Query 038899
Match_columns 95
No_of_seqs 100 out of 137
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 04:23:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038899.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038899hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03207 stomagen; Provisional 97.7 9.1E-05 2E-09 52.9 5.1 49 38-89 62-112 (113)
2 PF12273 RCR: Chitin synthesis 64.8 5.5 0.00012 27.6 2.1 12 10-21 7-18 (130)
3 PF08525 OapA_N: Opacity-assoc 50.3 19 0.00042 19.8 2.3 18 3-20 9-26 (30)
4 PF12911 OppC_N: N-terminal TM 47.3 28 0.0006 20.3 2.8 19 3-21 14-32 (56)
5 PF10589 NADH_4Fe-4S: NADH-ubi 44.8 3.7 8E-05 24.4 -1.3 10 55-64 15-24 (46)
6 TIGR03831 YgiT_finger YgiT-typ 44.2 9.3 0.0002 21.2 0.4 13 83-95 32-45 (46)
7 PF08094 Toxin_24: Conotoxin T 41.5 16 0.00034 21.2 1.0 10 43-52 3-13 (33)
8 COG2878 Predicted NADH:ubiquin 41.3 37 0.00081 26.6 3.4 46 8-60 8-53 (198)
9 PF12837 Fer4_6: 4Fe-4S bindin 38.4 5.1 0.00011 21.1 -1.2 13 53-65 6-18 (24)
10 PRK07118 ferredoxin; Validated 35.9 51 0.0011 26.0 3.5 49 8-64 8-59 (280)
11 COG0723 QcrA Rieske Fe-S prote 34.3 19 0.00041 25.9 0.8 16 80-95 122-137 (177)
12 PF15183 MRAP: Melanocortin-2 33.3 51 0.0011 23.0 2.8 23 8-31 46-68 (90)
13 PF05851 Lentivirus_VIF: Lenti 32.9 25 0.00055 28.4 1.4 18 78-95 210-227 (251)
14 PF11812 DUF3333: Domain of un 31.0 52 0.0011 24.3 2.7 24 8-31 21-44 (155)
15 PF11635 Med16: Mediator compl 29.6 27 0.00058 31.1 1.1 49 44-93 702-752 (753)
16 PF15347 PAG: Phosphoprotein a 29.4 46 0.00099 28.8 2.4 16 8-23 24-39 (428)
17 PRK11917 bifunctional adhesin/ 29.4 46 0.001 24.7 2.2 46 4-50 3-50 (259)
18 TIGR01944 rnfB electron transp 29.3 81 0.0017 22.7 3.4 47 8-61 6-52 (165)
19 PF09646 Gp37: Gp37 protein; 26.9 21 0.00045 26.4 -0.0 18 35-52 76-93 (144)
20 PF12797 Fer4_2: 4Fe-4S bindin 25.2 25 0.00054 18.6 0.1 11 54-64 8-18 (22)
21 COG3162 Predicted membrane pro 24.3 64 0.0014 23.0 2.0 18 2-19 19-36 (102)
22 TIGR02052 MerP mercuric transp 23.3 60 0.0013 18.7 1.5 9 9-17 5-13 (92)
23 PF03597 CcoS: Cytochrome oxid 23.1 1.4E+02 0.0031 17.9 3.1 26 9-34 10-35 (45)
24 cd01995 ExsB ExsB is a transcr 23.0 27 0.0006 24.2 -0.0 14 51-64 145-162 (169)
25 PF12800 Fer4_4: 4Fe-4S bindin 22.5 53 0.0012 15.8 1.0 11 54-64 2-12 (17)
26 PF01096 TFIIS_C: Transcriptio 22.4 87 0.0019 17.8 2.0 35 55-91 2-37 (39)
27 PF05207 zf-CSL: CSL zinc fing 20.7 39 0.00085 20.7 0.3 11 82-92 17-27 (55)
28 PF09749 HVSL: Uncharacterised 20.7 30 0.00065 26.2 -0.2 16 79-94 221-236 (239)
29 PF13623 SurA_N_2: SurA N-term 20.6 1.2E+02 0.0025 21.9 2.8 20 2-21 4-24 (145)
30 PF12191 stn_TNFRSF12A: Tumour 20.4 20 0.00043 26.5 -1.2 20 46-65 39-58 (129)
31 COG5207 UBP14 Isopeptidase T [ 20.3 92 0.002 28.5 2.7 11 82-92 476-487 (749)
32 PF13397 DUF4109: Domain of un 20.0 46 0.00099 23.7 0.6 12 79-90 46-58 (105)
No 1
>PLN03207 stomagen; Provisional
Probab=97.68 E-value=9.1e-05 Score=52.95 Aligned_cols=49 Identities=29% Similarity=0.714 Sum_probs=38.2
Q ss_pred hhhcccCCCCCCCccc-CCCCCC-CCCcceeeeCCCCCCCCCCccccceeeccC
Q 038899 38 DQKRISGPGSSPPTCR-SKCGRC-SPCKPVHVPIQPGLSMPLEYYPEAWRCNCG 89 (95)
Q Consensus 38 ~~~r~~~~GS~PP~C~-~KC~~C-~PC~aV~Vp~~~~~~~~~eY~P~~WKCkCg 89 (95)
.-.|..+|||+.|.|. |-|.+| .-|.+.|||+......++.| -|||-|+
T Consensus 62 k~srr~~igs~aptctynecrgcr~kc~~eqvpv~~~dp~nsay---hy~cvch 112 (113)
T PLN03207 62 KSSRRLMIGSTAPTCTYNECRGCRYKCRAEQVPVEGNDPINSAY---HYKCVCH 112 (113)
T ss_pred hhhhhhhhcCcCCccccccccCccccccceeccccCCCCCcccc---ccccCCC
Confidence 3445567999999997 689999 67999999998766655555 4788875
No 2
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=64.78 E-value=5.5 Score=27.63 Aligned_cols=12 Identities=25% Similarity=0.415 Sum_probs=5.1
Q ss_pred HHHHHHHHHHHH
Q 038899 10 SFTAFTFLFFVL 21 (95)
Q Consensus 10 ~~~~~~fl~~~~ 21 (95)
+||++.||+||+
T Consensus 7 iii~~i~l~~~~ 18 (130)
T PF12273_consen 7 IIIVAILLFLFL 18 (130)
T ss_pred HHHHHHHHHHHH
Confidence 334444444443
No 3
>PF08525 OapA_N: Opacity-associated protein A N-terminal motif; InterPro: IPR013731 This domain is found in the Haemophilus influenzae opacity-associated protein (OapA). It is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [, ]. This motif occurs at the N terminus of these proteins. It contains a conserved histidine followed by a run of hydrophobic residues. Many of the proteins in this entry are unassigned peptidases belonging to MEROPS peptidase family M23B.
Probab=50.27 E-value=19 Score=19.83 Aligned_cols=18 Identities=28% Similarity=0.573 Sum_probs=12.3
Q ss_pred chhhhHHHHHHHHHHHHH
Q 038899 3 RHRRLLSSFTAFTFLFFV 20 (95)
Q Consensus 3 ~~r~~l~~~~~~~fl~~~ 20 (95)
.||+.+..++.++.++++
T Consensus 9 ~Hr~~l~~l~~v~l~ll~ 26 (30)
T PF08525_consen 9 LHRRALIALSAVVLVLLL 26 (30)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 478887777777666544
No 4
>PF12911 OppC_N: N-terminal TM domain of oligopeptide transport permease C
Probab=47.30 E-value=28 Score=20.34 Aligned_cols=19 Identities=11% Similarity=0.258 Sum_probs=10.4
Q ss_pred chhhhHHHHHHHHHHHHHH
Q 038899 3 RHRRLLSSFTAFTFLFFVL 21 (95)
Q Consensus 3 ~~r~~l~~~~~~~fl~~~~ 21 (95)
|+|.++..++++.+++.++
T Consensus 14 ~nk~a~~gl~il~~~vl~a 32 (56)
T PF12911_consen 14 RNKLAVIGLIILLILVLLA 32 (56)
T ss_pred hCchHHHHHHHHHHHHHHH
Confidence 4455566666665555553
No 5
>PF10589 NADH_4Fe-4S: NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; InterPro: IPR019575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the F subunit of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2. This entry represents the iron-sulphur binding domain of the F subunit.; GO: 0055114 oxidation-reduction process; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1.
Probab=44.82 E-value=3.7 Score=24.44 Aligned_cols=10 Identities=50% Similarity=1.836 Sum_probs=4.7
Q ss_pred CCCCCCCCcc
Q 038899 55 KCGRCSPCKP 64 (95)
Q Consensus 55 KC~~C~PC~a 64 (95)
-||+|.||.-
T Consensus 15 SCGkC~PCR~ 24 (46)
T PF10589_consen 15 SCGKCTPCRE 24 (46)
T ss_dssp --S--HHHHC
T ss_pred CCCCCCCcHh
Confidence 5899999963
No 6
>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=44.16 E-value=9.3 Score=21.19 Aligned_cols=13 Identities=31% Similarity=0.764 Sum_probs=9.7
Q ss_pred ceeec-cCCCCCCC
Q 038899 83 AWRCN-CGNKLFMP 95 (95)
Q Consensus 83 ~WKCk-Cg~klf~P 95 (95)
+|+|. ||..+|++
T Consensus 32 ~~~C~~CGE~~~~~ 45 (46)
T TIGR03831 32 ALVCPQCGEEYLDA 45 (46)
T ss_pred ccccccCCCEeeCC
Confidence 67776 88888764
No 7
>PF08094 Toxin_24: Conotoxin TVIIA/GS family; InterPro: IPR012629 This family consists of conotoxins isolated from the venom of cone snail Conus tulipa and Conus geographus. Conotoxin TVIIA, isolated from Conus tulipa displays little sequence homology with other well-characterised pharmacological classes of peptides, but displays similarity with conotoxin GS, a peptide from Conus geographus. Both these peptides block skeletal muscle sodium channels and also share several biochemical features and represent a distinct subgroup of the four-loop conotoxins [].; GO: 0019871 sodium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1AG7_A 1EYO_A.
Probab=41.47 E-value=16 Score=21.23 Aligned_cols=10 Identities=70% Similarity=1.438 Sum_probs=7.2
Q ss_pred cCCCCC-CCcc
Q 038899 43 SGPGSS-PPTC 52 (95)
Q Consensus 43 ~~~GS~-PP~C 52 (95)
++.||+ ||.|
T Consensus 3 sgr~srcpp~c 13 (33)
T PF08094_consen 3 SGRGSRCPPQC 13 (33)
T ss_dssp B-TTSSSSSSB
T ss_pred cCCCCCCCchh
Confidence 457898 8887
No 8
>COG2878 Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]
Probab=41.32 E-value=37 Score=26.64 Aligned_cols=46 Identities=15% Similarity=0.374 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHhcCCCccchhhhhhhhhcccCCCCCCCcccCCCCCCC
Q 038899 8 LSSFTAFTFLFFVLTQLGTGGAQEKETRVLDQKRISGPGSSPPTCRSKCGRCS 60 (95)
Q Consensus 8 l~~~~~~~fl~~~~~~~~s~~~~~~~~~~~~~~r~~~~GS~PP~C~~KC~~C~ 60 (95)
+.++.+++|++++.+...|--+...+.-++|+--.-.+|| .|++|+
T Consensus 8 v~~l~~l~~~~G~~L~~As~rFkve~DP~Ve~I~~lLPqs-------qCgqCG 53 (198)
T COG2878 8 VAALALLGLAFGAMLGYASRRFKVEEDPVVEKIDALLPQT-------QCGQCG 53 (198)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhccccCcHHHHHHHhCCcc-------ccccCC
Confidence 4555666788888777777777766655555433223343 677774
No 9
>PF12837 Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding
Probab=38.41 E-value=5.1 Score=21.06 Aligned_cols=13 Identities=38% Similarity=0.828 Sum_probs=9.5
Q ss_pred cCCCCCCCCCcce
Q 038899 53 RSKCGRCSPCKPV 65 (95)
Q Consensus 53 ~~KC~~C~PC~aV 65 (95)
.+||..|+-|..+
T Consensus 6 ~~~C~~Cg~C~~~ 18 (24)
T PF12837_consen 6 PDKCIGCGDCVRV 18 (24)
T ss_pred hhhCcChhHHHHh
Confidence 3588888888653
No 10
>PRK07118 ferredoxin; Validated
Probab=35.94 E-value=51 Score=26.05 Aligned_cols=49 Identities=29% Similarity=0.490 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCCccchh-hhhhhhhcccCCCCCCCcccCCCCCCCC--Ccc
Q 038899 8 LSSFTAFTFLFFVLTQLGTGGAQEKE-TRVLDQKRISGPGSSPPTCRSKCGRCSP--CKP 64 (95)
Q Consensus 8 l~~~~~~~fl~~~~~~~~s~~~~~~~-~~~~~~~r~~~~GS~PP~C~~KC~~C~P--C~a 64 (95)
++++.+++|+|++++...|--+...+ .++.+ -....+|+ .|+.|+- |.+
T Consensus 8 ~~~~~~~g~~~g~~l~~a~~~f~v~~d~~~~~-i~~~lp~~-------nCg~Cg~~~C~~ 59 (280)
T PRK07118 8 VLSLGALGLVFGILLAFASKKFAVEEDPRVEA-VREVLPGA-------NCGGCGYPGCDG 59 (280)
T ss_pred HHHHHHHHHHHHHHHHHHeeeeeccCCCcHHH-HHHhCCCC-------CCCCCCccCHHH
Confidence 34455567777777777777665554 34433 22223454 4888865 644
No 11
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=34.33 E-value=19 Score=25.94 Aligned_cols=16 Identities=19% Similarity=0.544 Sum_probs=13.6
Q ss_pred cccceeeccCCCCCCC
Q 038899 80 YPEAWRCNCGNKLFMP 95 (95)
Q Consensus 80 ~P~~WKCkCg~klf~P 95 (95)
..-.|.|-|++..|+|
T Consensus 122 ~~~~~~CPCHGS~yd~ 137 (177)
T COG0723 122 AEGGFFCPCHGSRYDP 137 (177)
T ss_pred CCCeEEccCCCCeEcC
Confidence 3468999999999986
No 12
>PF15183 MRAP: Melanocortin-2 receptor accessory protein family
Probab=33.29 E-value=51 Score=23.01 Aligned_cols=23 Identities=30% Similarity=0.540 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHHHhcCCCccc
Q 038899 8 LSSFTAFTFLFFVLTQLGTGGAQE 31 (95)
Q Consensus 8 l~~~~~~~fl~~~~~~~~s~~~~~ 31 (95)
|++++.|.||.+.+ -+.||..|.
T Consensus 46 LA~FV~~lF~iL~~-ms~sgspq~ 68 (90)
T PF15183_consen 46 LAAFVVFLFLILLY-MSWSGSPQM 68 (90)
T ss_pred HHHHHHHHHHHHHH-HhccCCCCc
Confidence 44444444443332 233454444
No 13
>PF05851 Lentivirus_VIF: Lentivirus virion infectivity factor (VIF); InterPro: IPR008668 This family consists of several feline-specific Lentivirus virion infectivity factor (VIF) proteins. VIF is essential for productive Feline immunodeficiency virus infection of host target cells in vitro [].; GO: 0019058 viral infectious cycle
Probab=32.89 E-value=25 Score=28.39 Aligned_cols=18 Identities=28% Similarity=0.824 Sum_probs=15.2
Q ss_pred CccccceeeccCCCCCCC
Q 038899 78 EYYPEAWRCNCGNKLFMP 95 (95)
Q Consensus 78 eY~P~~WKCkCg~klf~P 95 (95)
.=+-.+|+|+|.-++|+|
T Consensus 210 Grk~~~W~~~~~~RF~~~ 227 (251)
T PF05851_consen 210 GRKLYSWYCKCNYRFFSP 227 (251)
T ss_pred CCcccceecCCCceecCc
Confidence 455679999999999987
No 14
>PF11812 DUF3333: Domain of unknown function (DUF3333); InterPro: IPR024573 This N-terminal domain is functionally uncharacterised and it is found in proteins annotated as putative phosphate ABC transporter permease proteins. This presumed domain is typically between 116 to 159 amino acids in length.
Probab=30.97 E-value=52 Score=24.26 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHhcCCCccc
Q 038899 8 LSSFTAFTFLFFVLTQLGTGGAQE 31 (95)
Q Consensus 8 l~~~~~~~fl~~~~~~~~s~~~~~ 31 (95)
.++++++.||++++.++.|.|..-
T Consensus 21 ~Ai~~~l~fL~~ll~sI~~~G~~A 44 (155)
T PF11812_consen 21 AAIAIALAFLVILLFSIVSKGYPA 44 (155)
T ss_pred HHHHHHHHHHHHHHHHHHhcchhh
Confidence 566677788888888887776443
No 15
>PF11635 Med16: Mediator complex subunit 16; InterPro: IPR021665 Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression []. Several members including the human protein, Q9Y2X0 from SWISSPROT, have one or more WD40 domains on them, PF00400 from PFAM.
Probab=29.55 E-value=27 Score=31.10 Aligned_cols=49 Identities=29% Similarity=0.550 Sum_probs=32.0
Q ss_pred CCCCCCCcccCCCCCCCCCcceeeeCCCCCCCCCCccccce--eeccCCCCC
Q 038899 44 GPGSSPPTCRSKCGRCSPCKPVHVPIQPGLSMPLEYYPEAW--RCNCGNKLF 93 (95)
Q Consensus 44 ~~GS~PP~C~~KC~~C~PC~aV~Vp~~~~~~~~~eY~P~~W--KCkCg~klf 93 (95)
.+|..|.. ..+...|..|-+|.+...+..+...-.-++.| +|-|||..+
T Consensus 702 ~l~~~~~~-~~~~RrC~RC~~vs~~~~~~~s~~~~~w~~~~~R~C~CGG~W~ 752 (753)
T PF11635_consen 702 HLGRSPTS-TGKWRRCVRCGSVSEDEDPFTSRATKRWTMRWQRNCICGGMWV 752 (753)
T ss_pred eeeecccC-CCceEEeccCCCcccccCCCCcchhhhhhhheeeeeccCCeeC
Confidence 35666644 66777777887777655554333344567777 699998653
No 16
>PF15347 PAG: Phosphoprotein associated with glycosphingolipid-enriched
Probab=29.42 E-value=46 Score=28.83 Aligned_cols=16 Identities=25% Similarity=0.683 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHHH
Q 038899 8 LSSFTAFTFLFFVLTQ 23 (95)
Q Consensus 8 l~~~~~~~fl~~~~~~ 23 (95)
+.+++.++||+|++++
T Consensus 24 v~~f~lis~LifLCsS 39 (428)
T PF15347_consen 24 VTTFLLISFLIFLCSS 39 (428)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 4555555777777643
No 17
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=29.40 E-value=46 Score=24.73 Aligned_cols=46 Identities=13% Similarity=0.172 Sum_probs=24.0
Q ss_pred hhhhHHHHHHHHHHHHHHHHhcCCCccchhhhhhhhhcc--cCCCCCCC
Q 038899 4 HRRLLSSFTAFTFLFFVLTQLGTGGAQEKETRVLDQKRI--SGPGSSPP 50 (95)
Q Consensus 4 ~r~~l~~~~~~~fl~~~~~~~~s~~~~~~~~~~~~~~r~--~~~GS~PP 50 (95)
.|..|..+.+|+|.|.++.+..+......+. +.++..+ +.....||
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-i~~~g~l~vg~~~~~pP 50 (259)
T PRK11917 3 FRKSLLKLAVFALGACVAFSNANAAEGKLES-IKSKGQLIVGVKNDVPH 50 (259)
T ss_pred hHHHHHHHHHHHhhccccccccCCccchHHH-HHhCCEEEEEECCCCCC
Confidence 4666777777766666655554444444332 3333332 33344566
No 18
>TIGR01944 rnfB electron transport complex, RnfABCDGE type, B subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit.
Probab=29.33 E-value=81 Score=22.69 Aligned_cols=47 Identities=11% Similarity=0.345 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCCccchhhhhhhhhcccCCCCCCCcccCCCCCCCC
Q 038899 8 LSSFTAFTFLFFVLTQLGTGGAQEKETRVLDQKRISGPGSSPPTCRSKCGRCSP 61 (95)
Q Consensus 8 l~~~~~~~fl~~~~~~~~s~~~~~~~~~~~~~~r~~~~GS~PP~C~~KC~~C~P 61 (95)
.+++.++++++++++...|-.....++-.++|- ..-.| ...|+.|+-
T Consensus 6 ~~~~~~~g~~~~~~l~~~~~~~~ve~~p~~~~i-----~~~lP--~~nCg~Cg~ 52 (165)
T TIGR01944 6 VAALSALGLALGAILGYAARRFPVEADPIVEEI-----DALLP--QTQCGQCGY 52 (165)
T ss_pred HHHHHHHHHHHHHHHHHheeeeeccCCChHHHH-----HHhCC--CCCCccCCC
Confidence 344555567777777777776555443222222 22233 556777743
No 19
>PF09646 Gp37: Gp37 protein; InterPro: IPR018602 This entry is represented by Burkholderia phage BcepMu, Gp37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein of 154 residues consists of a unit of helices and beta sheets that crystallises into a beautiful asymmetrical dodecameric barrel-structure, of two six-membered rings one on top of the other. It is expressed in bacteria but is of viral origin as it is found in Burkholderia phage BcepMu and is probably a pathogenesis factor []. ; PDB: 2GJV_D.
Probab=26.94 E-value=21 Score=26.38 Aligned_cols=18 Identities=44% Similarity=0.794 Sum_probs=12.0
Q ss_pred hhhhhhcccCCCCCCCcc
Q 038899 35 RVLDQKRISGPGSSPPTC 52 (95)
Q Consensus 35 ~~~~~~r~~~~GS~PP~C 52 (95)
.++|+-|+...|=+||+|
T Consensus 76 ~~LD~vRlaL~Gf~pp~c 93 (144)
T PF09646_consen 76 AVLDRVRLALVGFRPPGC 93 (144)
T ss_dssp HHHHHHHHHHTT---TT-
T ss_pred HHHHHHHHHhcCcCCCCC
Confidence 468888988899999999
No 20
>PF12797 Fer4_2: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding
Probab=25.25 E-value=25 Score=18.60 Aligned_cols=11 Identities=27% Similarity=0.969 Sum_probs=8.6
Q ss_pred CCCCCCCCCcc
Q 038899 54 SKCGRCSPCKP 64 (95)
Q Consensus 54 ~KC~~C~PC~a 64 (95)
+||.+|+-|+.
T Consensus 8 ~rCiGC~~C~~ 18 (22)
T PF12797_consen 8 ERCIGCGACEV 18 (22)
T ss_pred ccccCchhHHH
Confidence 68888988863
No 21
>COG3162 Predicted membrane protein [Function unknown]
Probab=24.30 E-value=64 Score=22.99 Aligned_cols=18 Identities=28% Similarity=0.373 Sum_probs=12.6
Q ss_pred cchhhhHHHHHHHHHHHH
Q 038899 2 WRHRRLLSSFTAFTFLFF 19 (95)
Q Consensus 2 ~~~r~~l~~~~~~~fl~~ 19 (95)
+|.|+.|+.++++.||.+
T Consensus 19 v~kr~~Fa~~ltl~flv~ 36 (102)
T COG3162 19 VRKRRRFAVPLTLIFLVV 36 (102)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 467888887777766654
No 22
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=23.35 E-value=60 Score=18.74 Aligned_cols=9 Identities=22% Similarity=0.357 Sum_probs=3.3
Q ss_pred HHHHHHHHH
Q 038899 9 SSFTAFTFL 17 (95)
Q Consensus 9 ~~~~~~~fl 17 (95)
+++..|.|+
T Consensus 5 ~~~~~~~~~ 13 (92)
T TIGR02052 5 ATLLALFVL 13 (92)
T ss_pred HHHHHHHHH
Confidence 333333333
No 23
>PF03597 CcoS: Cytochrome oxidase maturation protein cbb3-type; InterPro: IPR004714 Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO). Expression of cytochrome cbb3 oxidase allows human pathogens to colonise anoxic tissues and agronomically important diazotrophs to sustain nitrogen fixation []. Genes encoding a cytochrome cbb3 oxidase were initially designated fixNOQP (ccoNOQP), the ccoNOQP operon is always found close to a second gene cluster, known as fixGHIS (ccoGHIS) whose expression is necessary for the assembly of a functional cbb3 oxidase. On the basis of their derived amino acid sequences each of the four proteins encoded by the ccoGHIS operon are thought to be membrane-bound. It has been suggested that they may function in concert as a multi-subunit complex, possibly playing a role in the uptake and metabolism of copper required for the assembly of the binuclear centre of cytochrome cbb3 oxidase.
Probab=23.05 E-value=1.4e+02 Score=17.90 Aligned_cols=26 Identities=19% Similarity=0.114 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHhcCCCccchhh
Q 038899 9 SSFTAFTFLFFVLTQLGTGGAQEKET 34 (95)
Q Consensus 9 ~~~~~~~fl~~~~~~~~s~~~~~~~~ 34 (95)
+.+++..+|..|.-.++|++....++
T Consensus 10 sl~l~~~~l~~f~Wavk~GQfdD~e~ 35 (45)
T PF03597_consen 10 SLILGLIALAAFLWAVKSGQFDDLEG 35 (45)
T ss_pred HHHHHHHHHHHHHHHHccCCCCCCcc
Confidence 44555567777778888998877664
No 24
>cd01995 ExsB ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown
Probab=22.97 E-value=27 Score=24.17 Aligned_cols=14 Identities=36% Similarity=1.205 Sum_probs=10.7
Q ss_pred cccC----CCCCCCCCcc
Q 038899 51 TCRS----KCGRCSPCKP 64 (95)
Q Consensus 51 ~C~~----KC~~C~PC~a 64 (95)
+|.+ -||.|.||..
T Consensus 145 sC~~~~~~~CG~C~~C~~ 162 (169)
T cd01995 145 SCYNGGEKHCGECDSCLL 162 (169)
T ss_pred eccCCCCCCCCCCHHHHH
Confidence 4655 7999999964
No 25
>PF12800 Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1BD6_A 1BQX_A 1BWE_A 1BC6_A.
Probab=22.48 E-value=53 Score=15.80 Aligned_cols=11 Identities=27% Similarity=0.918 Sum_probs=7.5
Q ss_pred CCCCCCCCCcc
Q 038899 54 SKCGRCSPCKP 64 (95)
Q Consensus 54 ~KC~~C~PC~a 64 (95)
++|..|+-|..
T Consensus 2 ~~C~~C~~C~~ 12 (17)
T PF12800_consen 2 ERCIGCGSCVD 12 (17)
T ss_dssp CCCTTSSSSTT
T ss_pred CcCCCCchHHh
Confidence 56777777754
No 26
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=22.38 E-value=87 Score=17.82 Aligned_cols=35 Identities=31% Similarity=0.619 Sum_probs=18.5
Q ss_pred CCCCCCCCcceeeeCCCCCCCCCCccccceee-ccCCC
Q 038899 55 KCGRCSPCKPVHVPIQPGLSMPLEYYPEAWRC-NCGNK 91 (95)
Q Consensus 55 KC~~C~PC~aV~Vp~~~~~~~~~eY~P~~WKC-kCg~k 91 (95)
+|..|+.=+++-+-.+..+. +|--.+-++| .||.+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsa--DE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSA--DEPMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-SSEEEEEEESSSSS--SSSSEEEEEESSSTEE
T ss_pred CCcCCCCCeEEEEEeeccCC--CCCCeEEEEeCCCCCe
Confidence 57777776666664444332 3445566777 66643
No 27
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=20.68 E-value=39 Score=20.72 Aligned_cols=11 Identities=27% Similarity=1.063 Sum_probs=9.1
Q ss_pred cceeeccCCCC
Q 038899 82 EAWRCNCGNKL 92 (95)
Q Consensus 82 ~~WKCkCg~kl 92 (95)
..+.|+||+.+
T Consensus 17 ~~y~CRCG~~f 27 (55)
T PF05207_consen 17 YSYPCRCGGEF 27 (55)
T ss_dssp EEEEETTSSEE
T ss_pred EEEcCCCCCEE
Confidence 57889999974
No 28
>PF09749 HVSL: Uncharacterised conserved protein; InterPro: IPR019146 This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown.
Probab=20.68 E-value=30 Score=26.20 Aligned_cols=16 Identities=31% Similarity=0.756 Sum_probs=11.7
Q ss_pred ccccceeeccCCCCCC
Q 038899 79 YYPEAWRCNCGNKLFM 94 (95)
Q Consensus 79 Y~P~~WKCkCg~klf~ 94 (95)
.+--.=|||+||++|+
T Consensus 221 ~~v~~Ik~kiGn~v~~ 236 (239)
T PF09749_consen 221 FKVNSIKCKIGNKVFS 236 (239)
T ss_pred EEeeEEEEEECCEEEE
Confidence 3445678999999874
No 29
>PF13623 SurA_N_2: SurA N-terminal domain
Probab=20.58 E-value=1.2e+02 Score=21.90 Aligned_cols=20 Identities=20% Similarity=0.335 Sum_probs=10.4
Q ss_pred cchhhh-HHHHHHHHHHHHHH
Q 038899 2 WRHRRL-LSSFTAFTFLFFVL 21 (95)
Q Consensus 2 ~~~r~~-l~~~~~~~fl~~~~ 21 (95)
+|-|.+ |..+|+++++.|.+
T Consensus 4 IR~r~~lLi~vIglAL~aFIv 24 (145)
T PF13623_consen 4 IRQRGGLLIIVIGLALFAFIV 24 (145)
T ss_pred HhhcchHHHHHHHHHHHHHHH
Confidence 355656 44455555555554
No 30
>PF12191 stn_TNFRSF12A: Tumour necrosis factor receptor stn_TNFRSF12A_TNFR domain; InterPro: IPR022316 The tumour necrosis factor (TNF) receptor (TNFR) superfamily comprises more than 20 type-I transmembrane proteins. Family members are defined based on similarity in their extracellular domain - a region that contains many cysteine residues arranged in a specific repetitive pattern []. The cysteines allow formation of an extended rod-like structure, responsible for ligand binding []. Upon receptor activation, different intracellular signalling complexes are assembled for different members of the TNFR superfamily, depending on their intracellular domains and sequences []. Activation of TNFRs can therefore induce a range of disparate effects, including cell proliferation, differentiation, survival, or apoptotic cell death, depending upon the receptor involved []. TNFRs are widely distributed and play important roles in many crucial biological processes, such as lymphoid and neuronal development, innate and adaptive immunity, and maintenance of cellular homeostasis []. Drugs that manipulate their signalling have potential roles in the prevention and treatment of many diseases, such as viral infections, coronary heart disease, transplant rejection, and immune disease []. TNF receptor 12 (also known as TWEAK receptor, and fibroblast growth factor-inducible-14 (Fn14)) has been implicated in endothelial cell growth and migration []. The receptor may also play a role in cell-matrix interactions [].; PDB: 2KN0_A 2RPJ_A 2KMZ_A 2EQP_A.
Probab=20.38 E-value=20 Score=26.48 Aligned_cols=20 Identities=40% Similarity=0.622 Sum_probs=12.9
Q ss_pred CCCCCcccCCCCCCCCCcce
Q 038899 46 GSSPPTCRSKCGRCSPCKPV 65 (95)
Q Consensus 46 GS~PP~C~~KC~~C~PC~aV 65 (95)
|++.=.=-+||..|+-|+.-
T Consensus 39 G~sWs~dLdkCm~CssC~~~ 58 (129)
T PF12191_consen 39 GSSWSADLDKCMSCSSCPAY 58 (129)
T ss_dssp SEEEETTTTEEEECCCHCC-
T ss_pred CCcCcccccccccCccCCCC
Confidence 55543445588899988764
No 31
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=20.33 E-value=92 Score=28.49 Aligned_cols=11 Identities=36% Similarity=1.078 Sum_probs=9.0
Q ss_pred cceeec-cCCCC
Q 038899 82 EAWRCN-CGNKL 92 (95)
Q Consensus 82 ~~WKCk-Cg~kl 92 (95)
+-|+|- |+.|+
T Consensus 476 iE~~CenCk~K~ 487 (749)
T COG5207 476 IEWSCENCKGKK 487 (749)
T ss_pred eeeehhhhcCcc
Confidence 389998 98875
No 32
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=20.04 E-value=46 Score=23.65 Aligned_cols=12 Identities=42% Similarity=1.240 Sum_probs=10.0
Q ss_pred ccccceeec-cCC
Q 038899 79 YYPEAWRCN-CGN 90 (95)
Q Consensus 79 Y~P~~WKCk-Cg~ 90 (95)
=-|..|-|+ ||.
T Consensus 46 evP~~WeC~~cG~ 58 (105)
T PF13397_consen 46 EVPATWECPRCGL 58 (105)
T ss_pred CCCCceeCCCCCC
Confidence 349999999 985
Done!