAYKCFFTKDQ 37 (340) Q Consensus 16 sndcetvnfrgiaykcfftkdq 37 (340) ||||++|.++|..--||.-..+ T Consensus 4 ~n~c~~v~l~G~~i~~f~v~G~ 25 (101) T d1l8ra_ 4 NNECKMVDLRGAKVASFTVEGC 25 (101) T ss_dssp GGCCEEEEETTEEEEEEEETTE T ss_pred CCCEEEEEECCEEEEEEEECCC T ss_conf 7502688841326888886682 No 8 >d1l8ra_ a.6.1.4 (A:) Retinal determination protein Dachshund {Human (Homo sapiens)} Probab=21.88 E-value=1.8e+02 Score=12.52 Aligned_columns=22 Identities=27% Q ss_pred CCCCCEEEECEEEEEEEEECCC Q ss_conf 0220211101046777520110 Q Fun_Sp_NP_5946 16 SNDCETVNFRGIAYKCFFTKDQ 37 (340) Q Consensus 16 sndcetvnfrgiaykcfftkdq 37 (340) ||||++|.++|..--||.-..+ T Consensus 4 ~n~c~~v~l~G~~i~~f~v~G~ 25 (101) T d1l8ra_ 4 NNECKMVDLRGAKVASFTVEGC 25 (101) T ss_dssp GGCCEEEEETTEEEEEEEETTE T ss_pred CCCEEEEEECCEEEEEEEECCC T ss_conf 7502688841326888875682 No 9 >1l8r_A Dachshund; winged-helix; 1.65A {Homo sapiens} SCOP: a.6.1.4 Probab=19.73 E-value=2.2e+02 Score=12.05 Aligned_columns=22 Identities=27% Q ss_pred CCCCCEEEECEEEEEEEEECCC Q ss_conf 0220211101046777520110 Q Fun_Sp_NP_5946 16 SNDCETVNFRGIAYKCFFTKDQ 37 (340) Q Consensus 16 sndcetvnfrgiaykcfftkdq 37 (340) ||||++|.++|..--||.-+.+ T Consensus 4 ~n~c~~v~l~G~~i~~f~v~G~ 25 (101) T 1l8r_A 4 NNECKMVDLRGAKVASFTVEGC 25 (101) T ss_dssp GGCCEEEEETTEEEEEEEETTE T ss_pred CCCEEEEEECCEEEEEEEECCC T ss_conf 7512688742437888886691 No 10 >KOG3066 Translin-associated protein X [General function prediction only] Probab=18.54 E-value=7.1e+02 Score=8.75 Aligned_columns=68 Identities=26% Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHH-HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH Q ss_conf 8898777730011100133335567776057899-9999974577631001344335677778999860 Q Fun_Sp_NP_5946 272 ISLLLGLFDKSISMLNCHSSKISDGDIPYKSHQV-FLQELQNKYSEIKTYSSNKLNKSSIKSSLWKDLI 339 (340) Q Consensus 272 islllglfdksismlnchsskisdgdipykshqv-flqelqnkyseiktyssnklnkssiksslwkdli 339 (340) |..+||+-|-.-....---..+|+|+|..-..|+ ||..+....|+|..-.+.+..-++--+.+-..++ T Consensus 167 iDYvLGvaDlTGElMRm~I~~~s~g~I~~~~~~~qFlRqih~~~s~i~~~~~~~ye~~~Kl~vm~qSi~ 235 (271) T KOG3066 167 IDYVLGVADLTGELMRMLITNGSKGSIQQLTQQVQFLRQLHKNCSEIEHLPSKKYELQQKLSVMEQSIS 235 (271) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH T ss_conf 888886875579999998406887523548999999999863121001579864788899999999898 Done!