Query 034873
Match_columns 80
No_of_seqs 97 out of 99
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:15:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034873.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034873hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12014 DUF3506: Domain of un 100.0 1.7E-37 3.6E-42 216.4 8.4 74 1-77 59-134 (134)
2 cd04487 RecJ_OBF2_like RecJ_OB 72.7 2.8 6E-05 25.9 1.7 20 9-28 49-68 (73)
3 PF09460 Saf-Nte_pilin: Saf-pi 54.5 13 0.00028 26.7 2.5 22 8-29 119-140 (145)
4 PF08197 TT_ORF2a: pORF2a trun 54.1 6 0.00013 23.6 0.7 15 13-27 15-33 (49)
5 KOG2387 CTP synthase (UTP-ammo 52.2 4 8.6E-05 34.6 -0.4 20 4-23 74-93 (585)
6 PF11869 DUF3389: Protein of u 48.7 22 0.00048 22.9 2.7 31 3-33 28-61 (75)
7 PF07619 DUF1581: Protein of u 42.8 20 0.00044 23.6 1.8 14 7-20 43-56 (84)
8 PF09284 RhgB_N: Rhamnogalactu 40.6 40 0.00087 26.1 3.5 69 8-79 90-167 (249)
9 PF07495 Y_Y_Y: Y_Y_Y domain; 36.7 31 0.00067 19.5 1.8 13 17-29 35-47 (66)
10 PF12142 PPO1_DWL: Polyphenol 35.5 13 0.00028 22.5 0.1 18 62-79 2-19 (54)
11 PF04283 CheF-arch: Chemotaxis 34.8 62 0.0014 24.0 3.6 31 48-78 3-36 (221)
12 PF01186 Lysyl_oxidase: Lysyl 32.5 47 0.001 24.9 2.7 22 17-38 156-177 (205)
13 PF06883 RNA_pol_Rpa2_4: RNA p 28.6 2.5 5.4E-05 25.6 -3.9 17 4-20 13-29 (58)
14 PLN00115 pollen allergen group 28.6 59 0.0013 22.2 2.4 39 18-56 79-117 (118)
15 KOG3265 Histone chaperone invo 25.6 82 0.0018 24.5 3.0 43 17-63 64-118 (250)
16 PF01458 UPF0051: Uncharacteri 23.7 2.5E+02 0.0054 20.0 5.1 30 49-78 147-176 (229)
17 PF12892 FctA: T surface-antig 23.4 1E+02 0.0022 18.1 2.5 19 11-29 69-87 (88)
18 PRK06032 fliH flagellar assemb 22.9 81 0.0018 22.5 2.4 23 8-30 157-179 (199)
19 cd07990 LPLAT_LCLAT1-like Lyso 22.2 1.6E+02 0.0034 20.2 3.6 26 3-28 3-31 (193)
20 TIGR02499 HrpE_YscL_not type I 22.2 84 0.0018 20.9 2.2 21 10-30 141-161 (166)
No 1
>PF12014 DUF3506: Domain of unknown function (DUF3506); InterPro: IPR021894 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 131 to 148 amino acids in length. This domain has a conserved KLTGD sequence motif.
Probab=100.00 E-value=1.7e-37 Score=216.37 Aligned_cols=74 Identities=53% Similarity=0.809 Sum_probs=66.6
Q ss_pred CceeeEEEEEEeeCCCCccCceEEEEEE-cCCCcCCCCCCCCCCCCCCceE-EEeeeEEcCCCCCCCceeeeEEEEEcC
Q 034873 1 MEFFEYVEAVKLTGDLNVPAGEVTFRAK-IGKGSRLPNRGKFPDELGVVAS-YSGQGRIADFGFRNPKWVDGELLQLNG 77 (80)
Q Consensus 1 ~~~~e~leAvKLTGDpNVPrGevtf~A~-ig~~~~~~~~g~~~~e~~~~ar-~~g~G~VA~~Gf~~~~~i~~~Lilis~ 77 (80)
++|+|+|||||||||||||||||||+|+ |++.+++ .+..++++.|+| ||||||||++||+|++||+|||||||+
T Consensus 59 ~~~~~~leAiKLTGDpNVPrGevtF~A~DiG~~~~i---~~a~~~~f~G~r~vk~~G~vA~~GF~~~~~id~eLilis~ 134 (134)
T PF12014_consen 59 REFRGRLEAIKLTGDPNVPRGEVTFRADDIGPGGRI---RVAHEGPFPGARRVKGQGHVAEPGFRNDKWIDGELILISG 134 (134)
T ss_pred ccccceEEEEEecCCCCCcCccEEEEecccCCCccc---ccccCCCCCceEEEecCCeEcCcCcCCCcceeeEEEEecC
Confidence 3699999999999999999999999999 9999887 344455566777 999999999999999999999999996
No 2
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=72.72 E-value=2.8 Score=25.86 Aligned_cols=20 Identities=20% Similarity=0.524 Sum_probs=17.4
Q ss_pred EEEeeCCCCccCceEEEEEE
Q 034873 9 AVKLTGDLNVPAGEVTFRAK 28 (80)
Q Consensus 9 AvKLTGDpNVPrGevtf~A~ 28 (80)
.|.++|-.++|+|+++|.++
T Consensus 49 ~V~v~G~v~~~~G~~ql~v~ 68 (73)
T cd04487 49 IVRVTGEVEPRDGQLQIEVE 68 (73)
T ss_pred EEEEEEEEecCCeEEEEEEe
Confidence 46788889999999999987
No 3
>PF09460 Saf-Nte_pilin: Saf-pilin pilus formation protein; InterPro: IPR018569 This domain consists of the adjacent Saf-Nte and Saf-pilin chains of the pilus-forming complex. Pilus assembly in Gram-negative bacteria involves a Donor-strand exchange mechanism between the C- and the N-termini of this domain. The C-terminal subunit forms an incomplete Ig-fold which is then complemented by the 10-18 residue N terminus of another, incoming, pilus subunit which is not involved in the Ig-fold. The N terminus sequences contain a motif of alternating hydrophobic residues that occupy the P2 to P5 binding pockets in the groove of the first pilus subunit []. ; PDB: 2CNZ_A 2CO7_A 2CO3_A 2CO1_A 2CNY_A 3CRF_A 2CO4_A 3CRE_A 2CO6_A 2CO2_A ....
Probab=54.50 E-value=13 Score=26.71 Aligned_cols=22 Identities=32% Similarity=0.480 Sum_probs=15.9
Q ss_pred EEEEeeCCCCccCceEEEEEEc
Q 034873 8 EAVKLTGDLNVPAGEVTFRAKI 29 (80)
Q Consensus 8 eAvKLTGDpNVPrGevtf~A~i 29 (80)
..|||+||.|||+--+....++
T Consensus 119 ~~i~l~G~Q~V~aDTYPvTldv 140 (145)
T PF09460_consen 119 LDIILSGDQNVPADTYPVTLDV 140 (145)
T ss_dssp EEEEE-SS-EE-SEEEEEEEEE
T ss_pred EEEEEEcccccCCCceeEEEEE
Confidence 4799999999999988887773
No 4
>PF08197 TT_ORF2a: pORF2a truncated protein; InterPro: IPR013267 Most isolated ORF2 of TT virus (TTV) encode a 49 amino acid protein (pORF2a) because of an in-frame stop codon. ORF2s isolated from G1 TTV encode a 202 amino acid protein (pORF2ab) [].
Probab=54.06 E-value=6 Score=23.60 Aligned_cols=15 Identities=53% Similarity=0.846 Sum_probs=10.6
Q ss_pred eCCCCccC----ceEEEEE
Q 034873 13 TGDLNVPA----GEVTFRA 27 (80)
Q Consensus 13 TGDpNVPr----Gevtf~A 27 (80)
.|||+||| ||.|-+.
T Consensus 15 eg~prvPRAGAgGefthrs 33 (49)
T PF08197_consen 15 EGDPRVPRAGAGGEFTHRS 33 (49)
T ss_pred cCCCCCcccccccceeecc
Confidence 49999998 5555443
No 5
>KOG2387 consensus CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism]
Probab=52.16 E-value=4 Score=34.61 Aligned_cols=20 Identities=30% Similarity=0.547 Sum_probs=18.3
Q ss_pred eeEEEEEEeeCCCCccCceE
Q 034873 4 FEYVEAVKLTGDLNVPAGEV 23 (80)
Q Consensus 4 ~e~leAvKLTGDpNVPrGev 23 (80)
||+.-.|+||.|.|++-|++
T Consensus 74 YERfldi~Lt~dNNITtGKi 93 (585)
T KOG2387|consen 74 YERFLDITLTRDNNITTGKI 93 (585)
T ss_pred hhhhccceeeccCCcccchH
Confidence 78888999999999999986
No 6
>PF11869 DUF3389: Protein of unknown function (DUF3389); InterPro: IPR021811 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=48.72 E-value=22 Score=22.93 Aligned_cols=31 Identities=29% Similarity=0.485 Sum_probs=25.6
Q ss_pred eeeEEEEEEeeCCCCc---cCceEEEEEEcCCCc
Q 034873 3 FFEYVEAVKLTGDLNV---PAGEVTFRAKIGKGS 33 (80)
Q Consensus 3 ~~e~leAvKLTGDpNV---PrGevtf~A~ig~~~ 33 (80)
.+-..++|+|-|++|| -.|++.|-.+++.+-
T Consensus 28 LqA~~D~I~li~~anvi~A~g~~vkWSikLD~ee 61 (75)
T PF11869_consen 28 LQAQVDDITLIGGANVIIANGGEVKWSIKLDNEE 61 (75)
T ss_pred EEEeeeehhhcCCCcEEEEeCcceEEEEEcCCHH
Confidence 3556789999999998 579999999988654
No 7
>PF07619 DUF1581: Protein of unknown function (DUF1581); InterPro: IPR022660 Several Rhodopirellula baltica proteins share this domain. They also match PF07622 from PFAM
Probab=42.78 E-value=20 Score=23.60 Aligned_cols=14 Identities=21% Similarity=0.622 Sum_probs=11.9
Q ss_pred EEEEEeeCCCCccC
Q 034873 7 VEAVKLTGDLNVPA 20 (80)
Q Consensus 7 leAvKLTGDpNVPr 20 (80)
+.-+.|||||-+|+
T Consensus 43 frNlrItG~P~iP~ 56 (84)
T PF07619_consen 43 FRNLRITGSPEIPD 56 (84)
T ss_pred eeeeEEcCCCcCCC
Confidence 45688999999997
No 8
>PF09284 RhgB_N: Rhamnogalacturonase B, N-terminal; InterPro: IPR015364 This domain is found in prokaryotic enzyme rhamnogalacturonase B, it adopts a structure consisting of a beta supersandwich, with eighteen strands in two beta-sheets. The exact function of the domain is unknown, but a putative role includes carbohydrate-binding []. ; GO: 0016837 carbon-oxygen lyase activity, acting on polysaccharides, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process; PDB: 1NKG_A 2XHN_B 3NJX_A 3NJV_A.
Probab=40.59 E-value=40 Score=26.09 Aligned_cols=69 Identities=19% Similarity=0.341 Sum_probs=35.8
Q ss_pred EEEEeeCCCCccCceEEEEEEcCCCcCCCCCCC---CCCCCCC----c-eE-EEeeeEEcCCCCCCCceeeeEEEEEcCC
Q 034873 8 EAVKLTGDLNVPAGEVTFRAKIGKGSRLPNRGK---FPDELGV----V-AS-YSGQGRIADFGFRNPKWVDGELLQLNGK 78 (80)
Q Consensus 8 eAvKLTGDpNVPrGevtf~A~ig~~~~~~~~g~---~~~e~~~----~-ar-~~g~G~VA~~Gf~~~~~i~~~Lilis~~ 78 (80)
.|+-.|.||+| ||.-|.|+|.+. .+|+.+. +.+.-+. + -. ..+.|+=+..=|.+.++||-+..-+++.
T Consensus 90 maT~~~~e~~i--gelRfIaRL~~~-~lpn~~~~~~~~~~~g~taIEgsDVf~~~~G~TrSKfYSs~r~IDd~~hgv~g~ 166 (249)
T PF09284_consen 90 MATYITAEPSI--GELRFIARLNRS-ILPNEYPYGDVSTTDGGTAIEGSDVFLVSDGQTRSKFYSSQRFIDDDVHGVSGS 166 (249)
T ss_dssp EEEEESS--TT--S-EEEEEEE-TT-TS-EEETTGGGG--TT-EEEETTTEEEE-TTEEEEGGGG--BGGG-SEEEEE-S
T ss_pred EEeccCCCCCc--cceEEEEEcccc-cCCCCCCcccccccCCceEEeeccEEEecCceEeeeeccccceeccceEEEecC
Confidence 57788999887 799999999763 2232111 1100010 0 11 2236888888888889999888877765
Q ss_pred C
Q 034873 79 V 79 (80)
Q Consensus 79 ~ 79 (80)
.
T Consensus 167 ~ 167 (249)
T PF09284_consen 167 A 167 (249)
T ss_dssp S
T ss_pred C
Confidence 4
No 9
>PF07495 Y_Y_Y: Y_Y_Y domain; InterPro: IPR011123 This region is mostly found at the end of the beta propellers (IPR011110 from INTERPRO) in a family of two component regulators. However they are also found tandemly repeated in Q891H4 from SWISSPROT without other signal conduction domains being present. It is named after the conserved tyrosines found in the alignment. The exact function is not known.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=36.74 E-value=31 Score=19.47 Aligned_cols=13 Identities=31% Similarity=0.695 Sum_probs=10.0
Q ss_pred CccCceEEEEEEc
Q 034873 17 NVPAGEVTFRAKI 29 (80)
Q Consensus 17 NVPrGevtf~A~i 29 (80)
|.|.|.++|.+..
T Consensus 35 ~L~~G~Y~l~V~a 47 (66)
T PF07495_consen 35 NLPPGKYTLEVRA 47 (66)
T ss_dssp S--SEEEEEEEEE
T ss_pred eCCCEEEEEEEEE
Confidence 7899999999994
No 10
>PF12142 PPO1_DWL: Polyphenol oxidase middle domain; InterPro: IPR022739 This domain is found in bacteria and eukaryotes and is approximately 50 amino acids in length. It is found in association with PF00264 from PFAM and PF12143 from PFAM. Most members are annotated as being polyphenol oxidases, and many are from plants or plastids. There is a conserved DWL sequence motif. ; GO: 0004097 catechol oxidase activity, 0055114 oxidation-reduction process; PDB: 1BT3_A 1BUG_B 1BT1_B 1BT2_B 2P3X_A.
Probab=35.55 E-value=13 Score=22.46 Aligned_cols=18 Identities=22% Similarity=0.708 Sum_probs=11.6
Q ss_pred CCCCceeeeEEEEEcCCC
Q 034873 62 FRNPKWVDGELLQLNGKV 79 (80)
Q Consensus 62 f~~~~~i~~~Lilis~~~ 79 (80)
|.++.|.+++.++.++++
T Consensus 2 ~tD~dWLns~F~FYDen~ 19 (54)
T PF12142_consen 2 FTDPDWLNSSFLFYDENG 19 (54)
T ss_dssp ---HHHHT-EEEEE-TTS
T ss_pred CCccccccCeeEEECCCC
Confidence 678999999999998875
No 11
>PF04283 CheF-arch: Chemotaxis signal transduction system protein F from archaea; InterPro: IPR007381 This is an archaeal protein of unknown function.
Probab=34.81 E-value=62 Score=23.96 Aligned_cols=31 Identities=23% Similarity=0.372 Sum_probs=22.9
Q ss_pred ceEEEeeeEEcCCCC---CCCceeeeEEEEEcCC
Q 034873 48 VASYSGQGRIADFGF---RNPKWVDGELLQLNGK 78 (80)
Q Consensus 48 ~ar~~g~G~VA~~Gf---~~~~~i~~~Lilis~~ 78 (80)
.|.+.|++..+...= .+.+|++|+++|-+.+
T Consensus 3 iadf~Gkf~~~~~~~~~~~d~~W~~~rIiLs~~r 36 (221)
T PF04283_consen 3 IADFVGKFIQVVSDGRKLPDGKWVKGRIILSNDR 36 (221)
T ss_pred eEEEeCcEEEEccCCcccccCCcEEEEEEEecCE
Confidence 467888887765544 5689999999886643
No 12
>PF01186 Lysyl_oxidase: Lysyl oxidase ; InterPro: IPR001695 Lysyl oxidase (1.4.3.13 from EC) (LOX) [] is an extracellular copper-dependent enzyme that catalyses the oxidative deamination of peptidyl lysine residues in precursors of various collagens and elastins, yielding alpha-aminoadipic-delta-semialdehyde. The deaminated lysines are then able to form semialdehyde cross-links, resulting in the formation of insoluble collagen and elastin fibres in the extracellular matrix []. The active site of LOX resides towards the C terminus: this region also binds a single copper atom in an octahedral coordination complex involving at least 3 His residues []. Four histidine residues are clustered in a central region of the enzyme. This region is thought to be involved in cooper-binding and is called the 'copper-talon' [].; GO: 0005507 copper ion binding, 0016641 oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor, 0055114 oxidation-reduction process
Probab=32.51 E-value=47 Score=24.95 Aligned_cols=22 Identities=18% Similarity=0.451 Sum_probs=18.0
Q ss_pred CccCceEEEEEEcCCCcCCCCC
Q 034873 17 NVPAGEVTFRAKIGKGSRLPNR 38 (80)
Q Consensus 17 NVPrGevtf~A~ig~~~~~~~~ 38 (80)
-||-|.++|++.+.|...+++.
T Consensus 156 dvp~G~Y~l~V~vNP~~~v~Es 177 (205)
T PF01186_consen 156 DVPPGTYILQVTVNPEYRVAES 177 (205)
T ss_pred CCCCccEEEEEecCCccccccc
Confidence 4889999999999988776443
No 13
>PF06883 RNA_pol_Rpa2_4: RNA polymerase I, Rpa2 specific domain ; InterPro: IPR009674 This domain is found between domain 3 and domain 5, but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=28.62 E-value=2.5 Score=25.59 Aligned_cols=17 Identities=24% Similarity=0.481 Sum_probs=13.7
Q ss_pred eeEEEEEEeeCCCCccC
Q 034873 4 FEYVEAVKLTGDLNVPA 20 (80)
Q Consensus 4 ~e~leAvKLTGDpNVPr 20 (80)
.+.|...|+.|+.+||.
T Consensus 13 ~~~LR~~Kv~~~~~vP~ 29 (58)
T PF06883_consen 13 ADQLRYLKVEGEHGVPP 29 (58)
T ss_pred HHHHHHHHHcCCCCCCC
Confidence 45667789999999994
No 14
>PLN00115 pollen allergen group 3; Provisional
Probab=28.60 E-value=59 Score=22.21 Aligned_cols=39 Identities=13% Similarity=0.119 Sum_probs=24.8
Q ss_pred ccCceEEEEEEcCCCcCCCCCCCCCCCCCCceEEEeeeE
Q 034873 18 VPAGEVTFRAKIGKGSRLPNRGKFPDELGVVASYSGQGR 56 (80)
Q Consensus 18 VPrGevtf~A~ig~~~~~~~~g~~~~e~~~~ar~~g~G~ 56 (80)
.|+|-.|||........+....++|..-..|..|++.=|
T Consensus 79 pl~GPlS~R~t~~~G~~~va~nViPa~Wk~G~tY~s~vq 117 (118)
T PLN00115 79 PLKGPFSVRFLVKGGGYRVVDDVIPESFKAGSVYKTGIQ 117 (118)
T ss_pred CCCCceEEEEEEeCCCEEEECceECCCCCCCCEEecccc
Confidence 567888888875433333345667777667777776533
No 15
>KOG3265 consensus Histone chaperone involved in gene silencing [Transcription; Chromatin structure and dynamics]
Probab=25.60 E-value=82 Score=24.46 Aligned_cols=43 Identities=28% Similarity=0.508 Sum_probs=25.9
Q ss_pred CccCceEEEEEEcCCCcCCCCCCCCCCCC--C-----CceEEEee-----eEEcCCCCC
Q 034873 17 NVPAGEVTFRAKIGKGSRLPNRGKFPDEL--G-----VVASYSGQ-----GRIADFGFR 63 (80)
Q Consensus 17 NVPrGevtf~A~ig~~~~~~~~g~~~~e~--~-----~~ar~~g~-----G~VA~~Gf~ 63 (80)
-||.|..-|+-+.+++.. ..+|.+- + -.|+|+|| |-..+.+|.
T Consensus 64 PVP~G~~~FVf~AD~Pd~----~kIP~~d~vGVTviLltC~Y~gQEFIRvGYyVnNeY~ 118 (250)
T KOG3265|consen 64 PVPVGRHKFVFQADAPDP----SKIPEDDIVGVTVILLTCSYRGQEFIRVGYYVNNEYT 118 (250)
T ss_pred cccccceEEEEecCCCCc----ccCcccceeeeEEEEEEEEEcCceeEEEEEEecCCCC
Confidence 489999999888766432 2344331 2 24778887 344444444
No 16
>PF01458 UPF0051: Uncharacterized protein family (UPF0051); InterPro: IPR000825 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents SufB and SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0016226 iron-sulfur cluster assembly; PDB: 1VH4_B 2ZU0_A 4DN7_A.
Probab=23.73 E-value=2.5e+02 Score=20.04 Aligned_cols=30 Identities=13% Similarity=0.121 Sum_probs=26.3
Q ss_pred eEEEeeeEEcCCCCCCCceeeeEEEEEcCC
Q 034873 49 ASYSGQGRIADFGFRNPKWVDGELLQLNGK 78 (80)
Q Consensus 49 ar~~g~G~VA~~Gf~~~~~i~~~Lilis~~ 78 (80)
..++|.++|....-....+..++.+++|++
T Consensus 147 ~vf~G~i~i~~~a~~s~~~q~~~~llls~~ 176 (229)
T PF01458_consen 147 VVFRGRIKIEKGAQGSDAHQECRNLLLSDE 176 (229)
T ss_dssp EEEEEEEEEECTSTTEEEEEEEEEEE-STT
T ss_pred EEEEeEEEEhhhhhCChheeeEeeEEccCC
Confidence 449999999999999999999999999876
No 17
>PF12892 FctA: T surface-antigen of pili; InterPro: IPR022464 This entry describes a domain that occurs once in the major pilin of Streptococcus pyogenes, Spy0128, but in higher copy numbers in other streptococcal and related bacteria proteins. The domain occurs nine times in a surface-anchored protein of Bifidobacterium longum. All members of this family have LPXTG-type sortase target sequences. The Streptococcus pyogenes major pilin has been shown to undergo isopeptide bond cross-linking, mediated by sortases, that are critical to maintaining pilus structural integrity. One such Lys-to-Asn isopeptide bond is to a near-invariant Asn near the C-terminal end of this domain. A Glu in the S. pyogenes major pilin, invariant as Glu or Gln, is described as catalytic for isopeptide bond formation []. ; PDB: 3GLE_C 3B2M_B 3GLD_C 3KLQ_B.
Probab=23.43 E-value=1e+02 Score=18.14 Aligned_cols=19 Identities=26% Similarity=0.338 Sum_probs=11.1
Q ss_pred EeeCCCCccCceEEEEEEc
Q 034873 11 KLTGDLNVPAGEVTFRAKI 29 (80)
Q Consensus 11 KLTGDpNVPrGevtf~A~i 29 (80)
+|+|...-+.++.+|...+
T Consensus 69 ~l~G~~~~~~~~F~F~l~~ 87 (88)
T PF12892_consen 69 TLSGRDGLKDKEFTFTLTA 87 (88)
T ss_dssp EEESTT--TT--EEEEEEE
T ss_pred EeeCCCcCcCCcEEEEEEe
Confidence 3678877888888887753
No 18
>PRK06032 fliH flagellar assembly protein H; Validated
Probab=22.92 E-value=81 Score=22.49 Aligned_cols=23 Identities=13% Similarity=0.245 Sum_probs=19.2
Q ss_pred EEEEeeCCCCccCceEEEEEEcC
Q 034873 8 EAVKLTGDLNVPAGEVTFRAKIG 30 (80)
Q Consensus 8 eAvKLTGDpNVPrGevtf~A~ig 30 (80)
..++|.+||.+++|.+.....-|
T Consensus 157 ~~~~l~~D~~L~~G~c~vet~~G 179 (199)
T PRK06032 157 GRLVVLADPDMAPGDCRLEWADG 179 (199)
T ss_pred ccEEEeeCCCCCCCCeEEEeCCC
Confidence 45889999999999998877644
No 19
>cd07990 LPLAT_LCLAT1-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are such LPLATs as Lysocardiolipin acyltransferase 1 (LCLAT1) or 1-acyl-sn-glycerol-3-phosphate acyltransferase and similar proteins.
Probab=22.19 E-value=1.6e+02 Score=20.19 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=19.2
Q ss_pred eeeEE--EEEEeeCCCCc-cCceEEEEEE
Q 034873 3 FFEYV--EAVKLTGDLNV-PAGEVTFRAK 28 (80)
Q Consensus 3 ~~e~l--eAvKLTGDpNV-PrGevtf~A~ 28 (80)
++|.+ .-++++||.|. |.+.+-+.++
T Consensus 3 ~~~~~~g~~i~v~G~~~~~~~~~~iiv~N 31 (193)
T cd07990 3 LFEWLSGVKVVVYGDEPKLPKERALIISN 31 (193)
T ss_pred EEEEecCeEEEEEecCccCCCccEEEEEc
Confidence 45655 45789999999 7777777666
No 20
>TIGR02499 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family. This model is related to Pfam model pfam06188, but is broader. pfam06188 describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This model includes also the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This model excludes the related protein FliH of the bacterial flagellar apparatus (see pfam02108)
Probab=22.18 E-value=84 Score=20.88 Aligned_cols=21 Identities=19% Similarity=0.371 Sum_probs=17.9
Q ss_pred EEeeCCCCccCceEEEEEEcC
Q 034873 10 VKLTGDLNVPAGEVTFRAKIG 30 (80)
Q Consensus 10 vKLTGDpNVPrGevtf~A~ig 30 (80)
+.|..||++++|.+......|
T Consensus 141 ~~i~~D~~l~~G~c~vet~~G 161 (166)
T TIGR02499 141 WELEPDASLAPGACVLETESG 161 (166)
T ss_pred eEEeeCCCCCCCCEEEEeCCc
Confidence 789999999999998877654
Done!