Query psy9785
Match_columns 63
No_of_seqs 103 out of 236
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 19:31:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9785.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9785hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0696|consensus 99.6 1.3E-16 2.7E-21 124.1 0.2 50 14-63 18-67 (683)
2 KOG0694|consensus 99.1 1.9E-11 4.2E-16 97.2 2.1 41 23-63 140-180 (694)
3 KOG0695|consensus 98.9 2.1E-10 4.6E-15 88.4 -1.5 41 23-63 112-152 (593)
4 PF00130 C1_1: Phorbol esters/ 97.7 2.5E-05 5.5E-10 42.7 2.4 22 42-63 1-22 (53)
5 smart00109 C1 Protein kinase C 97.3 0.00012 2.7E-09 38.3 1.7 22 42-63 1-22 (49)
6 cd00029 C1 Protein kinase C co 97.3 9.1E-05 2E-09 39.3 1.1 22 42-63 1-22 (50)
7 KOG4236|consensus 94.0 0.011 2.3E-07 48.5 -0.8 27 37-63 141-167 (888)
8 KOG0696|consensus 92.6 0.03 6.5E-07 44.8 -0.3 24 40-63 109-132 (683)
9 KOG0694|consensus 85.1 0.23 5E-06 40.6 -0.4 24 40-63 229-252 (694)
10 KOG1011|consensus 79.9 0.64 1.4E-05 39.2 0.3 28 36-63 164-194 (1283)
11 KOG4239|consensus 68.3 1.5 3.2E-05 33.5 -0.3 28 36-63 46-73 (348)
12 KOG4236|consensus 60.7 1.7 3.8E-05 36.0 -1.2 23 40-62 266-288 (888)
13 COG4306 Uncharacterized protei 54.4 6.1 0.00013 27.1 0.8 26 38-63 54-80 (160)
14 PF02148 zf-UBP: Zn-finger in 50.3 9.8 0.00021 21.3 1.1 27 37-63 34-60 (63)
15 TIGR03831 YgiT_finger YgiT-typ 50.1 19 0.00042 18.2 2.2 24 37-62 18-42 (46)
16 PF14392 zf-CCHC_4: Zinc knuck 39.5 25 0.00055 18.9 1.7 15 46-60 25-39 (49)
17 PF07503 zf-HYPF: HypF finger; 38.7 16 0.00034 19.1 0.7 17 47-63 16-32 (35)
18 COG3627 PhnJ Uncharacterized e 36.8 23 0.0005 26.2 1.6 31 28-60 210-251 (291)
19 KOG2996|consensus 35.2 11 0.00024 31.5 -0.3 25 38-62 520-544 (865)
20 PF06007 PhnJ: Phosphonate met 34.9 22 0.00048 26.5 1.2 31 28-60 202-243 (277)
21 PF06220 zf-U1: U1 zinc finger 31.7 21 0.00046 18.7 0.5 10 53-62 4-13 (38)
22 KOG0190|consensus 30.5 21 0.00046 28.3 0.6 23 38-61 38-60 (493)
23 KOG3564|consensus 28.3 13 0.00028 30.3 -1.0 22 41-62 286-307 (604)
24 KOG3362|consensus 26.3 26 0.00057 24.1 0.4 10 50-59 116-125 (156)
25 KOG4684|consensus 24.6 29 0.00062 25.7 0.3 10 54-63 172-182 (275)
26 PF09788 Tmemb_55A: Transmembr 24.1 34 0.00074 25.2 0.6 11 53-63 158-169 (256)
27 PRK11582 flagella biosynthesis 23.1 32 0.0007 24.0 0.3 13 50-62 20-32 (169)
28 PF06463 Mob_synth_C: Molybden 22.9 33 0.00071 21.9 0.3 26 34-60 49-77 (128)
29 TIGR03823 FliZ flagellar regul 22.4 32 0.0007 24.0 0.2 13 50-62 20-32 (168)
30 PF13248 zf-ribbon_3: zinc-rib 22.2 34 0.00074 16.2 0.2 9 52-60 16-24 (26)
31 PF10083 DUF2321: Uncharacteri 21.9 53 0.0011 22.7 1.2 14 47-60 63-76 (158)
32 PF04828 GFA: Glutathione-depe 20.2 30 0.00065 19.3 -0.2 13 51-63 47-59 (92)
No 1
>KOG0696|consensus
Probab=99.60 E-value=1.3e-16 Score=124.09 Aligned_cols=50 Identities=64% Similarity=1.091 Sum_probs=44.7
Q ss_pred CccccccccccccccchhhhcceeecCCceeeeeecCCccccCCCCCccC
Q psy9785 14 NDMNTKFGLKIRGRKGALKKKNVYNVKDHKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 14 ~~~~~~~~~~~~~RrgA~r~kKVh~v~GH~F~a~~f~qptfCa~C~efIW 63 (63)
++.+....+..+.|+||+|++.||+|++|+|.++||+|||||+||.||||
T Consensus 18 ~e~~~~~~~~~f~RkGAlrqKnvhevk~HkF~aRFFKqPTfCsHCkDFiw 67 (683)
T KOG0696|consen 18 GESEGENSMKRFLRKGALRQKNVHEVKSHKFIARFFKQPTFCSHCKDFIW 67 (683)
T ss_pred CcccchhHHHHHHhhhhhhhcchhhhccceeeehhccCCchhhhhhhhee
Confidence 44455556667789999999999999999999999999999999999999
No 2
>KOG0694|consensus
Probab=99.13 E-value=1.9e-11 Score=97.16 Aligned_cols=41 Identities=41% Similarity=0.883 Sum_probs=37.6
Q ss_pred ccccccchhhhcceeecCCceeeeeecCCccccCCCCCccC
Q psy9785 23 KIRGRKGALKKKNVYNVKDHKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 23 ~~~~RrgA~r~kKVh~v~GH~F~a~~f~qptfCa~C~efIW 63 (63)
....|+||+.++|||+|.||+|++++|+|||+|++|++|||
T Consensus 140 ~~~~rrga~~~~kVhei~gH~F~aT~l~Qpt~Cs~C~kFi~ 180 (694)
T KOG0694|consen 140 SKPRRRGAISQSKVHEIDGHKFGATSLRQPTFCSWCQKFIW 180 (694)
T ss_pred cCcccccccccceeEEeeCcEEEEeeccCcchhhhhhhhee
Confidence 34458889888999999999999999999999999999999
No 3
>KOG0695|consensus
Probab=98.86 E-value=2.1e-10 Score=88.36 Aligned_cols=41 Identities=32% Similarity=0.705 Sum_probs=39.0
Q ss_pred ccccccchhhhcceeecCCceeeeeecCCccccCCCCCccC
Q psy9785 23 KIRGRKGALKKKNVYNVKDHKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 23 ~~~~RrgA~r~kKVh~v~GH~F~a~~f~qptfCa~C~efIW 63 (63)
....||||+||+|+|..|||.|.++.|+++++|..|.|.||
T Consensus 112 ksiyrrgarrwrkly~~ngh~fqakr~nrr~~c~ic~d~iw 152 (593)
T KOG0695|consen 112 KSIYRRGARRWRKLYRANGHLFQAKRFNRRAYCGICSDRIW 152 (593)
T ss_pred chHHHhHHHHHHHHHhhcCcchhhhhhccceeeeechhhhh
Confidence 35679999999999999999999999999999999999999
No 4
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=97.74 E-value=2.5e-05 Score=42.66 Aligned_cols=22 Identities=50% Similarity=1.389 Sum_probs=19.4
Q ss_pred ceeeeeecCCccccCCCCCccC
Q psy9785 42 HKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 42 H~F~a~~f~qptfCa~C~efIW 63 (63)
|.|+.+.|.+|++|++|+++||
T Consensus 1 H~f~~~~~~~~~~C~~C~~~i~ 22 (53)
T PF00130_consen 1 HHFVPTTFSKPTYCDVCGKFIW 22 (53)
T ss_dssp -EEEEEESSSTEB-TTSSSBEC
T ss_pred CeEEEccCCCCCCCcccCcccC
Confidence 8999999999999999999997
No 5
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=97.34 E-value=0.00012 Score=38.34 Aligned_cols=22 Identities=50% Similarity=1.164 Sum_probs=20.8
Q ss_pred ceeeeeecCCccccCCCCCccC
Q psy9785 42 HKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 42 H~F~a~~f~qptfCa~C~efIW 63 (63)
|.|+...+.+|++|.+|+++||
T Consensus 1 H~~~~~~~~~~~~C~~C~~~i~ 22 (49)
T smart00109 1 HHFVERTFKKPTKCCVCRKSIW 22 (49)
T ss_pred CceEEeccCCCCCccccccccC
Confidence 7899999999999999999998
No 6
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=97.33 E-value=9.1e-05 Score=39.32 Aligned_cols=22 Identities=45% Similarity=1.213 Sum_probs=21.0
Q ss_pred ceeeeeecCCccccCCCCCccC
Q psy9785 42 HKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 42 H~F~a~~f~qptfCa~C~efIW 63 (63)
|.|+...+.+|++|++|.++||
T Consensus 1 H~f~~~~~~~~~~C~~C~~~i~ 22 (50)
T cd00029 1 HRFVRKSFFKPTFCDVCRKSIW 22 (50)
T ss_pred CccEEeeCCCCCChhhcchhhh
Confidence 8899999999999999999998
No 7
>KOG4236|consensus
Probab=94.02 E-value=0.011 Score=48.46 Aligned_cols=27 Identities=26% Similarity=0.915 Sum_probs=24.0
Q ss_pred eecCCceeeeeecCCccccCCCCCccC
Q psy9785 37 YNVKDHKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 37 h~v~GH~F~a~~f~qptfCa~C~efIW 63 (63)
..|.-|.+-.+-++.||||++|+|.+|
T Consensus 141 ~~i~PH~l~vhSY~~PtFCD~CGEmL~ 167 (888)
T KOG4236|consen 141 FQIRPHTLFVHSYKAPTFCDFCGEMLF 167 (888)
T ss_pred eeeecceeeeecccCchHHHHHHHHHH
Confidence 356789999999999999999999887
No 8
>KOG0696|consensus
Probab=92.59 E-value=0.03 Score=44.83 Aligned_cols=24 Identities=38% Similarity=0.982 Sum_probs=20.8
Q ss_pred CCceeeeeecCCccccCCCCCccC
Q psy9785 40 KDHKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 40 ~GH~F~a~~f~qptfCa~C~efIW 63 (63)
.-|+|..+.+..||||+||+.+++
T Consensus 109 ~kHkf~~~tYssPTFCDhCGsLLy 132 (683)
T KOG0696|consen 109 SKHKFKIHTYSSPTFCDHCGSLLY 132 (683)
T ss_pred cccceeeeecCCCchhhhHHHHHH
Confidence 349999999999999999998653
No 9
>KOG0694|consensus
Probab=85.15 E-value=0.23 Score=40.63 Aligned_cols=24 Identities=33% Similarity=0.913 Sum_probs=21.9
Q ss_pred CCceeeeeecCCccccCCCCCccC
Q psy9785 40 KDHKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 40 ~GH~F~a~~f~qptfCa~C~efIW 63 (63)
+.|.|..+...+|+||.||+.++|
T Consensus 229 ~Phrf~~~~~q~ptFc~hCGs~L~ 252 (694)
T KOG0694|consen 229 NPHRFVKLNRQRPTFCDHCGSVLY 252 (694)
T ss_pred CCCcchhhhccCccHHHhcchhhh
Confidence 349999999999999999999876
No 10
>KOG1011|consensus
Probab=79.90 E-value=0.64 Score=39.20 Aligned_cols=28 Identities=36% Similarity=1.077 Sum_probs=24.8
Q ss_pred eeec---CCceeeeeecCCccccCCCCCccC
Q psy9785 36 VYNV---KDHKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 36 Vh~v---~GH~F~a~~f~qptfCa~C~efIW 63 (63)
+|.| ..|.|....|..||||.-|...+|
T Consensus 164 iypis~ttphnf~~~t~~tpt~cyecegllw 194 (1283)
T KOG1011|consen 164 IYPISATTPHNFATTTFQTPTFCYECEGLLW 194 (1283)
T ss_pred eeecccCCCCceeeeeccCCchhhhhhhHHH
Confidence 5555 469999999999999999999998
No 11
>KOG4239|consensus
Probab=68.33 E-value=1.5 Score=33.51 Aligned_cols=28 Identities=36% Similarity=0.912 Sum_probs=24.8
Q ss_pred eeecCCceeeeeecCCccccCCCCCccC
Q psy9785 36 VYNVKDHKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 36 Vh~v~GH~F~a~~f~qptfCa~C~efIW 63 (63)
+...+||.|-.....-|+-|+-|+||||
T Consensus 46 lv~~r~~~~~~~g~~~~~~~~~c~~~~~ 73 (348)
T KOG4239|consen 46 LVPLRGHNFYTAGLLLPTWCDKCGDFIW 73 (348)
T ss_pred eeeccccccccccccccccchhhhHHHH
Confidence 3445899999999999999999999998
No 12
>KOG4236|consensus
Probab=60.66 E-value=1.7 Score=36.02 Aligned_cols=23 Identities=35% Similarity=0.827 Sum_probs=20.3
Q ss_pred CCceeeeeecCCccccCCCCCcc
Q psy9785 40 KDHKFIPRFFKQPTFCSHCKDFI 62 (63)
Q Consensus 40 ~GH~F~a~~f~qptfCa~C~efI 62 (63)
--|.|+.+-+++||-|.+|+..+
T Consensus 266 vPHTf~vHSY~rpTVCq~CkkLL 288 (888)
T KOG4236|consen 266 VPHTFIVHSYTRPTVCQYCKKLL 288 (888)
T ss_pred CCeeEEEeeccCchHHHHHHHHH
Confidence 36999999999999999998653
No 13
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.41 E-value=6.1 Score=27.05 Aligned_cols=26 Identities=27% Similarity=0.691 Sum_probs=17.2
Q ss_pred ecCCceeeeeecCCccccCCCCC-ccC
Q psy9785 38 NVKDHKFIPRFFKQPTFCSHCKD-FIW 63 (63)
Q Consensus 38 ~v~GH~F~a~~f~qptfCa~C~e-fIW 63 (63)
.|.|=.-.-.-+..|+||..|+. |-|
T Consensus 54 ~vegvlglg~dye~psfchncgs~fpw 80 (160)
T COG4306 54 YVEGVLGLGGDYEPPSFCHNCGSRFPW 80 (160)
T ss_pred eeeeeeccCCCCCCcchhhcCCCCCCc
Confidence 34443334455678999999998 445
No 14
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=50.35 E-value=9.8 Score=21.34 Aligned_cols=27 Identities=19% Similarity=0.630 Sum_probs=21.1
Q ss_pred eecCCceeeeeecCCccccCCCCCccC
Q psy9785 37 YNVKDHKFIPRFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 37 h~v~GH~F~a~~f~qptfCa~C~efIW 63 (63)
++..||.+....=..-.+|..|.++|.
T Consensus 34 ~~~~~H~l~v~~~~~~i~C~~C~~~v~ 60 (63)
T PF02148_consen 34 YKETGHPLAVSLSTGSIWCYACDDYVY 60 (63)
T ss_dssp HHHHT--EEEETTTTCEEETTTTEEEE
T ss_pred hcccCCeEEEECCCCeEEEcCCCcEEe
Confidence 356799999988888899999999873
No 15
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=50.12 E-value=19 Score=18.16 Aligned_cols=24 Identities=17% Similarity=0.469 Sum_probs=16.9
Q ss_pred eecCCceeeeeecCCcc-ccCCCCCcc
Q psy9785 37 YNVKDHKFIPRFFKQPT-FCSHCKDFI 62 (63)
Q Consensus 37 h~v~GH~F~a~~f~qpt-fCa~C~efI 62 (63)
....|+..+.+.+ |. +|..|++.+
T Consensus 18 ~~~~~~~~~i~~v--p~~~C~~CGE~~ 42 (46)
T TIGR03831 18 YEYGGELIVIENV--PALVCPQCGEEY 42 (46)
T ss_pred EEeCCEEEEEeCC--CccccccCCCEe
Confidence 3456777766665 54 699999865
No 16
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=39.52 E-value=25 Score=18.88 Aligned_cols=15 Identities=33% Similarity=0.941 Sum_probs=12.1
Q ss_pred eeecCCccccCCCCC
Q psy9785 46 PRFFKQPTFCSHCKD 60 (63)
Q Consensus 46 a~~f~qptfCa~C~e 60 (63)
.++=+.|.||.+|+-
T Consensus 25 v~YE~lp~~C~~C~~ 39 (49)
T PF14392_consen 25 VKYERLPRFCFHCGR 39 (49)
T ss_pred EEECCcChhhcCCCC
Confidence 356688999999985
No 17
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=38.66 E-value=16 Score=19.07 Aligned_cols=17 Identities=29% Similarity=0.426 Sum_probs=9.9
Q ss_pred eecCCccccCCCCCccC
Q psy9785 47 RFFKQPTFCSHCKDFIW 63 (63)
Q Consensus 47 ~~f~qptfCa~C~efIW 63 (63)
+|..|++-|.+|+=.+|
T Consensus 16 R~~~~~isC~~CGPr~~ 32 (35)
T PF07503_consen 16 RFHYQFISCTNCGPRYS 32 (35)
T ss_dssp TTT-TT--BTTCC-SCC
T ss_pred cccCcCccCCCCCCCEE
Confidence 56679999999986554
No 18
>COG3627 PhnJ Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=36.80 E-value=23 Score=26.18 Aligned_cols=31 Identities=35% Similarity=0.749 Sum_probs=23.5
Q ss_pred cchhhhcceeec-----------CCceeeeeecCCccccCCCCC
Q psy9785 28 KGALKKKNVYNV-----------KDHKFIPRFFKQPTFCSHCKD 60 (63)
Q Consensus 28 rgA~r~kKVh~v-----------~GH~F~a~~f~qptfCa~C~e 60 (63)
-||.|.+++|-+ ..|-|-...+..| |+.|+.
T Consensus 210 fGAGREKRiYAvPP~T~V~SLDF~DHPFevq~wd~~--CalCgs 251 (291)
T COG3627 210 FGAGREKRIYAVPPFTRVESLDFDDHPFEVQQWDEP--CALCGS 251 (291)
T ss_pred hcCCcceeeEecCCcceeeecccCCCcceeeecccc--hhhhCc
Confidence 377888888866 3588888888665 888875
No 19
>KOG2996|consensus
Probab=35.22 E-value=11 Score=31.50 Aligned_cols=25 Identities=28% Similarity=0.615 Sum_probs=21.8
Q ss_pred ecCCceeeeeecCCccccCCCCCcc
Q psy9785 38 NVKDHKFIPRFFKQPTFCSHCKDFI 62 (63)
Q Consensus 38 ~v~GH~F~a~~f~qptfCa~C~efI 62 (63)
..++|.|.-+.|..+|-|..|.-++
T Consensus 520 ~an~H~fqmhtF~~~tsCkvC~mll 544 (865)
T KOG2996|consen 520 RANNHDFQMHTFKNTTSCKVCQMLL 544 (865)
T ss_pred cccCcceEEEeccCCcchHHHHHHh
Confidence 4589999999999999999997654
No 20
>PF06007 PhnJ: Phosphonate metabolism protein PhnJ; InterPro: IPR010306 This family consists of several bacterial phosphonate metabolism (PhnJ) sequences. The exact role that PhnJ plays in phosphonate utilisation is unknown.; GO: 0042916 alkylphosphonate transport
Probab=34.89 E-value=22 Score=26.48 Aligned_cols=31 Identities=32% Similarity=0.547 Sum_probs=23.0
Q ss_pred cchhhhcceeecCC-----------ceeeeeecCCccccCCCCC
Q psy9785 28 KGALKKKNVYNVKD-----------HKFIPRFFKQPTFCSHCKD 60 (63)
Q Consensus 28 rgA~r~kKVh~v~G-----------H~F~a~~f~qptfCa~C~e 60 (63)
=||.|.+|+|-|+- |-|....|.. .|+.|+.
T Consensus 202 fGAGREkrIYAvPPyT~V~sL~FeD~pF~~e~~~~--~C~~CGs 243 (277)
T PF06007_consen 202 FGAGREKRIYAVPPYTDVESLDFEDHPFEVERFDG--PCALCGS 243 (277)
T ss_pred hcCCcceeeeecCCCccccccCccCCCCccccccC--cccccCC
Confidence 48889999997754 5566666655 7999974
No 21
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=31.68 E-value=21 Score=18.65 Aligned_cols=10 Identities=30% Similarity=1.202 Sum_probs=4.4
Q ss_pred cccCCCCCcc
Q psy9785 53 TFCSHCKDFI 62 (63)
Q Consensus 53 tfCa~C~efI 62 (63)
-||.+|.-+|
T Consensus 4 yyCdyC~~~~ 13 (38)
T PF06220_consen 4 YYCDYCKKYL 13 (38)
T ss_dssp -B-TTT--B-
T ss_pred eeccccccee
Confidence 4899998765
No 22
>KOG0190|consensus
Probab=30.52 E-value=21 Score=28.32 Aligned_cols=23 Identities=35% Similarity=0.924 Sum_probs=18.6
Q ss_pred ecCCceeeeeecCCccccCCCCCc
Q psy9785 38 NVKDHKFIPRFFKQPTFCSHCKDF 61 (63)
Q Consensus 38 ~v~GH~F~a~~f~qptfCa~C~ef 61 (63)
.|.||.|+---|..| .|.||+..
T Consensus 38 ~i~~~~~vlVeFYAP-WCghck~L 60 (493)
T KOG0190|consen 38 TINGHEFVLVEFYAP-WCGHCKAL 60 (493)
T ss_pred HhccCceEEEEEEch-hhhhhhhh
Confidence 357999997777788 99999853
No 23
>KOG3564|consensus
Probab=28.27 E-value=13 Score=30.26 Aligned_cols=22 Identities=32% Similarity=0.591 Sum_probs=20.2
Q ss_pred CceeeeeecCCccccCCCCCcc
Q psy9785 41 DHKFIPRFFKQPTFCSHCKDFI 62 (63)
Q Consensus 41 GH~F~a~~f~qptfCa~C~efI 62 (63)
-|.|+.+.+..|-+|-+|+..|
T Consensus 286 ~htfi~kt~~~~~~Cv~C~krI 307 (604)
T KOG3564|consen 286 LHTFISKTVIKPENCVPCGKRI 307 (604)
T ss_pred cchhhHhhccCcccchhhhhhh
Confidence 4999999999999999999866
No 24
>KOG3362|consensus
Probab=26.33 E-value=26 Score=24.15 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=8.1
Q ss_pred CCccccCCCC
Q psy9785 50 KQPTFCSHCK 59 (63)
Q Consensus 50 ~qptfCa~C~ 59 (63)
-+.+||+.|+
T Consensus 116 P~r~fCaVCG 125 (156)
T KOG3362|consen 116 PLRKFCAVCG 125 (156)
T ss_pred CcchhhhhcC
Confidence 3568999998
No 25
>KOG4684|consensus
Probab=24.55 E-value=29 Score=25.68 Aligned_cols=10 Identities=40% Similarity=1.431 Sum_probs=7.2
Q ss_pred ccCCCCC-ccC
Q psy9785 54 FCSHCKD-FIW 63 (63)
Q Consensus 54 fCa~C~e-fIW 63 (63)
-|.||+| |+|
T Consensus 172 ~CgHC~~tFLf 182 (275)
T KOG4684|consen 172 KCGHCNETFLF 182 (275)
T ss_pred EecCccceeeh
Confidence 5788887 665
No 26
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=24.15 E-value=34 Score=25.22 Aligned_cols=11 Identities=36% Similarity=1.395 Sum_probs=7.7
Q ss_pred cccCCCCC-ccC
Q psy9785 53 TFCSHCKD-FIW 63 (63)
Q Consensus 53 tfCa~C~e-fIW 63 (63)
.-|+||.+ |+|
T Consensus 158 v~CghC~~~Fl~ 169 (256)
T PF09788_consen 158 VICGHCSNTFLF 169 (256)
T ss_pred EECCCCCCcEec
Confidence 36888877 666
No 27
>PRK11582 flagella biosynthesis protein FliZ; Provisional
Probab=23.12 E-value=32 Score=24.00 Aligned_cols=13 Identities=31% Similarity=1.053 Sum_probs=10.3
Q ss_pred CCccccCCCCCcc
Q psy9785 50 KQPTFCSHCKDFI 62 (63)
Q Consensus 50 ~qptfCa~C~efI 62 (63)
+..|.|+||...+
T Consensus 20 hsQthCshC~K~L 32 (169)
T PRK11582 20 HSQTHCAHCRKLL 32 (169)
T ss_pred ccccchhhhccch
Confidence 5689999998743
No 28
>PF06463 Mob_synth_C: Molybdenum Cofactor Synthesis C; InterPro: IPR010505 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism [, ]. In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which converts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner []. MoCF is the active co-factor in eukaryotic and some prokaryotic molybdo-enzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdo-enzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF []. Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 (Q39054 from SWISSPROT) of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) []. This entry represents MoaA, which belongs to a family of enzymes involved in the synthesis of metallo-cofactors (IPR000385 from INTERPRO). Each subunit of the MoaA dimer is comprised of an N-terminal SAM domain (IPR007197 from INTERPRO) that contains the [4Fe-4S] cluster typical for this family of enzymes, as well as an additional [4Fe-4S] cluster in the C-terminal domain that is unique to MoaA proteins []. The unique Fe site of the C-terminal [4Fe-4S] cluster is thought to be involved in the binding and activation of 5'-GTP. Mutations in the human MoCF biosynthesis proteins MOCS1, MOCS2 or GEPH cause MoCF Deficiency type A (MOCOD), causing the loss of activity of MoCF-containing enzymes, resulting in neurological abnormalities and death [].; GO: 0051539 4 iron, 4 sulfur cluster binding, 0006777 Mo-molybdopterin cofactor biosynthetic process, 0019008 molybdopterin synthase complex; PDB: 2FB2_A 2FB3_A 1TV8_B 1TV7_A.
Probab=22.94 E-value=33 Score=21.87 Aligned_cols=26 Identities=27% Similarity=0.600 Sum_probs=12.9
Q ss_pred cceeecCCce--e-eeeecCCccccCCCCC
Q psy9785 34 KNVYNVKDHK--F-IPRFFKQPTFCSHCKD 60 (63)
Q Consensus 34 kKVh~v~GH~--F-~a~~f~qptfCa~C~e 60 (63)
++.+.++|.. + +-.-+.+| ||+.|.-
T Consensus 49 a~~y~~~g~~g~vG~I~~~s~~-FC~~CNR 77 (128)
T PF06463_consen 49 ARYYRIPGGKGRVGFISPVSNP-FCSSCNR 77 (128)
T ss_dssp SEEEEETTT--EEEEE-TTTS---GGG--E
T ss_pred ceEEEECCCCcEEEEEeCCCCC-CCCcCCE
Confidence 3567777766 2 23556777 9999974
No 29
>TIGR03823 FliZ flagellar regulatory protein FliZ. FliZ is involved in the regulation of flagellar assembly and possibly also the down-regulation of the motile phenotype. FliZ interacts with the flagellar translational activator FlhCD complex.
Probab=22.41 E-value=32 Score=23.97 Aligned_cols=13 Identities=38% Similarity=1.027 Sum_probs=10.3
Q ss_pred CCccccCCCCCcc
Q psy9785 50 KQPTFCSHCKDFI 62 (63)
Q Consensus 50 ~qptfCa~C~efI 62 (63)
+..|.|+||...+
T Consensus 20 hsQthCshC~K~L 32 (168)
T TIGR03823 20 HSQTHCSHCHKLL 32 (168)
T ss_pred cccchhhhhcchh
Confidence 5689999998743
No 30
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=22.19 E-value=34 Score=16.20 Aligned_cols=9 Identities=33% Similarity=1.132 Sum_probs=5.9
Q ss_pred ccccCCCCC
Q psy9785 52 PTFCSHCKD 60 (63)
Q Consensus 52 ptfCa~C~e 60 (63)
-.||.+|+.
T Consensus 16 ~~fC~~CG~ 24 (26)
T PF13248_consen 16 AKFCPNCGA 24 (26)
T ss_pred cccChhhCC
Confidence 457777765
No 31
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.87 E-value=53 Score=22.68 Aligned_cols=14 Identities=21% Similarity=1.013 Sum_probs=11.5
Q ss_pred eecCCccccCCCCC
Q psy9785 47 RFFKQPTFCSHCKD 60 (63)
Q Consensus 47 ~~f~qptfCa~C~e 60 (63)
..+..|.||+.|+.
T Consensus 63 ~~~~~PsYC~~CGk 76 (158)
T PF10083_consen 63 GHYEAPSYCHNCGK 76 (158)
T ss_pred CCCCCChhHHhCCC
Confidence 44568999999997
No 32
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=20.17 E-value=30 Score=19.33 Aligned_cols=13 Identities=23% Similarity=0.795 Sum_probs=8.2
Q ss_pred CccccCCCCCccC
Q psy9785 51 QPTFCSHCKDFIW 63 (63)
Q Consensus 51 qptfCa~C~efIW 63 (63)
+..||..|+..||
T Consensus 47 ~r~FC~~CGs~l~ 59 (92)
T PF04828_consen 47 ERYFCPTCGSPLF 59 (92)
T ss_dssp EEEEETTT--EEE
T ss_pred cCcccCCCCCeee
Confidence 4569999998664
Done!