Query 031683
Match_columns 155
No_of_seqs 97 out of 99
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 03:55:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031683.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031683hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13474 cytochrome b6-f compl 99.9 3.5E-24 7.7E-29 169.3 2.7 90 54-143 3-92 (178)
2 PF08802 CytB6-F_Fe-S: Cytochr 99.8 2.3E-22 4.9E-27 129.7 -2.7 39 58-96 1-39 (39)
3 TIGR03171 soxL2 Rieske iron-su 99.7 1.3E-17 2.7E-22 145.0 2.1 84 60-145 58-143 (321)
4 KOG1671 Ubiquinol cytochrome c 99.3 1.2E-12 2.7E-17 109.0 4.9 132 1-139 2-135 (210)
5 cd03471 Rieske_cytochrome_b6f 99.0 9.5E-11 2.1E-15 89.9 1.9 40 104-143 1-40 (126)
6 COG0723 QcrA Rieske Fe-S prote 97.4 9.6E-05 2.1E-09 57.4 2.6 84 58-141 4-88 (177)
7 TIGR01416 Rieske_proteo ubiqui 96.6 0.00071 1.5E-08 53.8 1.0 38 64-101 1-38 (174)
8 PF10399 UCR_Fe-S_N: Ubiquitin 95.5 0.0011 2.3E-08 43.0 -2.5 38 57-94 3-40 (41)
9 TIGR02811 formate_TAT formate 86.3 0.35 7.6E-06 33.9 1.0 28 59-86 5-32 (66)
10 PF10518 TAT_signal: TAT (twin 84.5 0.55 1.2E-05 27.5 1.1 22 62-83 1-22 (26)
11 PF03935 SKN1: Beta-glucan syn 64.1 6.4 0.00014 37.2 2.9 76 61-136 35-116 (504)
12 PF06135 DUF965: Bacterial pro 61.3 3.2 6.9E-05 30.7 0.4 11 134-144 44-54 (79)
13 TIGR01409 TAT_signal_seq Tat ( 59.8 4.6 9.9E-05 23.8 0.8 19 63-81 1-19 (29)
14 PRK05473 hypothetical protein; 56.0 4.4 9.6E-05 30.4 0.4 11 134-144 47-57 (86)
15 PRK09476 napG quinol dehydroge 54.4 6.5 0.00014 33.1 1.2 25 60-84 6-30 (254)
16 PRK02888 nitrous-oxide reducta 40.9 22 0.00047 34.6 2.5 28 58-85 4-31 (635)
17 PF00970 FAD_binding_6: Oxidor 39.5 15 0.00032 24.9 0.9 51 88-140 47-99 (99)
18 PRK09898 hypothetical protein; 38.9 14 0.00029 29.7 0.7 20 130-150 108-127 (208)
19 PF06024 DUF912: Nucleopolyhed 34.2 7 0.00015 28.8 -1.5 31 63-93 55-85 (101)
20 PTZ00334 trans-sialidase; Prov 31.4 61 0.0013 32.3 3.9 66 31-99 8-89 (780)
21 COG4031 Predicted metal-bindin 30.6 32 0.0007 29.7 1.7 29 85-113 151-187 (227)
22 PLN02289 ribulose-bisphosphate 29.1 83 0.0018 26.5 3.8 29 44-72 49-85 (176)
23 COG4472 Uncharacterized protei 25.9 27 0.00058 26.5 0.4 11 134-144 47-57 (88)
24 PF05688 DUF824: Salmonella re 25.8 30 0.00065 23.1 0.6 20 104-123 19-38 (47)
25 PRK10882 hydrogenase 2 protein 25.7 36 0.00078 30.1 1.2 16 63-78 1-16 (328)
26 TIGR02659 TTQ_MADH_Lt methylam 25.3 36 0.00078 28.8 1.1 27 63-90 22-48 (186)
27 PLN00042 photosystem II oxygen 24.5 98 0.0021 27.2 3.6 27 46-75 36-62 (260)
28 PF00173 Cyt-b5: Cytochrome b5 24.0 35 0.00077 22.2 0.7 33 110-142 21-53 (76)
29 PRK11130 moaD molybdopterin sy 23.6 42 0.0009 23.0 1.0 8 92-99 74-81 (81)
No 1
>PRK13474 cytochrome b6-f complex iron-sulfur subunit; Provisional
Probab=99.89 E-value=3.5e-24 Score=169.26 Aligned_cols=90 Identities=47% Similarity=0.737 Sum_probs=85.6
Q ss_pred cCCCCCCCCchhHHHHHHHhhhccccccceeccceEEEeecCCCCCCCCccccccccCCcchhhhhhccCCCCCchhhcc
Q 031683 54 SIPADRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEG 133 (155)
Q Consensus 54 s~~~~~vPDM~RRqlMNlLl~Gava~~a~g~LyP~v~fFVPP~sgGggGGv~AKDalGNdI~as~wL~th~pGdR~LvqG 133 (155)
+..+++||||+||+|||.+++|++++.++++++|+++||+||.+++++|+.+|||++||+|++++|+++|++|++.++++
T Consensus 3 ~~~~~~~~d~~RR~FL~~~~~~~gg~~a~~~~~P~v~~~~Pp~~~~~~g~~~a~d~~G~~I~~s~~~~~~~~g~~~~v~~ 82 (178)
T PRK13474 3 QSGSSDVPSMGRRQFMNLLTFGTVTGVALGALYPVVKYFIPPSAGGAGGGTTAKDELGNDIPASQFLATHPAGDRSLVQG 82 (178)
T ss_pred ccccCCCCCccHHHHHHHHHHHHHHHHHHHHHHHhhheeCChhHccCCCcceeecccCCeeehhhccccCCCCCcEEEEE
Confidence 45568999999999999999999999999999999999999999989999999999999999999999999999999999
Q ss_pred cCCCceeeee
Q 031683 134 LKVQINFFEN 143 (155)
Q Consensus 134 LKGDpTYLi~ 143 (155)
++|+++|||-
T Consensus 83 ~~g~~~~lv~ 92 (178)
T PRK13474 83 LKGDPTYLVV 92 (178)
T ss_pred cCCCeEEEEE
Confidence 9999988874
No 2
>PF08802 CytB6-F_Fe-S: Cytochrome B6-F complex Fe-S subunit ; InterPro: IPR014909 The cytochrome b6-f complex mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions. The cytochrome b6-f complex has 4 large subunits, these are: cytochrome b6, subunit IV (17 kDa polypeptide, PetD), cytochrome f and the Rieske protein, while the 4 small subunits are: PetG, PetL, PetM and PetN. The complex functions as a dimer. This protein corresponds to the alpha helical transmembrane domain of the cytochrome b6-f complex Rieske iron-sulphur subunit. ; GO: 0009496 plastoquinol-plastocyanin reductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process, 0042651 thylakoid membrane; PDB: 1Q90_R 1VF5_D 2E75_D 2E74_D 2E76_D 2D2C_Q 2ZT9_D.
Probab=99.82 E-value=2.3e-22 Score=129.65 Aligned_cols=39 Identities=69% Similarity=1.169 Sum_probs=31.0
Q ss_pred CCCCCchhHHHHHHHhhhccccccceeccceEEEeecCC
Q 031683 58 DRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPG 96 (155)
Q Consensus 58 ~~vPDM~RRqlMNlLl~Gava~~a~g~LyP~v~fFVPP~ 96 (155)
|+|||||||||||+|++|++++++++++|||++|||||+
T Consensus 1 d~VPdm~RR~lmN~ll~Gava~~a~~~lyP~~~ffvPP~ 39 (39)
T PF08802_consen 1 DRVPDMSRRQLMNLLLGGAVAVPAGGMLYPYVKFFVPPS 39 (39)
T ss_dssp -----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS---
T ss_pred CCCCChhHHHHHHHHHHhhHHHHHHHHhhhheeEecCCC
Confidence 579999999999999999999999999999999999995
No 3
>TIGR03171 soxL2 Rieske iron-sulfur protein SoxL2. This iron-sulfur protein is found in a contiguous genomic region with subunits of cytochrome b558/566 in several archaeal species, and appears to be part of a cytochrome bc1-analogous system.
Probab=99.67 E-value=1.3e-17 Score=145.02 Aligned_cols=84 Identities=21% Similarity=0.302 Sum_probs=74.7
Q ss_pred CCCchhHHHHHHHhhhccccccceeccceEEEeecCCCCCCC--CccccccccCCcchhhhhhccCCCCCchhhcccCCC
Q 031683 60 VPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAG--GGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKVQ 137 (155)
Q Consensus 60 vPDM~RRqlMNlLl~Gava~~a~g~LyP~v~fFVPP~sgGgg--GGv~AKDalGNdI~as~wL~th~pGdR~LvqGLKGD 137 (155)
-|||+||+|||++++|++++++++ ++|+++||+||..+.++ +.++|+|++||||.+|+ |..|.+.++.+.+++++|
T Consensus 58 ~vD~~RR~fL~~al~gAga~a~~~-avPlv~~l~PP~~a~atG~pk~La~D~~GnPIKASd-L~vnSp~~~lfeyPl~gd 135 (321)
T TIGR03171 58 GVDEGRRKFLKGLIFGIAAAAVVG-IIPGLRVLVPPTVAAASGFPKSLLVDSSGNPIKASS-IPVNSPIITIFEYPMTGE 135 (321)
T ss_pred CCCccHHHHHHHHHHHHHHHHhhh-hhhheecccCchhhhccCCCceEEecCCCCeeeHHH-ccCCCcccccccCcCCCC
Confidence 479999999999999999976666 78999999999875544 45999999999999999 667999999999999999
Q ss_pred ceeeeeeh
Q 031683 138 INFFENYC 145 (155)
Q Consensus 138 pTYLi~~~ 145 (155)
|+|||+--
T Consensus 136 P~fLIklg 143 (321)
T TIGR03171 136 PNFLLNLG 143 (321)
T ss_pred cHHHHHhh
Confidence 99999863
No 4
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=99.33 E-value=1.2e-12 Score=108.96 Aligned_cols=132 Identities=17% Similarity=0.090 Sum_probs=120.4
Q ss_pred CCCCCCCCCCCcccccccCCCCCcccccccccccc--ccccccCCCcceeeeeeccCCCCCCCCchhHHHHHHHhhhccc
Q 031683 1 MASSSSLSSATPSQLCSSKGGMFCPSRAFLVKPAR--TQMVTKNPMGMKIKCQATSIPADRVPDMGKRQLMNLLLLGAVS 78 (155)
Q Consensus 1 mas~~~ls~~~psql~~~~~~~~~~~~~l~~k~~~--~~~~~k~~~~~~~~~~a~s~~~~~vPDM~RRqlMNlLl~Gava 78 (155)
|+| +++|....+||-++..-+..|.-...+++.. .++.+++.|+....||..+..+..+++++.+-+.++...+|.+
T Consensus 2 ~~s-~s~~~~~s~~l~~~~t~~~~p~~~~~~~~~~~~~~~~~~~~k~~~sy~~~g~~~~~~a~~ak~~v~~fi~smsAsa 80 (210)
T KOG1671|consen 2 MSS-SSLSRVLSTGLGSSHTDLMVPDFSDYRRESVKDHQDTGEERKGFRSYLMVGAGAAGRAYAAKNLVTTFISSMSASA 80 (210)
T ss_pred ccc-cccchhhccccccccccccCCCchhhhchhhhccccchhhhhceeeEEEecccceeehhhhhhhHHHHHHHhhhhh
Confidence 444 6777755679999999999999999998877 3556777667889999999999999999999999999999999
Q ss_pred cccceeccceEEEeecCCCCCCCCccccccccCCcchhhhhhccCCCCCchhhcccCCCce
Q 031683 79 LPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKVQIN 139 (155)
Q Consensus 79 ~~a~g~LyP~v~fFVPP~sgGggGGv~AKDalGNdI~as~wL~th~pGdR~LvqGLKGDpT 139 (155)
-+.+.+++||..++||+ |+..|++..|||+.+.+|+++|-+++|++-|+.++||+
T Consensus 81 dvlA~akiei~l~~IPe------Gk~~~~kwrGkpvfirhrt~~ei~~~r~V~~s~lrDPq 135 (210)
T KOG1671|consen 81 DVLAMAKIEIKLSDIPE------GKTVAFKWRGKPVFIRHRTKAEIEGERNVPQSTLRDPQ 135 (210)
T ss_pred hhhhheeeeeeeecCCC------CCCcceeccCCceEEeeccccccccccccchhhccCch
Confidence 99999999999999999 78999999999999999999999999999999999997
No 5
>cd03471 Rieske_cytochrome_b6f Iron-sulfur protein (ISP) component of the b6f complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The cytochrome b6f complex from Mastigocladus laminosus, a thermophilic cyanobacterium, contains four large subunits, including cytochrome f, cytochrome b6, the Rieske ISP, and subunit IV; as well as four small hydrophobic subunits, PetG, PetL, PetM, and PetN. Rieske ISP, one of the large subunits of the cytochrome bc-type complexes, is involved in respiratory and photosynthetic electron transfer. The core of the chloroplast b6f complex is similar to the analogous respiratory cytochrome bc(1) complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.
Probab=99.02 E-value=9.5e-11 Score=89.91 Aligned_cols=40 Identities=50% Similarity=0.865 Sum_probs=37.3
Q ss_pred cccccccCCcchhhhhhccCCCCCchhhcccCCCceeeee
Q 031683 104 TTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKVQINFFEN 143 (155)
Q Consensus 104 v~AKDalGNdI~as~wL~th~pGdR~LvqGLKGDpTYLi~ 143 (155)
+.|||||||||++++||+||.|||+.++|+..+++.++|-
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~ 40 (126)
T cd03471 1 VAAKDALGNDIKVSKWLATHNPGDRSLVQGLKGDPTYLIV 40 (126)
T ss_pred CccccccCCceeHHHHHhhCCCCCeEEEEEecCCeEEEEE
Confidence 4699999999999999999999999999999999988763
No 6
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=97.42 E-value=9.6e-05 Score=57.42 Aligned_cols=84 Identities=17% Similarity=0.066 Sum_probs=70.7
Q ss_pred CCCCCchhHHHHHHHhhhccccccceeccceEEEeecCCCC-CCCCccccccccCCcchhhhhhccCCCCCchhhcccCC
Q 031683 58 DRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLG-SAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKV 136 (155)
Q Consensus 58 ~~vPDM~RRqlMNlLl~Gava~~a~g~LyP~v~fFVPP~sg-GggGGv~AKDalGNdI~as~wL~th~pGdR~LvqGLKG 136 (155)
....++.||++|+.++.+.++..+..++||.+.++.|+..+ ..+..+.++|...+++.......+..|..+.+.....+
T Consensus 4 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~ 83 (177)
T COG0723 4 AAATGLSRRDFLVLLTTGVGAVGAGAALYPAVESVDPPAGGGLAGAPIEVDDSGIGPGPLVTVPWRGKPVFLLRRTEYAG 83 (177)
T ss_pred cccccccHHHhhhhhhccccccceeeeeeehhhcccCcccccccCCceeeeccCCccceEEEEecCCCCeeeEeeccccc
Confidence 35678999999999999999999999999999999997765 88888999999989999988888888888776665555
Q ss_pred Cceee
Q 031683 137 QINFF 141 (155)
Q Consensus 137 DpTYL 141 (155)
+..|.
T Consensus 84 ~~~~~ 88 (177)
T COG0723 84 PKGGV 88 (177)
T ss_pred ccccc
Confidence 44443
No 7
>TIGR01416 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix.
Probab=96.64 E-value=0.00071 Score=53.80 Aligned_cols=38 Identities=13% Similarity=0.159 Sum_probs=33.9
Q ss_pred hhHHHHHHHhhhccccccceeccceEEEeecCCCCCCC
Q 031683 64 GKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAG 101 (155)
Q Consensus 64 ~RRqlMNlLl~Gava~~a~g~LyP~v~fFVPP~sgGgg 101 (155)
+||+||+.++.+++++.++++++|+++|+-|.....++
T Consensus 1 ~RR~fl~~~~~~~~~~~~~~~~~p~v~~~~P~~~~~a~ 38 (174)
T TIGR01416 1 TRRDFLYAATGAVGAVGAAAAAVPFIDSMNPSASVKAA 38 (174)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHheeCcchhcccc
Confidence 59999999999999999999999999999887765554
No 8
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=95.50 E-value=0.0011 Score=43.05 Aligned_cols=38 Identities=11% Similarity=0.233 Sum_probs=28.7
Q ss_pred CCCCCCchhHHHHHHHhhhccccccceeccceEEEeec
Q 031683 57 ADRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAP 94 (155)
Q Consensus 57 ~~~vPDM~RRqlMNlLl~Gava~~a~g~LyP~v~fFVP 94 (155)
.++..|-+||.||.+.+.+++++-++++++|+++.+-|
T Consensus 3 ~~~~~~~~RRdFL~~at~~~gavG~~~~a~Pfv~s~~P 40 (41)
T PF10399_consen 3 SNEPVDPTRRDFLTIATSAVGAVGAAAAAWPFVSSMNP 40 (41)
T ss_dssp -------HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS
T ss_pred CCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 34567899999999999999999999999999887666
No 9
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=86.32 E-value=0.35 Score=33.86 Aligned_cols=28 Identities=21% Similarity=0.177 Sum_probs=19.5
Q ss_pred CCCCchhHHHHHHHhhhccccccceecc
Q 031683 59 RVPDMGKRQLMNLLLLGAVSLPTGFMLV 86 (155)
Q Consensus 59 ~vPDM~RRqlMNlLl~Gava~~a~g~Ly 86 (155)
.-++.+||+||-.|.+|++++.++...-
T Consensus 5 ~~~~~sRR~Flk~lg~~aaa~~aa~~~~ 32 (66)
T TIGR02811 5 QKADPSRRDLLKGLGVGAAAGAVAAATG 32 (66)
T ss_pred ccCCccHHHHHHHHHHHHHHHHHHHhcc
Confidence 4567899999998877666555544333
No 10
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=84.49 E-value=0.55 Score=27.53 Aligned_cols=22 Identities=18% Similarity=0.202 Sum_probs=15.5
Q ss_pred CchhHHHHHHHhhhccccccce
Q 031683 62 DMGKRQLMNLLLLGAVSLPTGF 83 (155)
Q Consensus 62 DM~RRqlMNlLl~Gava~~a~g 83 (155)
.|+|||||-.....+++..+++
T Consensus 1 ~~sRR~fLk~~~a~~a~~~~~~ 22 (26)
T PF10518_consen 1 NLSRRQFLKGGAAAAAAAALGG 22 (26)
T ss_pred CCcHHHHHHHHHHHHHHHHhcc
Confidence 4799999988766555554444
No 11
>PF03935 SKN1: Beta-glucan synthesis-associated protein (SKN1); InterPro: IPR005629 This family consists of the beta-glucan synthesis-associated proteins KRE6 and SKN1. Beta1,6-Glucan is a key component of the yeast cell wall, interconnecting cell wall proteins, beta1,3-glucan, and chitin. It has been postulated that the synthesis of beta1,6-glucan begins in the endoplasmic reticulum with the formation of protein-bound primer structures and that these primer structures are extended in the Golgi complex by two putative glucosyltransferases that are functionally redundant, Kre6 and Skn1. This is followed by maturation steps at the cell surface and by coupling to other cell wall macromolecules [].
Probab=64.09 E-value=6.4 Score=37.17 Aligned_cols=76 Identities=21% Similarity=0.152 Sum_probs=45.3
Q ss_pred CCchhHHHHHHHhhhccc--cccceeccceEEEeec---CCCCCCCCccccccccCCcchh-hhhhccCCCCCchhhccc
Q 031683 61 PDMGKRQLMNLLLLGAVS--LPTGFMLVPYATFFAP---PGLGSAGGGTTAKDAIGNDIIA-ADWLNTHGPGDRTLTEGL 134 (155)
Q Consensus 61 PDM~RRqlMNlLl~Gava--~~a~g~LyP~v~fFVP---P~sgGggGGv~AKDalGNdI~a-s~wL~th~pGdR~LvqGL 134 (155)
--|+||.++|+..+..++ ++++...||++.||-= +..++..+++.+.-..-+--.. ..|+.-..|-+.---++.
T Consensus 35 ~~~s~RGl~Nlg~LilL~lGLL~LFigyPIlt~~~~~~~~~~~~~~~~~~~~~~~p~l~~~~~~liDpdTP~~a~t~~~~ 114 (504)
T PF03935_consen 35 DIFSRRGLLNLGGLILLILGLLMLFIGYPILTFFGKTNHSTSGGNLGGINASGQYPLLSNIRTGLIDPDTPESAYTRTSS 114 (504)
T ss_pred cccchhhhhHHHHHHHHHHHHHHHHHHhhheeEEecccccccccccccccccccCcccccccccccCCCCCHHHhheeCC
Confidence 358999999997776544 6777789999999964 3334444555544332221111 246555555554444455
Q ss_pred CC
Q 031683 135 KV 136 (155)
Q Consensus 135 KG 136 (155)
.|
T Consensus 115 ~g 116 (504)
T PF03935_consen 115 DG 116 (504)
T ss_pred CC
Confidence 43
No 12
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=61.31 E-value=3.2 Score=30.75 Aligned_cols=11 Identities=9% Similarity=0.108 Sum_probs=9.4
Q ss_pred cCCCceeeeee
Q 031683 134 LKVQINFFENY 144 (155)
Q Consensus 134 LKGDpTYLi~~ 144 (155)
|-|||||+.+|
T Consensus 44 lSGDPaYItsh 54 (79)
T PF06135_consen 44 LSGDPAYITSH 54 (79)
T ss_pred ecCCCccccCc
Confidence 46999999886
No 13
>TIGR01409 TAT_signal_seq Tat (twin-arginine translocation) pathway signal sequence. Members with small amino acid side chains at the -1 and -3 positions from the C-terminus of the model should be predicted to be cleaved as are Sec pathway signal sequences. Members are almost exclusively bacterial, although archaeal sequences are also found. A large fraction of the members of this family may have bound redox-active cofactors.
Probab=59.79 E-value=4.6 Score=23.77 Aligned_cols=19 Identities=5% Similarity=0.128 Sum_probs=14.4
Q ss_pred chhHHHHHHHhhhcccccc
Q 031683 63 MGKRQLMNLLLLGAVSLPT 81 (155)
Q Consensus 63 M~RRqlMNlLl~Gava~~a 81 (155)
++||+||-+...+++++..
T Consensus 1 ~sRR~Flk~~~~~~a~~~~ 19 (29)
T TIGR01409 1 LSRRDFLKGAAAAGAAAGL 19 (29)
T ss_pred CchhhhHHHHHHHHHHHhc
Confidence 5899999999776665544
No 14
>PRK05473 hypothetical protein; Provisional
Probab=55.97 E-value=4.4 Score=30.43 Aligned_cols=11 Identities=9% Similarity=0.078 Sum_probs=9.3
Q ss_pred cCCCceeeeee
Q 031683 134 LKVQINFFENY 144 (155)
Q Consensus 134 LKGDpTYLi~~ 144 (155)
|-|||||+.+|
T Consensus 47 lSGDPaYItsh 57 (86)
T PRK05473 47 LSGDPAYIPRH 57 (86)
T ss_pred ccCCCCccCCc
Confidence 56999999886
No 15
>PRK09476 napG quinol dehydrogenase periplasmic component; Provisional
Probab=54.42 E-value=6.5 Score=33.09 Aligned_cols=25 Identities=20% Similarity=0.255 Sum_probs=15.6
Q ss_pred CCCchhHHHHHHHhhhcccccccee
Q 031683 60 VPDMGKRQLMNLLLLGAVSLPTGFM 84 (155)
Q Consensus 60 vPDM~RRqlMNlLl~Gava~~a~g~ 84 (155)
.-.++||+||-..+.+++.+.++++
T Consensus 6 ~~~~~rr~f~~~~~~~~~~~~~~~~ 30 (254)
T PRK09476 6 KPQNGRRRFLRDVVRTAGGLAAVGV 30 (254)
T ss_pred cCCccHHHHHHHHHHHHHHHHHHHH
Confidence 4569999999766544444434444
No 16
>PRK02888 nitrous-oxide reductase; Validated
Probab=40.92 E-value=22 Score=34.64 Aligned_cols=28 Identities=14% Similarity=0.205 Sum_probs=21.2
Q ss_pred CCCCCchhHHHHHHHhhhccccccceec
Q 031683 58 DRVPDMGKRQLMNLLLLGAVSLPTGFML 85 (155)
Q Consensus 58 ~~vPDM~RRqlMNlLl~Gava~~a~g~L 85 (155)
+.-++++||+|||--.++++++.++++.
T Consensus 4 ~~~~~~~rr~~~~~~~~~~~~~~~~~~~ 31 (635)
T PRK02888 4 EAPSGLSRRQFLGTAALAGAAGAAGSTG 31 (635)
T ss_pred cccCCccHHHhhhHHHHHhhhhhhhccc
Confidence 4578899999999877766666666543
No 17
>PF00970 FAD_binding_6: Oxidoreductase FAD-binding domain; InterPro: IPR008333 These sequences contain an oxidoreductase FAD-binding domain. To date, the 3D-structures of the flavoprotein domain of Zea mays (Maize) nitrate reductase [] and of pig NADH:cytochrome b5 reductase [] have been solved. The overall fold is similar to that of ferredoxin:NADP+ reductase []: the FAD-binding domain (N-terminal) has the topology of an anti-parallel beta-barrel, while the NAD(P)-binding domain (C-terminal) has the topology of a classical pyridine dinucleotide-binding fold (i.e. a central parallel beta-sheet flanked by 2 helices on each side).; PDB: 1JB9_A 3LVB_A 3LO8_A 1FRN_A 1FND_A 1BX1_A 1FNC_A 1FNB_A 1BX0_A 1FRQ_A ....
Probab=39.50 E-value=15 Score=24.90 Aligned_cols=51 Identities=16% Similarity=0.210 Sum_probs=33.8
Q ss_pred eEEEeecCCCCCCCCcc--ccccccCCcchhhhhhccCCCCCchhhcccCCCcee
Q 031683 88 YATFFAPPGLGSAGGGT--TAKDAIGNDIIAADWLNTHGPGDRTLTEGLKVQINF 140 (155)
Q Consensus 88 ~v~fFVPP~sgGggGGv--~AKDalGNdI~as~wL~th~pGdR~LvqGLKGDpTY 140 (155)
..+.|-|.+.....|-+ ..|-. ++=.+++||.+-.+||+-.+.|=.|+-+|
T Consensus 47 ~~R~yS~~s~~~~~~~~~~~ik~~--~~G~~S~~L~~l~~Gd~v~i~gP~G~f~y 99 (99)
T PF00970_consen 47 VSRPYSPASSPDDKGYLEFAIKRY--PNGRVSRYLHQLKPGDEVEIRGPYGNFTY 99 (99)
T ss_dssp EEEEEEBCSSTTSSSEEEEEEEEC--TTSHHHHHHHTSCTTSEEEEEEEESSEEE
T ss_pred eecceeEeeecCCCCcEEEEEEec--cCCHHHHHHHhCCCCCEEEEEEcccccCC
Confidence 45556655544333322 33333 22246889999999999999999998887
No 18
>PRK09898 hypothetical protein; Provisional
Probab=38.94 E-value=14 Score=29.68 Aligned_cols=20 Identities=30% Similarity=0.622 Sum_probs=14.6
Q ss_pred hhcccCCCceeeeeeheehee
Q 031683 130 LTEGLKVQINFFENYCLVHCK 150 (155)
Q Consensus 130 LvqGLKGDpTYLi~~~~~~~~ 150 (155)
..+|..|++.|....| .||.
T Consensus 108 ~~~~~~g~~~~~~~~C-~~C~ 127 (208)
T PRK09898 108 SGGGLYGDLNYTADTC-RQCK 127 (208)
T ss_pred cCCCccCcEEEeCccC-CCcc
Confidence 3456678888888888 5885
No 19
>PF06024 DUF912: Nucleopolyhedrovirus protein of unknown function (DUF912); InterPro: IPR009261 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf78; it is a family of uncharacterised viral proteins.
Probab=34.16 E-value=7 Score=28.76 Aligned_cols=31 Identities=16% Similarity=0.277 Sum_probs=25.7
Q ss_pred chhHHHHHHHhhhccccccceeccceEEEee
Q 031683 63 MGKRQLMNLLLLGAVSLPTGFMLVPYATFFA 93 (155)
Q Consensus 63 M~RRqlMNlLl~Gava~~a~g~LyP~v~fFV 93 (155)
-+..+.+|.++++.++.++...+.-+++|||
T Consensus 55 ~~~~~~~~iili~lls~v~IlVily~IyYFV 85 (101)
T PF06024_consen 55 ASKQNNGNIILISLLSFVCILVILYAIYYFV 85 (101)
T ss_pred ccccccccchHHHHHHHHHHHHHHhhheEEE
Confidence 3567889999999999999887777777776
No 20
>PTZ00334 trans-sialidase; Provisional
Probab=31.38 E-value=61 Score=32.34 Aligned_cols=66 Identities=20% Similarity=0.246 Sum_probs=32.8
Q ss_pred cccccccccccCCCc--ceeeeeeccCCCCCCCCchhHHHHHH----H-hh---hccccccc------eeccceEEEeec
Q 031683 31 VKPARTQMVTKNPMG--MKIKCQATSIPADRVPDMGKRQLMNL----L-LL---GAVSLPTG------FMLVPYATFFAP 94 (155)
Q Consensus 31 ~k~~~~~~~~k~~~~--~~~~~~a~s~~~~~vPDM~RRqlMNl----L-l~---Gava~~a~------g~LyP~v~fFVP 94 (155)
+|..|+|-|.|- -+ .|.+ --.-+...=|.|+||-|=-. | +. |+.++.+. -...|--.||.|
T Consensus 8 VKAPRTHNRRRV-TGSSGRRR--EGrESEpQRPNMSRrvF~SAVLLLLVVMMCCgsggAaa~~~~~~~~~~~p~~~~~w~ 84 (780)
T PTZ00334 8 VKAPRTHNRRRV-TGSSGRRR--EGRESEPQRPNMSRRVFTSAVLLLLVVMMCCGSGGAAATENGASGQGSSPSKSFVWR 84 (780)
T ss_pred hcCccccCcCcC-CCCCCCcC--CCCCCCCCCCCcchhhHHHHHHHHhhheeeCCCchhhhcccCCCccccCCcccceec
Confidence 577777765442 11 0111 12234456899999987422 1 11 33222121 223454468888
Q ss_pred CCCCC
Q 031683 95 PGLGS 99 (155)
Q Consensus 95 P~sgG 99 (155)
+..++
T Consensus 85 ~~~~~ 89 (780)
T PTZ00334 85 DKNGG 89 (780)
T ss_pred CCCCC
Confidence 87654
No 21
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=30.56 E-value=32 Score=29.74 Aligned_cols=29 Identities=41% Similarity=0.613 Sum_probs=19.7
Q ss_pred ccceEEEeecC---CCC-CCCCccccc----cccCCc
Q 031683 85 LVPYATFFAPP---GLG-SAGGGTTAK----DAIGND 113 (155)
Q Consensus 85 LyP~v~fFVPP---~sg-GggGGv~AK----DalGNd 113 (155)
--||+|-.||- ..| ++|||+-+| |+.||-
T Consensus 151 ~~P~VKkVIPg~I~~~gs~~g~Gvr~KvtRaD~~GNl 187 (227)
T COG4031 151 QHPYVKKVIPGVISAKGSAGGGGVRLKVTRADARGNL 187 (227)
T ss_pred cCCceeecccceeecCcccCCCceEEEEEeecCCCCE
Confidence 46999999992 223 344556555 999985
No 22
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=29.13 E-value=83 Score=26.46 Aligned_cols=29 Identities=21% Similarity=0.440 Sum_probs=20.0
Q ss_pred CcceeeeeeccCCC--------CCCCCchhHHHHHHH
Q 031683 44 MGMKIKCQATSIPA--------DRVPDMGKRQLMNLL 72 (155)
Q Consensus 44 ~~~~~~~~a~s~~~--------~~vPDM~RRqlMNlL 72 (155)
++.|+.|+..-.+. ...|+|..+|+.-=+
T Consensus 49 ng~rv~cmqvw~~~~~kkfETfSYLPpLtdeqI~kQV 85 (176)
T PLN02289 49 NGGRVSCMQVWPPIGKKKFETLSYLPDLTDEELAKEV 85 (176)
T ss_pred CCceeEEEEeecccCccceeeeecCCCCCHHHHHHHH
Confidence 46788887655441 358999999987543
No 23
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.90 E-value=27 Score=26.50 Aligned_cols=11 Identities=18% Similarity=0.380 Sum_probs=9.4
Q ss_pred cCCCceeeeee
Q 031683 134 LKVQINFFENY 144 (155)
Q Consensus 134 LKGDpTYLi~~ 144 (155)
|-|||+|+-+|
T Consensus 47 lSGDPaYIpr~ 57 (88)
T COG4472 47 LSGDPAYIPRY 57 (88)
T ss_pred ccCCccccCcc
Confidence 57999999876
No 24
>PF05688 DUF824: Salmonella repeat of unknown function (DUF824); InterPro: IPR008542 This family consists of a series of repeated sequences (of around 180 residues) which are found in Salmonella typhimurium, Salmonella typhi and Escherichia coli. These repeats are almost always found with this entry. The repeats are associated with RatA and RatB, the coding sequences of which are found in the pathogeneicity island of Salmonella. The sequences may be determinants of pathogenicity [, ].
Probab=25.82 E-value=30 Score=23.09 Aligned_cols=20 Identities=40% Similarity=0.403 Sum_probs=15.3
Q ss_pred cccccccCCcchhhhhhccC
Q 031683 104 TTAKDAIGNDIIAADWLNTH 123 (155)
Q Consensus 104 v~AKDalGNdI~as~wL~th 123 (155)
|+.||+.||+++=..|--+.
T Consensus 19 Vt~kda~G~pv~n~~f~l~r 38 (47)
T PF05688_consen 19 VTVKDANGNPVPNAPFTLTR 38 (47)
T ss_pred EEEECCCCCCcCCceEEEEe
Confidence 57899999999877665443
No 25
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=25.70 E-value=36 Score=30.07 Aligned_cols=16 Identities=25% Similarity=0.447 Sum_probs=11.6
Q ss_pred chhHHHHHHHhhhccc
Q 031683 63 MGKRQLMNLLLLGAVS 78 (155)
Q Consensus 63 M~RRqlMNlLl~Gava 78 (155)
|+||.||-.+..++++
T Consensus 1 ~~RR~fl~~~~~~~~~ 16 (328)
T PRK10882 1 MNRRNFLKAASAGALL 16 (328)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 7899999987544433
No 26
>TIGR02659 TTQ_MADH_Lt methylamine dehydrogenase light chain. This family consists of the light chain of methylamine dehydrogenase light chain, a periplasmic enzyme. This subunit contains a tryptophan tryptophylquinone (TTQ) prothetic group derived from Trp-114 and Trp-165 of the precursor, numbered according to the sequence from Paracoccus denitrificans. The enzyme forms a complex with the type I blue copper protein amicyanin and cytochrome. Electron transfer procedes from TQQ to the copper and then to the heme group of the cytochrome.
Probab=25.28 E-value=36 Score=28.77 Aligned_cols=27 Identities=19% Similarity=0.180 Sum_probs=18.4
Q ss_pred chhHHHHHHHhhhccccccceeccceEE
Q 031683 63 MGKRQLMNLLLLGAVSLPTGFMLVPYAT 90 (155)
Q Consensus 63 M~RRqlMNlLl~Gava~~a~g~LyP~v~ 90 (155)
-+||.||..| ++++++.++..|.||-+
T Consensus 22 tsRRs~l~~l-G~~l~g~a~~PlLPv~R 48 (186)
T TIGR02659 22 TSRRGFIGRL-GTALAGSALVPLLPVDR 48 (186)
T ss_pred cchHHHHHHH-HHHHhhhhhccccccch
Confidence 4799999987 55555555556666654
No 27
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=24.49 E-value=98 Score=27.24 Aligned_cols=27 Identities=19% Similarity=0.315 Sum_probs=17.3
Q ss_pred ceeeeeeccCCCCCCCCchhHHHHHHHhhh
Q 031683 46 MKIKCQATSIPADRVPDMGKRQLMNLLLLG 75 (155)
Q Consensus 46 ~~~~~~a~s~~~~~vPDM~RRqlMNlLl~G 75 (155)
..+.|.+-.. +-...+||..|-++.+.
T Consensus 36 ~~~~~~~~~~---~~~~~srr~~l~~~~ga 62 (260)
T PLN00042 36 SQVVCRAQEE---DNSAVSRRAALALLAGA 62 (260)
T ss_pred cceeeecccc---ccccccHHHHHHHHHHH
Confidence 3455655322 33568999999888665
No 28
>PF00173 Cyt-b5: Cytochrome b5-like Heme/Steroid binding domain This prints entry is a subset of the Pfam entry; InterPro: IPR001199 Cytochromes b5 are ubiquitous electron transport proteins found in animals, plants and yeasts []. The microsomal and mitochondrial variants are membrane-bound, while those from erythrocytes and other animal tissues are water-soluble [, ]. The 3D structure of bovine cyt b5 is known, the fold belonging to the alpha+beta class, with 5 strands and 5 short helices forming a framework for supporting a central haem group []. The cytochrome b5 domain is similar to that of a number of oxidoreductases, such as plant and fungal nitrate reductases, sulphite oxidase, yeast flavocytochrome b2 (L-lactate dehydrogenase) and plant cyt b5/acyl lipid desaturase fusion protein.; GO: 0020037 heme binding; PDB: 2I96_A 3KS0_A 1KBI_B 1KBJ_B 1LTD_A 1SZG_B 1SZF_A 1LDC_B 2OZ0_B 1LCO_A ....
Probab=24.04 E-value=35 Score=22.16 Aligned_cols=33 Identities=18% Similarity=0.066 Sum_probs=25.1
Q ss_pred cCCcchhhhhhccCCCCCchhhcccCCCceeee
Q 031683 110 IGNDIIAADWLNTHGPGDRTLTEGLKVQINFFE 142 (155)
Q Consensus 110 lGNdI~as~wL~th~pGdR~LvqGLKGDpTYLi 142 (155)
.|+--.+++|+..||.|...+.+-.-.|.|...
T Consensus 21 ~g~VYDvt~~~~~hpgg~~~~~~~aG~D~T~~f 53 (76)
T PF00173_consen 21 DGKVYDVTDFLDRHPGGADILKKYAGRDATDAF 53 (76)
T ss_dssp TTEEEECTTTTTTSTTTSHHHHTTTTSBTHHHH
T ss_pred CCEEcccccccccccchhHHHHHhccccccHHH
Confidence 356677889999999997777666666777665
No 29
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=23.58 E-value=42 Score=23.05 Aligned_cols=8 Identities=50% Similarity=0.928 Sum_probs=6.3
Q ss_pred eecCCCCC
Q 031683 92 FAPPGLGS 99 (155)
Q Consensus 92 FVPP~sgG 99 (155)
|+||-+||
T Consensus 74 i~PPVsGG 81 (81)
T PRK11130 74 FFPPVTGG 81 (81)
T ss_pred EeCCCCCC
Confidence 67888876
Done!