Query 032276
Match_columns 144
No_of_seqs 97 out of 99
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 11:57:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032276.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032276hhsearch_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 1.9E-24 4.1E-29 169.4 3.0 90 54-143 3-92 (178)
2 PF08802 CytB6-F_Fe-S: Cytochr 99.8 1.6E-22 3.4E-27 129.1 -2.7 39 58-96 1-39 (39)
3 TIGR03171 soxL2 Rieske iron-su 99.7 1.7E-17 3.7E-22 142.9 1.6 83 60-144 58-142 (321)
4 KOG1671 Ubiquinol cytochrome c 99.3 1.4E-12 3.1E-17 107.6 4.9 132 1-139 2-135 (210)
5 COG0723 QcrA Rieske Fe-S prote 97.4 0.0001 2.2E-09 56.8 2.6 85 58-142 4-89 (177)
6 TIGR01416 Rieske_proteo ubiqui 95.8 0.0025 5.4E-08 50.3 0.2 38 64-101 1-38 (174)
7 PF10399 UCR_Fe-S_N: Ubiquitin 95.5 0.001 2.3E-08 42.7 -2.4 38 57-94 3-40 (41)
8 TIGR02811 formate_TAT formate 85.9 0.39 8.4E-06 33.3 1.1 28 59-86 5-32 (66)
9 PF10518 TAT_signal: TAT (twin 84.6 0.55 1.2E-05 27.2 1.1 22 62-83 1-22 (26)
10 PF03935 SKN1: Beta-glucan syn 63.1 7.3 0.00016 36.4 3.1 82 61-143 35-122 (504)
11 TIGR01409 TAT_signal_seq Tat ( 59.3 4.7 0.0001 23.4 0.8 19 63-81 1-19 (29)
12 PRK09476 napG quinol dehydroge 53.0 7.1 0.00015 32.5 1.2 25 60-84 6-30 (254)
13 PF00970 FAD_binding_6: Oxidor 40.3 14 0.0003 24.8 0.9 51 88-140 47-99 (99)
14 PRK09898 hypothetical protein; 37.7 14 0.0003 29.3 0.6 21 63-83 13-33 (208)
15 PRK02888 nitrous-oxide reducta 37.6 27 0.00058 33.7 2.5 28 58-85 4-31 (635)
16 PF06024 DUF912: Nucleopolyhed 34.3 7 0.00015 28.5 -1.4 31 63-93 55-85 (101)
17 COG4031 Predicted metal-bindin 30.3 33 0.00072 29.4 1.7 29 85-113 151-187 (227)
18 PTZ00334 trans-sialidase; Prov 26.9 81 0.0018 31.2 3.9 66 31-99 8-89 (780)
19 PLN02289 ribulose-bisphosphate 26.6 98 0.0021 25.8 3.8 29 44-72 49-85 (176)
20 PF05688 DUF824: Salmonella re 26.5 29 0.00062 22.9 0.6 19 104-122 19-37 (47)
21 PF06135 DUF965: Bacterial pro 26.4 25 0.00055 25.8 0.3 9 134-142 44-52 (79)
22 PLN00042 photosystem II oxygen 26.0 90 0.0019 27.2 3.6 27 46-75 36-62 (260)
23 PRK10882 hydrogenase 2 protein 24.6 39 0.00084 29.6 1.2 15 63-77 1-15 (328)
24 PRK05473 hypothetical protein; 24.4 29 0.00063 25.8 0.4 9 134-142 47-55 (86)
25 TIGR02659 TTQ_MADH_Lt methylam 23.3 42 0.0009 28.1 1.1 27 63-90 22-48 (186)
26 PRK11130 moaD molybdopterin sy 23.2 43 0.00093 22.8 1.0 8 92-99 74-81 (81)
27 PF00173 Cyt-b5: Cytochrome b5 23.1 40 0.00086 21.7 0.8 30 110-139 21-50 (76)
No 1
>PRK13474 cytochrome b6-f complex iron-sulfur subunit; Provisional
Probab=99.89 E-value=1.9e-24 Score=169.36 Aligned_cols=90 Identities=47% Similarity=0.739 Sum_probs=86.3
Q ss_pred cCCCCCCCCchhHHHHHHHhhhccccccceeccceEEEeecCCCCCCCCccccccccCCcchhhhhhhhCCCCCchhhcc
Q 032276 54 SIPADRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEG 133 (144)
Q Consensus 54 s~~~~~vPDm~RRqlMNlLl~Gava~~a~g~LyP~v~fFvPP~sgG~gGGv~AKDalGNdI~as~wL~th~~GdR~LvqG 133 (144)
+..+++||||+||+|||.+++|++++.++++++|+++||+||.+.+++|+..|||++||+|++++|+++|++|++.++++
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 032276 134 LKDFSHLQLI 143 (144)
Q Consensus 134 LKGDpTYLiv 143 (144)
++|+++|||+
T Consensus 83 ~~g~~~~lv~ 92 (178)
T PRK13474 83 LKGDPTYLVV 92 (178)
T ss_pred cCCCeEEEEE
Confidence 9999999986
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=99.83 E-value=1.6e-22 Score=129.08 Aligned_cols=39 Identities=69% Similarity=1.169 Sum_probs=31.0
Q ss_pred CCCCCchhHHHHHHHhhhccccccceeccceEEEeecCC
Q 032276 58 DRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPG 96 (144)
Q Consensus 58 ~~vPDm~RRqlMNlLl~Gava~~a~g~LyP~v~fFvPP~ 96 (144)
|+||||+||||||+|++|++++++++++|||++|||||+
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=99.66 E-value=1.7e-17 Score=142.92 Aligned_cols=83 Identities=20% Similarity=0.288 Sum_probs=73.7
Q ss_pred CCCchhHHHHHHHhhhccccccceeccceEEEeecCCCCCCC--CccccccccCCcchhhhhhhhCCCCCchhhccCCCC
Q 032276 60 VPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAG--GGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKDF 137 (144)
Q Consensus 60 vPDm~RRqlMNlLl~Gava~~a~g~LyP~v~fFvPP~sgG~g--GGv~AKDalGNdI~as~wL~th~~GdR~LvqGLKGD 137 (144)
-|||+||+|||++++|++++++++ ++|+++||+||..+.++ +.++|+|++||||.+|+ |..|.+.++.+.+++++|
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 ceeEEeC
Q 032276 138 SHLQLIL 144 (144)
Q Consensus 138 pTYLiv~ 144 (144)
|+|||.+
T Consensus 136 P~fLIkl 142 (321)
T TIGR03171 136 PNFLLNL 142 (321)
T ss_pred cHHHHHh
Confidence 9999863
No 4
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=99.32 E-value=1.4e-12 Score=107.55 Aligned_cols=132 Identities=17% Similarity=0.089 Sum_probs=120.2
Q ss_pred CCCCCCCCCCCcccccccCCCCCcccccccccccc--ccccccCCCcceeeeeeccCCCCCCCCchhHHHHHHHhhhccc
Q 032276 1 MASSSSLSSATPSQLCSSKGGMFCPSRAFLVKPAR--TQMVTKNPMGMKIKCQATSIPADRVPDMGKRQLMNLLLLGAVS 78 (144)
Q Consensus 1 mas~~~ls~~~~sql~~~~~~~~~~~~~l~~k~~~--~~~~~~~~~~~~~~~~a~s~~~~~vPDm~RRqlMNlLl~Gava 78 (144)
|+| +++|....+||-++..-+..|.-...+++.. .++.+++.|+....||..+..+..+++++.+-+.++...++.+
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 344 6777755679999999999999999998877 3556677567889999999999999999999999999999999
Q ss_pred cccceeccceEEEeecCCCCCCCCccccccccCCcchhhhhhhhCCCCCchhhccCCCCce
Q 032276 79 LPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKDFSH 139 (144)
Q Consensus 79 ~~a~g~LyP~v~fFvPP~sgG~gGGv~AKDalGNdI~as~wL~th~~GdR~LvqGLKGDpT 139 (144)
-+.+.+++||..++||+ |+..+++..|||+.+.+|+++|-+++|++-|+.++||+
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 78999999999999999999999999999999999998
No 5
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=97.41 E-value=0.0001 Score=56.76 Aligned_cols=85 Identities=16% Similarity=0.058 Sum_probs=72.5
Q ss_pred CCCCCchhHHHHHHHhhhccccccceeccceEEEeecCCCC-CCCCccccccccCCcchhhhhhhhCCCCCchhhccCCC
Q 032276 58 DRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLG-SAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKD 136 (144)
Q Consensus 58 ~~vPDm~RRqlMNlLl~Gava~~a~g~LyP~v~fFvPP~sg-G~gGGv~AKDalGNdI~as~wL~th~~GdR~LvqGLKG 136 (144)
....++.||++|+.++.+.++..+..++||.+.++.|+..+ ..+..+.++|...+++..........|..+.+....++
T Consensus 4 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~ 83 (177)
T COG0723 4 AAATGLSRRDFLVLLTTGVGAVGAGAALYPAVESVDPPAGGGLAGAPIEVDDSGIGPGPLVTVPWRGKPVFLLRRTEYAG 83 (177)
T ss_pred cccccccHHHhhhhhhccccccceeeeeeehhhcccCcccccccCCceeeeccCCccceEEEEecCCCCeeeEeeccccc
Confidence 35678999999999999999999999999999999997765 88888999999989999988888888888876666666
Q ss_pred CceeEE
Q 032276 137 FSHLQL 142 (144)
Q Consensus 137 DpTYLi 142 (144)
+..|.+
T Consensus 84 ~~~~~~ 89 (177)
T COG0723 84 PKGGVT 89 (177)
T ss_pred ccccce
Confidence 665543
No 6
>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=95.84 E-value=0.0025 Score=50.28 Aligned_cols=38 Identities=13% Similarity=0.159 Sum_probs=34.0
Q ss_pred hhHHHHHHHhhhccccccceeccceEEEeecCCCCCCC
Q 032276 64 GKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAG 101 (144)
Q Consensus 64 ~RRqlMNlLl~Gava~~a~g~LyP~v~fFvPP~sgG~g 101 (144)
+||+||+..+.+++++.++++++|+++|+-|.....++
T Consensus 1 ~RR~fl~~~~~~~~~~~~~~~~~p~v~~~~P~~~~~a~ 38 (174)
T TIGR01416 1 TRRDFLYAATGAVGAVGAAAAAVPFIDSMNPSASVKAA 38 (174)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHheeCcchhcccc
Confidence 59999999999999999999999999999997765554
No 7
>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=95.53 E-value=0.001 Score=42.67 Aligned_cols=38 Identities=11% Similarity=0.233 Sum_probs=28.7
Q ss_pred CCCCCCchhHHHHHHHhhhccccccceeccceEEEeec
Q 032276 57 ADRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAP 94 (144)
Q Consensus 57 ~~~vPDm~RRqlMNlLl~Gava~~a~g~LyP~v~fFvP 94 (144)
.++..|-+||.||.+.+.+++++-++++++|+++.+-|
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 34567899999999999999999999999999887766
No 8
>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=85.86 E-value=0.39 Score=33.29 Aligned_cols=28 Identities=21% Similarity=0.177 Sum_probs=19.5
Q ss_pred CCCCchhHHHHHHHhhhccccccceecc
Q 032276 59 RVPDMGKRQLMNLLLLGAVSLPTGFMLV 86 (144)
Q Consensus 59 ~vPDm~RRqlMNlLl~Gava~~a~g~Ly 86 (144)
.-++.+||+||-.+.+|++++.++...-
T Consensus 5 ~~~~~sRR~Flk~lg~~aaa~~aa~~~~ 32 (66)
T TIGR02811 5 QKADPSRRDLLKGLGVGAAAGAVAAATG 32 (66)
T ss_pred ccCCccHHHHHHHHHHHHHHHHHHHhcc
Confidence 4567899999998877666555544333
No 9
>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=84.58 E-value=0.55 Score=27.23 Aligned_cols=22 Identities=18% Similarity=0.202 Sum_probs=15.5
Q ss_pred CchhHHHHHHHhhhccccccce
Q 032276 62 DMGKRQLMNLLLLGAVSLPTGF 83 (144)
Q Consensus 62 Dm~RRqlMNlLl~Gava~~a~g 83 (144)
.|+|||||-.-...+++..+.+
T Consensus 1 ~~sRR~fLk~~~a~~a~~~~~~ 22 (26)
T PF10518_consen 1 NLSRRQFLKGGAAAAAAAALGG 22 (26)
T ss_pred CCcHHHHHHHHHHHHHHHHhcc
Confidence 4799999988766655554444
No 10
>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=63.08 E-value=7.3 Score=36.42 Aligned_cols=82 Identities=21% Similarity=0.188 Sum_probs=49.2
Q ss_pred CCchhHHHHHHHhhhccc--cccceeccceEEEeec---CCCCCCCCccccccccCCcchh-hhhhhhCCCCCchhhccC
Q 032276 61 PDMGKRQLMNLLLLGAVS--LPTGFMLVPYATFFAP---PGLGSAGGGTTAKDAIGNDIIA-ADWLNTHGPGDRTLTEGL 134 (144)
Q Consensus 61 PDm~RRqlMNlLl~Gava--~~a~g~LyP~v~fFvP---P~sgG~gGGv~AKDalGNdI~a-s~wL~th~~GdR~LvqGL 134 (144)
--|+||.++|+..+..+. ++++...||++.||-= ...++..+++.+.-..-+--.. ..|+.-..|-+.---++.
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 348999999997776544 6777789999999964 3334444555554333222212 256666666655555555
Q ss_pred CCCceeEEe
Q 032276 135 KDFSHLQLI 143 (144)
Q Consensus 135 KGDpTYLiv 143 (144)
.| .+|-+|
T Consensus 115 ~g-~~~~Lv 122 (504)
T PF03935_consen 115 DG-RTYKLV 122 (504)
T ss_pred CC-CEeeEE
Confidence 43 344333
No 11
>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=59.33 E-value=4.7 Score=23.45 Aligned_cols=19 Identities=5% Similarity=0.128 Sum_probs=14.4
Q ss_pred chhHHHHHHHhhhcccccc
Q 032276 63 MGKRQLMNLLLLGAVSLPT 81 (144)
Q Consensus 63 m~RRqlMNlLl~Gava~~a 81 (144)
++||+||-+...+++++..
T Consensus 1 ~sRR~Flk~~~~~~a~~~~ 19 (29)
T TIGR01409 1 LSRRDFLKGAAAAGAAAGL 19 (29)
T ss_pred CchhhhHHHHHHHHHHHhc
Confidence 5899999999776665444
No 12
>PRK09476 napG quinol dehydrogenase periplasmic component; Provisional
Probab=53.02 E-value=7.1 Score=32.53 Aligned_cols=25 Identities=20% Similarity=0.255 Sum_probs=15.6
Q ss_pred CCCchhHHHHHHHhhhcccccccee
Q 032276 60 VPDMGKRQLMNLLLLGAVSLPTGFM 84 (144)
Q Consensus 60 vPDm~RRqlMNlLl~Gava~~a~g~ 84 (144)
.-+++||+||-..+.+++.+.++++
T Consensus 6 ~~~~~rr~f~~~~~~~~~~~~~~~~ 30 (254)
T PRK09476 6 KPQNGRRRFLRDVVRTAGGLAAVGV 30 (254)
T ss_pred cCCccHHHHHHHHHHHHHHHHHHHH
Confidence 4569999999766544444434444
No 13
>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=40.27 E-value=14 Score=24.81 Aligned_cols=51 Identities=16% Similarity=0.144 Sum_probs=33.4
Q ss_pred eEEEeecCCCCCCCCcc--ccccccCCcchhhhhhhhCCCCCchhhccCCCCcee
Q 032276 88 YATFFAPPGLGSAGGGT--TAKDAIGNDIIAADWLNTHGPGDRTLTEGLKDFSHL 140 (144)
Q Consensus 88 ~v~fFvPP~sgG~gGGv--~AKDalGNdI~as~wL~th~~GdR~LvqGLKGDpTY 140 (144)
..+.|-|.+.....|-+ ..|-. ++=.+++||.+-.+||+-.+.|=.|+=+|
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 45555555444333322 33333 22246889999999999999999998877
No 14
>PRK09898 hypothetical protein; Provisional
Probab=37.68 E-value=14 Score=29.31 Aligned_cols=21 Identities=10% Similarity=0.150 Sum_probs=14.5
Q ss_pred chhHHHHHHHhhhccccccce
Q 032276 63 MGKRQLMNLLLLGAVSLPTGF 83 (144)
Q Consensus 63 m~RRqlMNlLl~Gava~~a~g 83 (144)
++||+||-+...+++++.+++
T Consensus 13 ~~RR~flk~~~~~~~g~~~~~ 33 (208)
T PRK09898 13 LTRLEFLRISGKGLAGLTIAP 33 (208)
T ss_pred hhHHHHHHhhcchhhhhhhhh
Confidence 999999998755555444433
No 15
>PRK02888 nitrous-oxide reductase; Validated
Probab=37.58 E-value=27 Score=33.72 Aligned_cols=28 Identities=14% Similarity=0.205 Sum_probs=21.4
Q ss_pred CCCCCchhHHHHHHHhhhccccccceec
Q 032276 58 DRVPDMGKRQLMNLLLLGAVSLPTGFML 85 (144)
Q Consensus 58 ~~vPDm~RRqlMNlLl~Gava~~a~g~L 85 (144)
+.-++++||+|||--.++++++.++++.
T Consensus 4 ~~~~~~~rr~~~~~~~~~~~~~~~~~~~ 31 (635)
T PRK02888 4 EAPSGLSRRQFLGTAALAGAAGAAGSTG 31 (635)
T ss_pred cccCCccHHHhhhHHHHHhhhhhhhccc
Confidence 4578899999999887777666666543
No 16
>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=34.26 E-value=7 Score=28.47 Aligned_cols=31 Identities=16% Similarity=0.277 Sum_probs=25.6
Q ss_pred chhHHHHHHHhhhccccccceeccceEEEee
Q 032276 63 MGKRQLMNLLLLGAVSLPTGFMLVPYATFFA 93 (144)
Q Consensus 63 m~RRqlMNlLl~Gava~~a~g~LyP~v~fFv 93 (144)
-+..+.+|.++++.++.++...+.-+++|||
T Consensus 55 ~~~~~~~~iili~lls~v~IlVily~IyYFV 85 (101)
T PF06024_consen 55 ASKQNNGNIILISLLSFVCILVILYAIYYFV 85 (101)
T ss_pred ccccccccchHHHHHHHHHHHHHHhhheEEE
Confidence 3567889999999999999887777777776
No 17
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=30.31 E-value=33 Score=29.36 Aligned_cols=29 Identities=41% Similarity=0.613 Sum_probs=19.7
Q ss_pred ccceEEEeecC---CCC-CCCCccccc----cccCCc
Q 032276 85 LVPYATFFAPP---GLG-SAGGGTTAK----DAIGND 113 (144)
Q Consensus 85 LyP~v~fFvPP---~sg-G~gGGv~AK----DalGNd 113 (144)
--||+|-.||- ..| ++|||+-+| |+.||-
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 999984
No 18
>PTZ00334 trans-sialidase; Provisional
Probab=26.92 E-value=81 Score=31.20 Aligned_cols=66 Identities=20% Similarity=0.246 Sum_probs=32.6
Q ss_pred cccccccccccCCCc--ceeeeeeccCCCCCCCCchhHHHHHH----H-hh---hccccccc------eeccceEEEeec
Q 032276 31 VKPARTQMVTKNPMG--MKIKCQATSIPADRVPDMGKRQLMNL----L-LL---GAVSLPTG------FMLVPYATFFAP 94 (144)
Q Consensus 31 ~k~~~~~~~~~~~~~--~~~~~~a~s~~~~~vPDm~RRqlMNl----L-l~---Gava~~a~------g~LyP~v~fFvP 94 (144)
+|..|+|-+.|- -+ .|.+ --.-+...=|.|+||-|=-. | +. |+.++.+. -...|--.||.|
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 11233456799999987422 1 11 33222121 223454468888
Q ss_pred CCCCC
Q 032276 95 PGLGS 99 (144)
Q Consensus 95 P~sgG 99 (144)
+..++
T Consensus 85 ~~~~~ 89 (780)
T PTZ00334 85 DKNGG 89 (780)
T ss_pred CCCCC
Confidence 87654
No 19
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=26.60 E-value=98 Score=25.75 Aligned_cols=29 Identities=21% Similarity=0.440 Sum_probs=20.0
Q ss_pred CcceeeeeeccCCC--------CCCCCchhHHHHHHH
Q 032276 44 MGMKIKCQATSIPA--------DRVPDMGKRQLMNLL 72 (144)
Q Consensus 44 ~~~~~~~~a~s~~~--------~~vPDm~RRqlMNlL 72 (144)
++.|+.|+..-.+. ...|+|..+|+..=+
T Consensus 49 ng~rv~cmqvw~~~~~kkfETfSYLPpLtdeqI~kQV 85 (176)
T PLN02289 49 NGGRVSCMQVWPPIGKKKFETLSYLPDLTDEELAKEV 85 (176)
T ss_pred CCceeEEEEeecccCccceeeeecCCCCCHHHHHHHH
Confidence 46788887655441 358999999987543
No 20
>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=26.47 E-value=29 Score=22.90 Aligned_cols=19 Identities=42% Similarity=0.414 Sum_probs=14.7
Q ss_pred cccccccCCcchhhhhhhh
Q 032276 104 TTAKDAIGNDIIAADWLNT 122 (144)
Q Consensus 104 v~AKDalGNdI~as~wL~t 122 (144)
|+.||+.||+++=..|--+
T Consensus 19 Vt~kda~G~pv~n~~f~l~ 37 (47)
T PF05688_consen 19 VTVKDANGNPVPNAPFTLT 37 (47)
T ss_pred EEEECCCCCCcCCceEEEE
Confidence 5789999999987666543
No 21
>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=26.42 E-value=25 Score=25.76 Aligned_cols=9 Identities=11% Similarity=-0.141 Sum_probs=6.9
Q ss_pred CCCCceeEE
Q 032276 134 LKDFSHLQL 142 (144)
Q Consensus 134 LKGDpTYLi 142 (144)
|-|||||+.
T Consensus 44 lSGDPaYIt 52 (79)
T PF06135_consen 44 LSGDPAYIT 52 (79)
T ss_pred ecCCCcccc
Confidence 459999974
No 22
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=26.04 E-value=90 Score=27.20 Aligned_cols=27 Identities=19% Similarity=0.315 Sum_probs=17.4
Q ss_pred ceeeeeeccCCCCCCCCchhHHHHHHHhhh
Q 032276 46 MKIKCQATSIPADRVPDMGKRQLMNLLLLG 75 (144)
Q Consensus 46 ~~~~~~a~s~~~~~vPDm~RRqlMNlLl~G 75 (144)
..+.|.+-.. +-...+||..|-++.+.
T Consensus 36 ~~~~~~~~~~---~~~~~srr~~l~~~~ga 62 (260)
T PLN00042 36 SQVVCRAQEE---DNSAVSRRAALALLAGA 62 (260)
T ss_pred cceeeecccc---ccccccHHHHHHHHHHH
Confidence 3456655322 33568999999888665
No 23
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=24.62 E-value=39 Score=29.57 Aligned_cols=15 Identities=27% Similarity=0.523 Sum_probs=11.2
Q ss_pred chhHHHHHHHhhhcc
Q 032276 63 MGKRQLMNLLLLGAV 77 (144)
Q Consensus 63 m~RRqlMNlLl~Gav 77 (144)
|+||.||-.+..+++
T Consensus 1 ~~RR~fl~~~~~~~~ 15 (328)
T PRK10882 1 MNRRNFLKAASAGAL 15 (328)
T ss_pred CCHHHHHHHHHHHHH
Confidence 789999997754433
No 24
>PRK05473 hypothetical protein; Provisional
Probab=24.45 E-value=29 Score=25.82 Aligned_cols=9 Identities=11% Similarity=-0.178 Sum_probs=6.8
Q ss_pred CCCCceeEE
Q 032276 134 LKDFSHLQL 142 (144)
Q Consensus 134 LKGDpTYLi 142 (144)
|-|||||+.
T Consensus 47 lSGDPaYIt 55 (86)
T PRK05473 47 LSGDPAYIP 55 (86)
T ss_pred ccCCCCccC
Confidence 458999974
No 25
>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=23.34 E-value=42 Score=28.10 Aligned_cols=27 Identities=19% Similarity=0.180 Sum_probs=18.3
Q ss_pred chhHHHHHHHhhhccccccceeccceEE
Q 032276 63 MGKRQLMNLLLLGAVSLPTGFMLVPYAT 90 (144)
Q Consensus 63 m~RRqlMNlLl~Gava~~a~g~LyP~v~ 90 (144)
-+||.||..| ++++++.++.-|.||-+
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 26
>PRK11130 moaD molybdopterin synthase small subunit; Provisional
Probab=23.22 E-value=43 Score=22.75 Aligned_cols=8 Identities=50% Similarity=0.928 Sum_probs=6.2
Q ss_pred eecCCCCC
Q 032276 92 FAPPGLGS 99 (144)
Q Consensus 92 FvPP~sgG 99 (144)
|+||-+||
T Consensus 74 i~PPVsGG 81 (81)
T PRK11130 74 FFPPVTGG 81 (81)
T ss_pred EeCCCCCC
Confidence 67888876
No 27
>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=23.08 E-value=40 Score=21.71 Aligned_cols=30 Identities=20% Similarity=0.162 Sum_probs=20.8
Q ss_pred cCCcchhhhhhhhCCCCCchhhccCCCCce
Q 032276 110 IGNDIIAADWLNTHGPGDRTLTEGLKDFSH 139 (144)
Q Consensus 110 lGNdI~as~wL~th~~GdR~LvqGLKGDpT 139 (144)
.|+--.+++|+..||.|...+-+-.-.|.|
T Consensus 21 ~g~VYDvt~~~~~hpgg~~~~~~~aG~D~T 50 (76)
T PF00173_consen 21 DGKVYDVTDFLDRHPGGADILKKYAGRDAT 50 (76)
T ss_dssp TTEEEECTTTTTTSTTTSHHHHTTTTSBTH
T ss_pred CCEEcccccccccccchhHHHHHhcccccc
Confidence 356677888999999996666554444554
Done!