Query 032198
Match_columns 145
No_of_seqs 86 out of 88
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 10:55:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032198.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032198hhsearch_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 4.3E-24 9.3E-29 167.0 3.4 91 54-144 3-93 (178)
2 PF08802 CytB6-F_Fe-S: Cytochr 99.8 1.6E-22 3.4E-27 129.3 -2.6 39 58-96 1-39 (39)
3 TIGR03171 soxL2 Rieske iron-su 99.7 2.5E-17 5.4E-22 141.8 1.4 83 60-144 58-142 (321)
4 KOG1671 Ubiquinol cytochrome c 99.4 7.1E-13 1.5E-17 109.4 4.9 132 1-139 2-135 (210)
5 cd03471 Rieske_cytochrome_b6f 99.1 5.5E-11 1.2E-15 90.3 2.4 41 104-144 1-41 (126)
6 COG0723 QcrA Rieske Fe-S prote 97.3 0.00014 3E-09 55.9 2.6 86 58-143 4-90 (177)
7 TIGR01416 Rieske_proteo ubiqui 95.1 0.0069 1.5E-07 47.7 0.4 38 64-101 1-38 (174)
8 PF10399 UCR_Fe-S_N: Ubiquitin 93.7 0.0062 1.3E-07 39.1 -2.2 37 58-94 4-40 (41)
9 TIGR02811 formate_TAT formate 82.5 0.74 1.6E-05 31.9 1.3 28 59-86 5-32 (66)
10 PF10518 TAT_signal: TAT (twin 81.0 1.1 2.3E-05 26.0 1.4 23 62-84 1-23 (26)
11 PF03935 SKN1: Beta-glucan syn 68.3 5.5 0.00012 37.2 3.4 77 61-137 35-117 (504)
12 PF00970 FAD_binding_6: Oxidor 47.2 8.3 0.00018 25.9 0.6 51 88-140 47-99 (99)
13 TIGR01409 TAT_signal_seq Tat ( 44.8 13 0.00029 21.5 1.1 19 63-81 1-19 (29)
14 PRK09476 napG quinol dehydroge 40.7 16 0.00035 30.4 1.4 14 60-73 6-19 (254)
15 PRK02888 nitrous-oxide reducta 38.4 27 0.00058 33.7 2.7 28 58-85 4-31 (635)
16 PF06135 DUF965: Bacterial pro 31.7 18 0.0004 26.5 0.4 9 134-142 44-52 (79)
17 PF06024 DUF912: Nucleopolyhed 31.6 8.6 0.00019 28.0 -1.4 31 63-93 55-85 (101)
18 PLN02289 ribulose-bisphosphate 31.4 73 0.0016 26.5 3.8 27 44-70 49-83 (176)
19 PRK05473 hypothetical protein; 29.4 21 0.00046 26.6 0.4 9 134-142 47-55 (86)
20 PF05688 DUF824: Salmonella re 25.0 32 0.00068 22.7 0.6 20 104-123 19-38 (47)
21 PF00173 Cyt-b5: Cytochrome b5 24.0 36 0.00077 21.9 0.7 29 111-139 22-50 (76)
22 PF00996 GDI: GDP dissociation 22.7 33 0.00072 31.1 0.4 45 31-75 102-147 (438)
23 PRK09898 hypothetical protein; 21.6 39 0.00084 26.8 0.6 22 63-84 13-34 (208)
24 PLN00042 photosystem II oxygen 21.1 1.4E+02 0.003 26.1 3.8 27 46-75 36-62 (260)
No 1
>PRK13474 cytochrome b6-f complex iron-sulfur subunit; Provisional
Probab=99.89 E-value=4.3e-24 Score=167.01 Aligned_cols=91 Identities=48% Similarity=0.738 Sum_probs=87.0
Q ss_pred cCCCCCCCCcchHHHHHHHHhhhcccccceecceeEEEeecCCCCCCCCccccccccCCcchhhhhhccCCCCChhhhcc
Q 032198 54 SIPADRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEG 133 (145)
Q Consensus 54 s~~~~~vPdM~RRqlMNlL~~Gav~~~a~g~lyP~~~fFvPP~~gG~gGGv~AKDalGNdI~as~wL~th~pGdR~LvqG 133 (145)
+..+++||||+||+|||.+++|+.++.++++++|+++||+||...+++|+..|||++||+|++++|+++|++|++.++++
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 45568999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCceeEEEe
Q 032198 134 LKQDFSHLQLI 144 (145)
Q Consensus 134 LKGDpTYLiV~ 144 (145)
++|+++||++.
T Consensus 83 ~~g~~~~lv~~ 93 (178)
T PRK13474 83 LKGDPTYLVVE 93 (178)
T ss_pred cCCCeEEEEEe
Confidence 99999999985
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=129.29 Aligned_cols=39 Identities=69% Similarity=1.169 Sum_probs=31.0
Q ss_pred CCCCCcchHHHHHHHHhhhcccccceecceeEEEeecCC
Q 032198 58 DRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPG 96 (145)
Q Consensus 58 ~~vPdM~RRqlMNlL~~Gav~~~a~g~lyP~~~fFvPP~ 96 (145)
|+||||+||||||+|++|++++++++++|||++||+||+
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 579999999999999999999999999999999999996
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=99.65 E-value=2.5e-17 Score=141.82 Aligned_cols=83 Identities=19% Similarity=0.278 Sum_probs=73.8
Q ss_pred CCCcchHHHHHHHHhhhcccccceecceeEEEeecCCCCCCC--CccccccccCCcchhhhhhccCCCCChhhhcccCCC
Q 032198 60 VPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAG--GGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKQD 137 (145)
Q Consensus 60 vPdM~RRqlMNlL~~Gav~~~a~g~lyP~~~fFvPP~~gG~g--GGv~AKDalGNdI~as~wL~th~pGdR~LvqGLKGD 137 (145)
-+||+||+|||++++|++++++++ ++|++.||+||....++ +.++|+|++||||.+|+ |..|.+.++.+.+++++|
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 479999999999999999977666 67999999999875544 45999999999999999 667999999999999999
Q ss_pred ceeEEEe
Q 032198 138 FSHLQLI 144 (145)
Q Consensus 138 pTYLiV~ 144 (145)
|+|||+.
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=99.35 E-value=7.1e-13 Score=109.37 Aligned_cols=132 Identities=17% Similarity=0.104 Sum_probs=120.2
Q ss_pred CCCCCCCCCCCcccccccCCCCCcccccceecccc--ccccccCCCcceeeeeeccCCCCCCCCcchHHHHHHHHhhhcc
Q 032198 1 MASSSSLSSATPSQLCSSKGGMFCPSRAFLVKPAR--TQMVTKNPMGMKIKCQATSIPADRVPDMGKRQLMNLLLLGAVS 78 (145)
Q Consensus 1 mas~~~ls~~~psql~~~k~~~~~~~~~l~~k~~~--~~~~~k~~~~~~~~~~a~s~~~~~vPdM~RRqlMNlL~~Gav~ 78 (145)
|+| +++|....+||-++..-+-.|.-...+++.. .++.+++.|+....||..+..+..+++|..+...|+...+|.+
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 6777755679999999999999999998876 3556677667889999999999999999999999999999999
Q ss_pred cccceecceeEEEeecCCCCCCCCccccccccCCcchhhhhhccCCCCChhhhcccCCCce
Q 032198 79 LPTGFMLVPYATFFAPPGLGSAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKQDFS 139 (145)
Q Consensus 79 ~~a~g~lyP~~~fFvPP~~gG~gGGv~AKDalGNdI~as~wL~th~pGdR~LvqGLKGDpT 139 (145)
-+.+.+.+||..++||+ |+..+++..|||+.+.+|+++|-+++|++-|+.++||+
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 88999999999999999999999999999999999998
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=99.07 E-value=5.5e-11 Score=90.28 Aligned_cols=41 Identities=54% Similarity=0.866 Sum_probs=38.8
Q ss_pred cccccccCCcchhhhhhccCCCCChhhhcccCCCceeEEEe
Q 032198 104 TTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKQDFSHLQLI 144 (145)
Q Consensus 104 v~AKDalGNdI~as~wL~th~pGdR~LvqGLKGDpTYLiV~ 144 (145)
+.|||+|||||++++||+||.|||+.++|+..+++.++++.
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~~ 41 (126)
T cd03471 1 VAAKDALGNDIKVSKWLATHNPGDRSLVQGLKGDPTYLIVE 41 (126)
T ss_pred CccccccCCceeHHHHHhhCCCCCeEEEEEecCCeEEEEEe
Confidence 46999999999999999999999999999999999999874
No 6
>COG0723 QcrA Rieske Fe-S protein [Energy production and conversion]
Probab=97.34 E-value=0.00014 Score=55.89 Aligned_cols=86 Identities=16% Similarity=0.080 Sum_probs=73.3
Q ss_pred CCCCCcchHHHHHHHHhhhcccccceecceeEEEeecCCCC-CCCCccccccccCCcchhhhhhccCCCCChhhhcccCC
Q 032198 58 DRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLG-SAGGGTTAKDAIGNDIIAADWLNTHGPGDRTLTEGLKQ 136 (145)
Q Consensus 58 ~~vPdM~RRqlMNlL~~Gav~~~a~g~lyP~~~fFvPP~~g-G~gGGv~AKDalGNdI~as~wL~th~pGdR~LvqGLKG 136 (145)
....+++||++|++++.+..+.....++||...++.|+..+ ..+..+.++|...+++..........|..+.+....++
T Consensus 4 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~ 83 (177)
T COG0723 4 AAATGLSRRDFLVLLTTGVGAVGAGAALYPAVESVDPPAGGGLAGAPIEVDDSGIGPGPLVTVPWRGKPVFLLRRTEYAG 83 (177)
T ss_pred cccccccHHHhhhhhhccccccceeeeeeehhhcccCcccccccCCceeeeccCCccceEEEEecCCCCeeeEeeccccc
Confidence 35678999999999999999999999999999999997765 78888999999989999988888888888877666666
Q ss_pred CceeEEE
Q 032198 137 DFSHLQL 143 (145)
Q Consensus 137 DpTYLiV 143 (145)
+..|.+.
T Consensus 84 ~~~~~~~ 90 (177)
T COG0723 84 PKGGVTR 90 (177)
T ss_pred cccccee
Confidence 6665543
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=95.09 E-value=0.0069 Score=47.72 Aligned_cols=38 Identities=13% Similarity=0.159 Sum_probs=33.8
Q ss_pred chHHHHHHHHhhhcccccceecceeEEEeecCCCCCCC
Q 032198 64 GKRQLMNLLLLGAVSLPTGFMLVPYATFFAPPGLGSAG 101 (145)
Q Consensus 64 ~RRqlMNlL~~Gav~~~a~g~lyP~~~fFvPP~~gG~g 101 (145)
+||+||+..+.++.++-++++++|++.||-|.....++
T Consensus 1 ~RR~fl~~~~~~~~~~~~~~~~~p~v~~~~P~~~~~a~ 38 (174)
T TIGR01416 1 TRRDFLYAATGAVGAVGAAAAAVPFIDSMNPSASVKAA 38 (174)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHheeCcchhcccc
Confidence 59999999999999999999999999999887766555
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=93.69 E-value=0.0062 Score=39.14 Aligned_cols=37 Identities=11% Similarity=0.230 Sum_probs=28.2
Q ss_pred CCCCCcchHHHHHHHHhhhcccccceecceeEEEeec
Q 032198 58 DRVPDMGKRQLMNLLLLGAVSLPTGFMLVPYATFFAP 94 (145)
Q Consensus 58 ~~vPdM~RRqlMNlL~~Gav~~~a~g~lyP~~~fFvP 94 (145)
++..|-+||.||-+.+.+..++-++++++|++..+-|
T Consensus 4 ~~~~~~~RRdFL~~at~~~gavG~~~~a~Pfv~s~~P 40 (41)
T PF10399_consen 4 NEPVDPTRRDFLTIATSAVGAVGAAAAAWPFVSSMNP 40 (41)
T ss_dssp ------HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS
T ss_pred CCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 4567889999999999999999999999999877766
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=82.54 E-value=0.74 Score=31.90 Aligned_cols=28 Identities=21% Similarity=0.177 Sum_probs=19.7
Q ss_pred CCCCcchHHHHHHHHhhhcccccceecc
Q 032198 59 RVPDMGKRQLMNLLLLGAVSLPTGFMLV 86 (145)
Q Consensus 59 ~vPdM~RRqlMNlL~~Gav~~~a~g~ly 86 (145)
.-++++||+||-.|.+|++++.+....-
T Consensus 5 ~~~~~sRR~Flk~lg~~aaa~~aa~~~~ 32 (66)
T TIGR02811 5 QKADPSRRDLLKGLGVGAAAGAVAAATG 32 (66)
T ss_pred ccCCccHHHHHHHHHHHHHHHHHHHhcc
Confidence 4567899999998887776555544333
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=80.97 E-value=1.1 Score=26.03 Aligned_cols=23 Identities=17% Similarity=0.180 Sum_probs=16.4
Q ss_pred CcchHHHHHHHHhhhccccccee
Q 032198 62 DMGKRQLMNLLLLGAVSLPTGFM 84 (145)
Q Consensus 62 dM~RRqlMNlL~~Gav~~~a~g~ 84 (145)
.|+|||||-.....+++..+++.
T Consensus 1 ~~sRR~fLk~~~a~~a~~~~~~~ 23 (26)
T PF10518_consen 1 NLSRRQFLKGGAAAAAAAALGGC 23 (26)
T ss_pred CCcHHHHHHHHHHHHHHHHhccc
Confidence 47999999887776665555443
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=68.34 E-value=5.5 Score=37.19 Aligned_cols=77 Identities=21% Similarity=0.164 Sum_probs=47.0
Q ss_pred CCcchHHHHHHHHhhhcc--cccceecceeEEEeecCC---CCCCCCccccccccCCcchh-hhhhccCCCCChhhhccc
Q 032198 61 PDMGKRQLMNLLLLGAVS--LPTGFMLVPYATFFAPPG---LGSAGGGTTAKDAIGNDIIA-ADWLNTHGPGDRTLTEGL 134 (145)
Q Consensus 61 PdM~RRqlMNlL~~Gav~--~~a~g~lyP~~~fFvPP~---~gG~gGGv~AKDalGNdI~a-s~wL~th~pGdR~LvqGL 134 (145)
--|+||-++|+..+..+. +.++.+.||++.||-=-. .++..+++.+.-..-+--.. ..|+.-..|-+.---++.
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 348999999998776544 677778999999995433 33444555544332222112 256666666655555566
Q ss_pred CCC
Q 032198 135 KQD 137 (145)
Q Consensus 135 KGD 137 (145)
.|+
T Consensus 115 ~g~ 117 (504)
T PF03935_consen 115 DGR 117 (504)
T ss_pred CCC
Confidence 544
No 12
>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=47.21 E-value=8.3 Score=25.87 Aligned_cols=51 Identities=18% Similarity=0.232 Sum_probs=33.7
Q ss_pred eEEEeecCCCCCCCCcc--ccccccCCcchhhhhhccCCCCChhhhcccCCCcee
Q 032198 88 YATFFAPPGLGSAGGGT--TAKDAIGNDIIAADWLNTHGPGDRTLTEGLKQDFSH 140 (145)
Q Consensus 88 ~~~fFvPP~~gG~gGGv--~AKDalGNdI~as~wL~th~pGdR~LvqGLKGDpTY 140 (145)
....|-|-+.....|-+ ..|-. ++=.+++||.+-.+||+-.+.|=.|+-+|
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 44555555554333322 33333 22246889999999999999999999888
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=44.81 E-value=13 Score=21.55 Aligned_cols=19 Identities=5% Similarity=0.128 Sum_probs=14.3
Q ss_pred cchHHHHHHHHhhhccccc
Q 032198 63 MGKRQLMNLLLLGAVSLPT 81 (145)
Q Consensus 63 M~RRqlMNlL~~Gav~~~a 81 (145)
++||+||-+...++.++..
T Consensus 1 ~sRR~Flk~~~~~~a~~~~ 19 (29)
T TIGR01409 1 LSRRDFLKGAAAAGAAAGL 19 (29)
T ss_pred CchhhhHHHHHHHHHHHhc
Confidence 5899999998776665444
No 14
>PRK09476 napG quinol dehydrogenase periplasmic component; Provisional
Probab=40.72 E-value=16 Score=30.43 Aligned_cols=14 Identities=21% Similarity=0.591 Sum_probs=10.3
Q ss_pred CCCcchHHHHHHHH
Q 032198 60 VPDMGKRQLMNLLL 73 (145)
Q Consensus 60 vPdM~RRqlMNlL~ 73 (145)
.-.|+||+||=...
T Consensus 6 ~~~~~rr~f~~~~~ 19 (254)
T PRK09476 6 KPQNGRRRFLRDVV 19 (254)
T ss_pred cCCccHHHHHHHHH
Confidence 34699999995554
No 15
>PRK02888 nitrous-oxide reductase; Validated
Probab=38.43 E-value=27 Score=33.69 Aligned_cols=28 Identities=14% Similarity=0.205 Sum_probs=21.6
Q ss_pred CCCCCcchHHHHHHHHhhhcccccceec
Q 032198 58 DRVPDMGKRQLMNLLLLGAVSLPTGFML 85 (145)
Q Consensus 58 ~~vPdM~RRqlMNlL~~Gav~~~a~g~l 85 (145)
+.-++++||+|||--.++++++.++++.
T Consensus 4 ~~~~~~~rr~~~~~~~~~~~~~~~~~~~ 31 (635)
T PRK02888 4 EAPSGLSRRQFLGTAALAGAAGAAGSTG 31 (635)
T ss_pred cccCCccHHHhhhHHHHHhhhhhhhccc
Confidence 4578899999999887777777666554
No 16
>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=31.68 E-value=18 Score=26.51 Aligned_cols=9 Identities=22% Similarity=0.213 Sum_probs=7.0
Q ss_pred cCCCceeEE
Q 032198 134 LKQDFSHLQ 142 (145)
Q Consensus 134 LKGDpTYLi 142 (145)
|-|||||+.
T Consensus 44 lSGDPaYIt 52 (79)
T PF06135_consen 44 LSGDPAYIT 52 (79)
T ss_pred ecCCCcccc
Confidence 469999974
No 17
>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=31.62 E-value=8.6 Score=28.01 Aligned_cols=31 Identities=16% Similarity=0.277 Sum_probs=26.2
Q ss_pred cchHHHHHHHHhhhcccccceecceeEEEee
Q 032198 63 MGKRQLMNLLLLGAVSLPTGFMLVPYATFFA 93 (145)
Q Consensus 63 M~RRqlMNlL~~Gav~~~a~g~lyP~~~fFv 93 (145)
-+..+.+|.++++.++..+...+.-+++|||
T Consensus 55 ~~~~~~~~iili~lls~v~IlVily~IyYFV 85 (101)
T PF06024_consen 55 ASKQNNGNIILISLLSFVCILVILYAIYYFV 85 (101)
T ss_pred ccccccccchHHHHHHHHHHHHHHhhheEEE
Confidence 4567889999999999999888887888886
No 18
>PLN02289 ribulose-bisphosphate carboxylase small chain
Probab=31.39 E-value=73 Score=26.50 Aligned_cols=27 Identities=22% Similarity=0.485 Sum_probs=18.9
Q ss_pred CcceeeeeeccCCC--------CCCCCcchHHHHH
Q 032198 44 MGMKIKCQATSIPA--------DRVPDMGKRQLMN 70 (145)
Q Consensus 44 ~~~~~~~~a~s~~~--------~~vPdM~RRqlMN 70 (145)
++.|+.|+..-.+. ...|+|..+|+.-
T Consensus 49 ng~rv~cmqvw~~~~~kkfETfSYLPpLtdeqI~k 83 (176)
T PLN02289 49 NGGRVSCMQVWPPIGKKKFETLSYLPDLTDEELAK 83 (176)
T ss_pred CCceeEEEEeecccCccceeeeecCCCCCHHHHHH
Confidence 46788887655441 3589999998864
No 19
>PRK05473 hypothetical protein; Provisional
Probab=29.43 E-value=21 Score=26.58 Aligned_cols=9 Identities=22% Similarity=0.205 Sum_probs=6.9
Q ss_pred cCCCceeEE
Q 032198 134 LKQDFSHLQ 142 (145)
Q Consensus 134 LKGDpTYLi 142 (145)
|-|||||+.
T Consensus 47 lSGDPaYIt 55 (86)
T PRK05473 47 LSGDPAYIP 55 (86)
T ss_pred ccCCCCccC
Confidence 469999973
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=25.02 E-value=32 Score=22.74 Aligned_cols=20 Identities=40% Similarity=0.403 Sum_probs=15.3
Q ss_pred cccccccCCcchhhhhhccC
Q 032198 104 TTAKDAIGNDIIAADWLNTH 123 (145)
Q Consensus 104 v~AKDalGNdI~as~wL~th 123 (145)
|+.||+.||+++=..|--+.
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 21
>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=36 Score=21.88 Aligned_cols=29 Identities=24% Similarity=0.319 Sum_probs=20.7
Q ss_pred CCcchhhhhhccCCCCChhhhcccCCCce
Q 032198 111 GNDIIAADWLNTHGPGDRTLTEGLKQDFS 139 (145)
Q Consensus 111 GNdI~as~wL~th~pGdR~LvqGLKGDpT 139 (145)
|+--.+++|+..||.|...+-+-.-.|.|
T Consensus 22 g~VYDvt~~~~~hpgg~~~~~~~aG~D~T 50 (76)
T PF00173_consen 22 GKVYDVTDFLDRHPGGADILKKYAGRDAT 50 (76)
T ss_dssp TEEEECTTTTTTSTTTSHHHHTTTTSBTH
T ss_pred CEEcccccccccccchhHHHHHhcccccc
Confidence 56677888999999997666554445554
No 22
>PF00996 GDI: GDP dissociation inhibitor; InterPro: IPR018203 Rab proteins constitute a family of small GTPases that serve a regulatory role in vesicular membrane traffic [, ]; C-terminal geranylgeranylation is crucial for their membrane association and function. This post-translational modification is catalysed by Rab geranylgeranyl transferase (Rab-GGTase), a multi-subunit enzyme that contains a catalytic heterodimer and an accessory component, termed Rab escort protein (REP)-1 []. REP-1 presents newly- synthesised Rab proteins to the catalytic component, and forms a stable complex with the prenylated proteins following the transfer reaction. The mechanism of REP-1-mediated membrane association of Rab5 is similar to that mediated by Rab GDP dissociation inhibitor (GDI). REP-1 and Rab GDI also share other functional properties, including the ability to inhibit the release of GDP and to remove Rab proteins from membranes. The crystal structure of the bovine alpha-isoform of Rab GDI has been determined to a resolution of 1.81A []. The protein is composed of two main structural units: a large complex multi-sheet domain I, and a smaller alpha-helical domain II. The structural organisation of domain I is closely related to FAD-containing monooxygenases and oxidases []. Conserved regions common to GDI and the choroideraemia gene product, which delivers Rab to catalytic subunits of Rab geranylgeranyltransferase II, are clustered on one face of the domain []. The two most conserved regions form a compact structure at the apex of the molecule; site-directed mutagenesis has shown these regions to play a critical role in the binding of Rab proteins [].; PDB: 1VG9_C 1VG0_A 1LTX_R 3P1W_A 3CPH_H 3CPJ_G 3CPI_H 1UKV_G 2BCG_G 1GND_A ....
Probab=22.66 E-value=33 Score=31.09 Aligned_cols=45 Identities=24% Similarity=0.307 Sum_probs=26.0
Q ss_pred eccccccccccCCCcceeeeeeccC-CCCCCCCcchHHHHHHHHhh
Q 032198 31 VKPARTQMVTKNPMGMKIKCQATSI-PADRVPDMGKRQLMNLLLLG 75 (145)
Q Consensus 31 ~k~~~~~~~~k~~~~~~~~~~a~s~-~~~~vPdM~RRqlMNlL~~G 75 (145)
.|+..+..+-++.+-.++.|....+ ....+.-++||+||+||.+-
T Consensus 102 Fk~V~~~~v~~~~~l~kVP~sr~dvf~s~~lsl~eKR~lmkFl~~v 147 (438)
T PF00996_consen 102 FKAVDGSYVYKNGKLHKVPCSREDVFKSKLLSLFEKRRLMKFLKFV 147 (438)
T ss_dssp EEEESEEEEEETTEEEE--SSHHHHHC-TTS-HHHHHHHHHHHHHH
T ss_pred EEEcceeEEEeCCEEeeCCCCHHHhhcCCCccHHHHHHHHHHHHHH
Confidence 3444444444444556777764433 34567778999999999874
No 23
>PRK09898 hypothetical protein; Provisional
Probab=21.65 E-value=39 Score=26.77 Aligned_cols=22 Identities=9% Similarity=0.132 Sum_probs=14.8
Q ss_pred cchHHHHHHHHhhhccccccee
Q 032198 63 MGKRQLMNLLLLGAVSLPTGFM 84 (145)
Q Consensus 63 M~RRqlMNlL~~Gav~~~a~g~ 84 (145)
|+||+||=....+++++.+++.
T Consensus 13 ~~RR~flk~~~~~~~g~~~~~~ 34 (208)
T PRK09898 13 LTRLEFLRISGKGLAGLTIAPA 34 (208)
T ss_pred hhHHHHHHhhcchhhhhhhhhH
Confidence 9999999887555554444333
No 24
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=21.10 E-value=1.4e+02 Score=26.05 Aligned_cols=27 Identities=19% Similarity=0.315 Sum_probs=17.0
Q ss_pred ceeeeeeccCCCCCCCCcchHHHHHHHHhh
Q 032198 46 MKIKCQATSIPADRVPDMGKRQLMNLLLLG 75 (145)
Q Consensus 46 ~~~~~~a~s~~~~~vPdM~RRqlMNlL~~G 75 (145)
..+.|.+-.. +-...+||..|-++...
T Consensus 36 ~~~~~~~~~~---~~~~~srr~~l~~~~ga 62 (260)
T PLN00042 36 SQVVCRAQEE---DNSAVSRRAALALLAGA 62 (260)
T ss_pred cceeeecccc---ccccccHHHHHHHHHHH
Confidence 3456655322 33568899999877655
Done!