Query gi|254780448|ref|YP_003064861.1| hypothetical protein CLIBASIA_01665 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 311
No_of_seqs 5 out of 7
Neff 2.1
Searched_HMMs 39220
Date Sun May 29 16:26:42 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780448.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK01683 trans-aconitate 2-met 59.2 8 0.0002 19.4 2.5 68 171-245 40-112 (252)
2 KOG2757 consensus 57.9 3.6 9.3E-05 21.7 0.5 43 203-257 226-268 (411)
3 cd06312 PBP1_ABC_sugar_binding 48.0 22 0.00056 16.5 3.4 99 143-246 77-185 (271)
4 cd06307 PBP1_uncharacterized_s 45.8 24 0.00061 16.3 4.4 103 143-249 78-192 (275)
5 KOG4463 consensus 43.1 8.2 0.00021 19.4 0.4 22 159-180 71-93 (323)
6 TIGR01090 apt adenine phosphor 43.1 9.4 0.00024 19.0 0.7 33 152-185 6-39 (175)
7 TIGR00243 Dxr 1-deoxy-D-xylulo 40.6 15 0.00039 17.6 1.5 66 142-213 155-236 (406)
8 PRK01622 OxaA-like protein pre 34.9 18 0.00047 17.0 1.2 25 11-35 55-79 (266)
9 COG4759 Uncharacterized protei 32.7 26 0.00066 16.0 1.6 25 249-273 272-296 (316)
10 PRK09437 bcp thioredoxin-depen 32.3 38 0.00098 14.9 3.7 15 196-211 70-84 (156)
11 pfam05125 Phage_cap_P2 Phage m 31.5 8.1 0.00021 19.4 -1.1 41 165-208 118-162 (333)
12 pfam04640 PLATZ PLATZ transcri 28.4 36 0.00091 15.1 1.7 25 176-200 13-37 (72)
13 COG0035 Upp Uracil phosphoribo 27.2 40 0.001 14.8 1.8 92 152-250 90-183 (210)
14 cd03019 DsbA_DsbA DsbA family, 26.2 35 0.00089 15.2 1.4 33 171-203 129-161 (178)
15 PRK02463 OxaA-like protein pre 25.9 34 0.00088 15.2 1.3 23 12-34 56-78 (307)
16 TIGR01017 rpsD_bact ribosomal 25.6 38 0.00097 14.9 1.5 16 184-200 123-138 (217)
17 KOG4389 consensus 25.3 14 0.00036 17.8 -0.8 79 150-229 310-404 (601)
18 pfam11681 DUF3277 Protein of u 24.9 28 0.00072 15.8 0.7 78 77-155 26-124 (146)
19 COG3068 Uncharacterized protei 24.4 41 0.001 14.7 1.4 52 169-225 40-91 (194)
20 TIGR01382 PfpI intracellular p 24.2 25 0.00064 16.1 0.3 54 152-213 89-150 (189)
21 PRK11582 flagella biosynthesis 24.2 40 0.001 14.8 1.3 77 163-242 13-99 (179)
22 pfam10787 YfmQ Uncharacterized 23.3 55 0.0014 13.9 2.5 32 181-213 40-71 (149)
23 pfam01289 Thiol_cytolysin Thio 23.2 55 0.0014 13.8 3.1 85 175-288 275-366 (467)
24 pfam02520 DUF148 Domain of unk 23.1 39 0.001 14.8 1.1 43 182-224 65-107 (114)
25 COG4106 Tam Trans-aconitate me 22.8 56 0.0014 13.8 3.2 74 171-251 39-117 (257)
26 TIGR00512 aIF-2BI_fam translat 22.6 33 0.00084 15.3 0.7 22 44-65 211-232 (306)
27 cd03023 DsbA_Com1_like DsbA fa 21.6 59 0.0015 13.6 2.6 28 181-208 125-152 (154)
28 pfam11190 DUF2976 Protein of u 21.6 48 0.0012 14.2 1.3 24 4-27 46-69 (87)
29 TIGR02739 TraF type-F conjugat 21.5 42 0.0011 14.6 1.1 38 219-259 101-139 (270)
30 TIGR03489 cas_csp1 CRISPR-asso 21.2 42 0.0011 14.6 1.0 102 143-261 125-232 (292)
31 pfam11477 PM0188 Sialyltransfe 21.1 61 0.0015 13.6 3.2 53 146-200 200-253 (381)
32 KOG0102 consensus 21.1 61 0.0015 13.6 1.9 79 168-247 496-578 (640)
33 KOG1355 consensus 20.6 34 0.00088 15.2 0.4 27 89-115 249-275 (455)
34 PRK02944 OxaA-like protein pre 20.5 52 0.0013 14.0 1.4 26 11-36 54-79 (255)
35 pfam08283 Gemini_AL1_M Geminiv 20.2 60 0.0015 13.6 1.6 39 195-233 12-50 (106)
36 cd02178 GH16_beta_agarase Beta 20.2 54 0.0014 13.9 1.4 19 188-206 197-215 (270)
37 CHL00113 rps4 ribosomal protei 20.2 58 0.0015 13.7 1.5 18 184-202 112-129 (201)
38 PHA01635 hypothetical protein 20.1 57 0.0015 13.7 1.5 46 176-227 52-97 (231)
No 1
>PRK01683 trans-aconitate 2-methyltransferase; Provisional
Probab=59.21 E-value=8 Score=19.42 Aligned_cols=68 Identities=25% Similarity=0.269 Sum_probs=28.4
Q ss_pred HCCCCHHHHHHHHHCCCEEEECCCEECCCCHHHHHHHHHHHCCCCHHHHHH-HHHH----CCHHHHHHHHHHHHHHCCCH
Q ss_conf 266704678876305767998381322368899999999751269746555-6654----07466545899998837231
Q gi|254780448|r 171 LGTNKVYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIFPKDFEKVQL-ISSY----AHEHIFCKPFTKDLLNLANK 245 (311)
Q Consensus 171 lg~nk~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~vPkd~e~~QL-ISSY----AhQ~If~qs~~~L~s~hPe~ 245 (311)
||+|.+-..+.+..-+ +.-+-+|++++||..-+...| +.+++|- +.++ .---||+-+.+|-+..|+.+
T Consensus 40 CG~G~~t~~l~~r~p~------a~v~GiD~S~~Ml~~Ar~~~~-~~~f~~~D~~~~~~~~~~D~ifSNaalhW~~d~~~~ 112 (252)
T PRK01683 40 CGPGNSTALLHQRWPA------ARITGIDSSPAMLAEARQALP-DCQFVEADIRNWQPEQALDLIYANASLQWLPDHYEL 112 (252)
T ss_pred CCCCHHHHHHHHHCCC------CEEEEEECCHHHHHHHHHHCC-CCEEEECCHHCCCCCCCCCEEEEEEEHHHCCCHHHH
T ss_conf 7498999999997799------879999898999999997589-983872504207876787889561004507877999
No 2
>KOG2757 consensus
Probab=57.91 E-value=3.6 Score=21.69 Aligned_cols=43 Identities=28% Similarity=0.404 Sum_probs=32.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHCCCCCCCCEEE
Q ss_conf 9999999751269746555665407466545899998837231002116872379
Q gi|254780448|r 203 NMLAELNKIFPKDFEKVQLISSYAHEHIFCKPFTKDLLNLANKNIYQLSNPRYSY 257 (311)
Q Consensus 203 ~mL~dfkt~vPkd~e~~QLISSYAhQ~If~qs~~~L~s~hPe~~kyq~sns~ysY 257 (311)
+.+..++++||-| -++|+-.|.|++.=+|+-+.|---|.---|
T Consensus 226 eli~~l~kqfP~D------------IGvfs~~FlN~~~L~PGEA~yL~AnepHAY 268 (411)
T KOG2757 226 ELILKLNKQFPGD------------IGVFSPFFLNYVRLNPGEAIYLEANEPHAY 268 (411)
T ss_pred HHHHHHHHHCCCC------------CEEEEHHHHHHEECCCCCEEEECCCCCCEE
T ss_conf 9999987348996------------315517645443157873465337886323
No 3
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=48.02 E-value=22 Score=16.49 Aligned_cols=99 Identities=11% Similarity=0.056 Sum_probs=53.6
Q ss_pred HHHHHCCCHH----------HCCCCHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCEEEECCCEECCCCHHHHHHHHHHHC
Q ss_conf 7765408866----------743430118002323444266704678876305767998381322368899999999751
Q gi|254780448|r 143 QAIFQKMPLE----------EYPRLQKIGINYFRDFKLLGTNKVYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIF 212 (311)
Q Consensus 143 ~ai~~k~p~~----------e~~~~~~~~~~~frdf~Llg~nk~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~v 212 (311)
+|..+.||.- ..+++..++.+.+.-=++++ +.++++..++..++-.......+...-.+-|+..+
T Consensus 77 ~a~~agIpVv~~ds~~~~~~~~~~~~~vg~dn~~~G~~~a-----~~l~~~~g~~~v~~~~~~~~~~~~~~R~~Gf~~~l 151 (271)
T cd06312 77 RAVAAGIPVISFNAGDPKYKELGALAYVGQDEYAAGEAAG-----ERLAELKGGKNVLCVIHEPGNVTLEDRCAGFADGL 151 (271)
T ss_pred HHHHCCCEEEEEECCCCCCCCCCEEEEECCCHHHHHHHHH-----HHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHHH
T ss_conf 9996598699994788643445538997278899999999-----99998659983999982799869999999999998
Q ss_pred CCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHH
Q ss_conf 2697465556654074665458999988372310
Q gi|254780448|r 213 PKDFEKVQLISSYAHEHIFCKPFTKDLLNLANKN 246 (311)
Q Consensus 213 Pkd~e~~QLISSYAhQ~If~qs~~~L~s~hPe~~ 246 (311)
.+.....+.+.+-..+.--......++++||+++
T Consensus 152 ~~~~~~~~~~~~~~d~~~a~~~~~~~L~~~pdi~ 185 (271)
T cd06312 152 GGAGITEEVIETGADPTEVASRIAAYLRANPDVD 185 (271)
T ss_pred HHCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 7559807998579999999999999998498988
No 4
>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes.
Probab=45.84 E-value=24 Score=16.27 Aligned_cols=103 Identities=13% Similarity=0.153 Sum_probs=54.4
Q ss_pred HHHHHCCCH-------HHCCCCHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCEEEECCCEECCCCHHHHHHHHHHH----
Q ss_conf 776540886-------674343011800232344426670467887630576799838132236889999999975----
Q gi|254780448|r 143 QAIFQKMPL-------EEYPRLQKIGINYFRDFKLLGTNKVYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKI---- 211 (311)
Q Consensus 143 ~ai~~k~p~-------~e~~~~~~~~~~~frdf~Llg~nk~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~---- 211 (311)
+|..+.||. .+.+++.-++.+.+.-=++++. +-.++|...+++-.++.|..-+. +..+-++-|+..
T Consensus 78 ~a~~~GIPVV~~~~~~~~~~~~~~Vg~Dn~~aG~~aa~--~l~~~l~~~~g~i~ii~g~~~~~-~~~~R~~Gf~~~l~~~ 154 (275)
T cd06307 78 RLAAAGVPVVTLVSDLPGSPRAGYVGIDNRAAGRTAAW--LIGRFLGRRPGKVAVLAGSHRFR-GHEEREMGFRSVLREE 154 (275)
T ss_pred HHHHCCCEEEEECCCCCCCCCCEEECCCHHHHHHHHHH--HHHHHHCCCCCEEEEEECCCCCH-HHHHHHHHHHHHHHHH
T ss_conf 99987984999728888877433991487999999999--99996076897799990798753-2999999999999865
Q ss_pred CCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHH-CCC
Q ss_conf 12697465556654074665458999988372310-021
Q gi|254780448|r 212 FPKDFEKVQLISSYAHEHIFCKPFTKDLLNLANKN-IYQ 249 (311)
Q Consensus 212 vPkd~e~~QLISSYAhQ~If~qs~~~L~s~hPe~~-kyq 249 (311)
.| +++-+......-.+..-.+...+++.+||++. .|.
T Consensus 155 ~p-~~~iv~~~~~~~~~~~a~~~~~~lL~~~Pdi~ai~~ 192 (275)
T cd06307 155 FP-GLRVLETLEGLDDPARAYEATRKLLARHPDLVGIYN 192 (275)
T ss_pred CC-CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf 88-874024661788659999999999974999629998
No 5
>KOG4463 consensus
Probab=43.13 E-value=8.2 Score=19.35 Aligned_cols=22 Identities=36% Similarity=0.522 Sum_probs=15.4
Q ss_pred HCCCHHHHHHH-HHCCCCHHHHH
Q ss_conf 11800232344-42667046788
Q gi|254780448|r 159 KIGINYFRDFK-LLGTNKVYKNL 180 (311)
Q Consensus 159 ~~~~~~frdf~-Llg~nk~~q~~ 180 (311)
+-=+-|||||| |||++|---++
T Consensus 71 l~I~Y~fR~~ERlLGShky~~fi 93 (323)
T KOG4463 71 LYILYYFRVFERLLGSHKYSVFI 93 (323)
T ss_pred HHHHHHHHHHHHHHCCCCCEEEH
T ss_conf 99999999999986455311203
No 6
>TIGR01090 apt adenine phosphoribosyltransferase; InterPro: IPR005764 Adenine phosphoribosyltransferase (APRTase, 2.4.2.7 from EC) is a widely distributed enzyme, and its deficiency in humans causes the accumulation of 2,8-dihydroxyadenine. It is the sole catalyst for adenine recycling in most eukaryotes. AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate ; GO: 0003999 adenine phosphoribosyltransferase activity, 0006168 adenine salvage.
Probab=43.08 E-value=9.4 Score=18.96 Aligned_cols=33 Identities=33% Similarity=0.607 Sum_probs=26.7
Q ss_pred HHCCCCHHCCCHHHHHHH-HHCCCCHHHHHHHHHC
Q ss_conf 674343011800232344-4266704678876305
Q gi|254780448|r 152 EEYPRLQKIGINYFRDFK-LLGTNKVYKNLLDASR 185 (311)
Q Consensus 152 ~e~~~~~~~~~~~frdf~-Llg~nk~~q~~LD~~r 185 (311)
-.+|--|+-|| +|||+- ||.....+++.+|++-
T Consensus 6 r~ipDfP~~GI-lFrDITplL~~~~~f~~~id~l~ 39 (175)
T TIGR01090 6 RSIPDFPKKGI-LFRDITPLLNNPELFRFLIDLLV 39 (175)
T ss_pred CCCCCCCCCCE-EEEECCCCCCCHHHHHHHHHHHH
T ss_conf 62578877966-77661701068778999999999
No 7
>TIGR00243 Dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase; InterPro: IPR003821 1-deoxy-D-xylulose 5-phosphate reductoisomerase synthesizes 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose 5-phosphate in a single step by intramolecular rearrangement and reduction and is responsible for terpenoid biosynthesis in some organisms . In Arabidopsis thaliana 1-deoxy-D-xylulose 5-phosphate reductoisomerase is the first committed enzyme of the non-mevalonate pathway for isoprenoid biosynthesis.; GO: 0003824 catalytic activity, 0008299 isoprenoid biosynthetic process.
Probab=40.59 E-value=15 Score=17.57 Aligned_cols=66 Identities=36% Similarity=0.530 Sum_probs=38.1
Q ss_pred HHHHHHCCCHHH-----CCCCHHCCC---------HHHHHHHH--HCCCCHHHHHHHHHCCCEEEECCCEECCCCHHHHH
Q ss_conf 777654088667-----434301180---------02323444--26670467887630576799838132236889999
Q gi|254780448|r 142 SQAIFQKMPLEE-----YPRLQKIGI---------NYFRDFKL--LGTNKVYKNLLDASRATEFIIDGKKINIDSAQNML 205 (311)
Q Consensus 142 ~~ai~~k~p~~e-----~~~~~~~~~---------~~frdf~L--lg~nk~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL 205 (311)
.-||||-.|-+- |--++.-+. --|||--| |-.-- -|.=|-|--=| =|+||++||| +||
T Consensus 155 H~AiFq~LP~~~Q~~~G~~~~~~~~~~~iiltaSGG~FRd~Ple~l~~~t-~~~AlkHPNWS----MG~KItiDSA-tmm 228 (406)
T TIGR00243 155 HSAIFQSLPQEIQNKLGYAGLKELGVKRIILTASGGAFRDTPLEELPIVT-VEDALKHPNWS----MGKKITIDSA-TMM 228 (406)
T ss_pred HHHHHHCCCHHHHHHCCCCCCCCCCCCEEEEECCCCCCCCCHHHHHCCCC-HHHHHCCCCCC----CCCCCCCCCH-HHH
T ss_conf 68897607977886168677221684078985688521022156512678-58873587866----7483220017-678
Q ss_pred HHHHHHCC
Q ss_conf 99997512
Q gi|254780448|r 206 AELNKIFP 213 (311)
Q Consensus 206 ~dfkt~vP 213 (311)
|+.-+.+-
T Consensus 229 NKGLE~iE 236 (406)
T TIGR00243 229 NKGLEVIE 236 (406)
T ss_pred HHHHHHHH
T ss_conf 66899999
No 8
>PRK01622 OxaA-like protein precursor; Validated
Probab=34.92 E-value=18 Score=17.00 Aligned_cols=25 Identities=28% Similarity=0.404 Sum_probs=16.2
Q ss_pred HCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 3167744204666400247777787
Q gi|254780448|r 11 FKKGNYGWGALGIVSDVALLAIPAA 35 (311)
Q Consensus 11 fkkgnygwg~~g~~sd~all~~~~~ 35 (311)
+--|||||+|+-..-=+-++..|..
T Consensus 55 ~~~gnyGlaIIl~TiivRlil~PL~ 79 (266)
T PRK01622 55 HIHGSYGIAIIIVTLIIRSLMIPLA 79 (266)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 7588499999999999999998702
No 9
>COG4759 Uncharacterized protein conserved in bacteria containing thioredoxin-like domain [Posttranslational modification, protein turnover, chaperones]
Probab=32.72 E-value=26 Score=16.04 Aligned_cols=25 Identities=4% Similarity=0.133 Sum_probs=15.1
Q ss_pred CCCCCCEEEEEEEECCCEEEEEEEE
Q ss_conf 1168723799985357659999960
Q gi|254780448|r 249 QLSNPRYSYQFNTLKDKTISFVAKE 273 (311)
Q Consensus 249 q~sns~ysY~ineL~dg~vkftAt~ 273 (311)
+++++-+.|..+-+++..-..++.+
T Consensus 272 ~pDg~i~~~~~~rVE~~g~v~t~~~ 296 (316)
T COG4759 272 SPDGDIWGYYLARVEVEGSVMTVRS 296 (316)
T ss_pred CCCCCEEEEEEEEEEECCCEEEEEE
T ss_conf 5789753699999995381899982
No 10
>PRK09437 bcp thioredoxin-dependent thiol peroxidase; Reviewed
Probab=32.28 E-value=38 Score=14.89 Aligned_cols=15 Identities=20% Similarity=0.330 Sum_probs=5.4
Q ss_pred ECCCCHHHHHHHHHHH
Q ss_conf 2236889999999975
Q gi|254780448|r 196 INIDSAQNMLAELNKI 211 (311)
Q Consensus 196 Is~Dsa~~mL~dfkt~ 211 (311)
||.|++. -+++|.+.
T Consensus 70 IS~D~~~-~~~~f~~~ 84 (156)
T PRK09437 70 ISPDKPE-KLSKFAEK 84 (156)
T ss_pred ECCCCHH-HHHHHHHH
T ss_conf 7688899-99999997
No 11
>pfam05125 Phage_cap_P2 Phage major capsid protein, P2 family.
Probab=31.45 E-value=8.1 Score=19.38 Aligned_cols=41 Identities=20% Similarity=0.279 Sum_probs=23.4
Q ss_pred HHHHH-HHCCCCHHHHHHHHHCCCEEEECCCEECCCC---HHHHHHHH
Q ss_conf 32344-4266704678876305767998381322368---89999999
Q gi|254780448|r 165 FRDFK-LLGTNKVYKNLLDASRATEFIIDGKKINIDS---AQNMLAEL 208 (311)
Q Consensus 165 frdf~-Llg~nk~~q~~LD~~ra~~FiiNGKKIs~Ds---a~~mL~df 208 (311)
|.||+ +....+..+.-||..+-- +||..++.++ ++-+++|-
T Consensus 118 ~~dF~~ri~~~i~~~~ALD~i~IG---fNG~s~A~~Td~~~nPllqDV 162 (333)
T pfam05125 118 FPDFQERIRDAIQKRQALDRIMIG---FNGTSRADTSNRADNPLLQDV 162 (333)
T ss_pred CHHHHHHHHHHHHHHHHHHHHEEC---CCCEEECCCCCCCCCCCHHHH
T ss_conf 788999999999999876561103---476540367882238662020
No 12
>pfam04640 PLATZ PLATZ transcription factor. Plant AT-rich sequence and zinc-binding proteins (PLATZ) are zinc dependant DNA binding proteins. They bind to AT rich sequences and functions in transcriptional repression.
Probab=28.42 E-value=36 Score=15.09 Aligned_cols=25 Identities=20% Similarity=0.379 Sum_probs=21.1
Q ss_pred HHHHHHHHHCCCEEEECCCEECCCC
Q ss_conf 4678876305767998381322368
Q gi|254780448|r 176 VYKNLLDASRATEFIIDGKKINIDS 200 (311)
Q Consensus 176 ~~q~~LD~~ra~~FiiNGKKIs~Ds 200 (311)
+-|+++|.+.--++++|+.||.-=|
T Consensus 13 d~qkl~D~s~VQtY~iNsakVvfLn 37 (72)
T pfam04640 13 DIQKLIDCSGVQTYVINSAKVVFLN 37 (72)
T ss_pred HHHHHCCCCCCEEEEECCCEEEEEC
T ss_conf 9886425145178897781699846
No 13
>COG0035 Upp Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]
Probab=27.24 E-value=40 Score=14.80 Aligned_cols=92 Identities=21% Similarity=0.204 Sum_probs=66.2
Q ss_pred HHCCCCHHCCCHHHHHHHHHCCCCHHHHHHH-HHCCCEEEECCCEECCCCHHHHHHHHHHH-CCCCHHHHHHHHHHCCHH
Q ss_conf 6743430118002323444266704678876-30576799838132236889999999975-126974655566540746
Q gi|254780448|r 152 EEYPRLQKIGINYFRDFKLLGTNKVYKNLLD-ASRATEFIIDGKKINIDSAQNMLAELNKI-FPKDFEKVQLISSYAHEH 229 (311)
Q Consensus 152 ~e~~~~~~~~~~~frdf~Llg~nk~~q~~LD-~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~-vPkd~e~~QLISSYAhQ~ 229 (311)
+.+|.....-+..+||.|-+---..|.++-+ ..-..-|+++.-.-.-.+.-.+++.+++. =|++....-+|++ -
T Consensus 90 ~~~P~a~vG~ig~~Rdeet~~p~~yy~KLP~~~~~~~viv~DPMLATG~s~i~ai~~L~~~G~~~~I~~v~~vAa--p-- 165 (210)
T COG0035 90 KLIPSARVGHIGIYRDEETLEPVLYYEKLPEDIDERTVIVLDPMLATGGSAIAAIDLLKKRGGPKNIKVVSLVAA--P-- 165 (210)
T ss_pred HHCCCCEEEEEEEEECCCCCCEEHHHHHCCCCCCCCEEEEECCHHHCCHHHHHHHHHHHHHCCCCEEEEEEEEEC--H--
T ss_conf 869766388988884376676003587589864688599978614126769999999997189752899999964--8--
Q ss_pred HHHHHHHHHHHHCCCHHCCCC
Q ss_conf 654589999883723100211
Q gi|254780448|r 230 IFCKPFTKDLLNLANKNIYQL 250 (311)
Q Consensus 230 If~qs~~~L~s~hPe~~kyq~ 250 (311)
+....+.+.||++..|+-
T Consensus 166 ---eGi~~v~~~~p~v~I~ta 183 (210)
T COG0035 166 ---EGIKAVEKAHPDVEIYTA 183 (210)
T ss_pred ---HHHHHHHHHCCCCEEEEE
T ss_conf ---999999986899759999
No 14
>cd03019 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain.
Probab=26.23 E-value=35 Score=15.15 Aligned_cols=33 Identities=15% Similarity=0.243 Sum_probs=19.7
Q ss_pred HCCCCHHHHHHHHHCCCEEEECCCEECCCCHHH
Q ss_conf 266704678876305767998381322368899
Q gi|254780448|r 171 LGTNKVYKNLLDASRATEFIIDGKKINIDSAQN 203 (311)
Q Consensus 171 lg~nk~~q~~LD~~ra~~FiiNGKKIs~Dsa~~ 203 (311)
+..+....+-+....--+|+||||.+...+.-.
T Consensus 129 i~~~~~~a~~~gI~gTPtfiINGKy~i~~~~~~ 161 (178)
T cd03019 129 VAKAEKLAKKYKITGVPAFVVNGKYVVNPSAIG 161 (178)
T ss_pred HHHHHHHHHHHCCCCCCEEEECCEEEECCCCCC
T ss_conf 999999999958986787999999998788788
No 15
>PRK02463 OxaA-like protein precursor; Provisional
Probab=25.91 E-value=34 Score=15.21 Aligned_cols=23 Identities=17% Similarity=0.193 Sum_probs=14.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 16774420466640024777778
Q gi|254780448|r 12 KKGNYGWGALGIVSDVALLAIPA 34 (311)
Q Consensus 12 kkgnygwg~~g~~sd~all~~~~ 34 (311)
--|||||+|+-..-=+-++..|.
T Consensus 56 ~g~nyG~aIIl~TiiIRlillPL 78 (307)
T PRK02463 56 LGLGFGLAIIIVTIIVRTLILPL 78 (307)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 38773389999999999999830
No 16
>TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=25.57 E-value=38 Score=14.90 Aligned_cols=16 Identities=38% Similarity=0.748 Sum_probs=13.0
Q ss_pred HCCCEEEECCCEECCCC
Q ss_conf 05767998381322368
Q gi|254780448|r 184 SRATEFIIDGKKINIDS 200 (311)
Q Consensus 184 ~ra~~FiiNGKKIs~Ds 200 (311)
+||- +.+||++|++-|
T Consensus 123 sHGh-i~vNGk~VdIPS 138 (217)
T TIGR01017 123 SHGH-ILVNGKKVDIPS 138 (217)
T ss_pred HCCE-EEECCEEECCCE
T ss_conf 0880-787981852240
No 17
>KOG4389 consensus
Probab=25.30 E-value=14 Score=17.82 Aligned_cols=79 Identities=15% Similarity=0.176 Sum_probs=45.4
Q ss_pred CHHHCCCCHHCCCHHHH-------------HHH-HHCCCCHHHHHHHHHCCCEEE--ECCCEECCCCHHHHHHHHHHHCC
Q ss_conf 86674343011800232-------------344-426670467887630576799--83813223688999999997512
Q gi|254780448|r 150 PLEEYPRLQKIGINYFR-------------DFK-LLGTNKVYKNLLDASRATEFI--IDGKKINIDSAQNMLAELNKIFP 213 (311)
Q Consensus 150 p~~e~~~~~~~~~~~fr-------------df~-Llg~nk~~q~~LD~~ra~~Fi--iNGKKIs~Dsa~~mL~dfkt~vP 213 (311)
++-+||-+|.+|.+.|. |.+ |.|.||||-...-.--.-.|- -|.-.+.+|-=.+.++.+...+|
T Consensus 310 ~~l~FpfvpvvDg~Fl~~~~~~~L~~g~fkd~~il~G~nkDEGtyfl~Y~lp~ff~~~n~~~itR~ef~e~~~~~f~~~~ 389 (601)
T KOG4389 310 TPLSFPFVPVVDGDFLSDDPFALLKEGDFKDVQILVGVNKDEGTYFLVYGLPGFFDKHNASLITRDEFLEGVRVFFPGVS 389 (601)
T ss_pred CCCCCCEEEEECCCCCCCCHHHHHHCCCCCCEEEEEEEECCCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCC
T ss_conf 74320106642321025786889743786650489876436640687615744343346544778999999987512431
Q ss_pred CCHHHHHHHHHHCCHH
Q ss_conf 6974655566540746
Q gi|254780448|r 214 KDFEKVQLISSYAHEH 229 (311)
Q Consensus 214 kd~e~~QLISSYAhQ~ 229 (311)
|++..-++--|.-.+
T Consensus 390 -~~~r~a~~~~ytd~~ 404 (601)
T KOG4389 390 -DLAREAIKFHYTDWH 404 (601)
T ss_pred -HHHHHHHHHHCCCHH
T ss_conf -789998887107611
No 18
>pfam11681 DUF3277 Protein of unknown function (DUF3277). This family of proteins represents a putative bacteriophage protein. No function is currently known.
Probab=24.94 E-value=28 Score=15.79 Aligned_cols=78 Identities=18% Similarity=0.210 Sum_probs=33.3
Q ss_pred HHHHHCCCCEEEEEECCCEEEECCCCCHHHHHHCCCCCCHHHHCCCCHHHHHH------------------HHHHHHHHH
Q ss_conf 34543064225787167125410122326543102452011110540121111------------------011000234
Q gi|254780448|r 77 ALLAKEGIEATHIMEGGSTAIKSESVGAKELISASQNSQTVTQTGNISDATKA------------------SSTIKDAQS 138 (311)
Q Consensus 77 a~l~kegi~~~~~~eg~s~~ikses~g~k~~is~~~~~~~~t~~g~~~~~tka------------------s~tik~~~~ 138 (311)
++.+.|||+-...-+..+.+|-+.--|- .+..+.+.-+-+-..=||+.+-+. .-||.|.++
T Consensus 26 ~a~aeEGItv~m~~dkntMtiGaDGe~M-HSLhA~ksG~VTv~lLKTSP~N~kL~~~yn~Qs~ss~~WG~N~i~i~~~~s 104 (146)
T pfam11681 26 SATAEEGITVAMAGDKNTMTVGADGEVM-HSLHADKSGQITIRLLKTSPVNAKLMALYNAQSLSSALWGKNVIVIRNSAS 104 (146)
T ss_pred CCCCCCCEEEEEECCCCEEEECCCCHHH-HHCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCHHHHCCCEEEEECCCC
T ss_conf 5334465478962587426752685224-330269986499998734877899999876512064553573899934665
Q ss_pred HHH---HHHHHHCCCHHHCC
Q ss_conf 456---77765408866743
Q gi|254780448|r 139 IDR---SQAIFQKMPLEEYP 155 (311)
Q Consensus 139 i~~---~~ai~~k~p~~e~~ 155 (311)
=|. .+.-|||.|=..|.
T Consensus 105 GD~~tar~cAF~K~PD~~~a 124 (146)
T pfam11681 105 GDIATARSCAFKKQPDLQYA 124 (146)
T ss_pred CCEEEEEEEEEEECCCCCCC
T ss_conf 77348634266627875444
No 19
>COG3068 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.36 E-value=41 Score=14.70 Aligned_cols=52 Identities=25% Similarity=0.537 Sum_probs=37.4
Q ss_pred HHHCCCCHHHHHHHHHCCCEEEECCCEECCCCHHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf 442667046788763057679983813223688999999997512697465556654
Q gi|254780448|r 169 KLLGTNKVYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIFPKDFEKVQLISSY 225 (311)
Q Consensus 169 ~Llg~nk~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~vPkd~e~~QLISSY 225 (311)
--.+.+++||++||+---. ..+.+-||+-+| -|.++-+++| +..--++-.-|
T Consensus 40 ~e~~~~~~Yr~ILdlvWE~-ltVK~aKvNFe~---QLEKLE~~IP-~~dd~~~ygv~ 91 (194)
T COG3068 40 TEFGDGQIYRRILDLVWET-LTVKDAKVNFES---QLEKLEEAIP-SADDFDLYGVY 91 (194)
T ss_pred HHCCCCHHHHHHHHHHHHH-HHHCCCCCCHHH---HHHHHHHHCC-CCCHHHHHCCC
T ss_conf 7103308999999999999-741110135687---9999998689-93023564224
No 20
>TIGR01382 PfpI intracellular protease, PfpI family; InterPro: IPR006286 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad . This group of cysteine peptidases belong to MEROPS peptidase family C56 (Pfp1 endopeptidase, clan PC(C)). The member of this family from Pyrococcus horikoshii has been solved to 2 Angstrom resolution. It is an ATP-independent intracellular protease that crystallises as a hexameric ring. Cys-101 is proposed as the active site residue in a catalytic triad with the adjacent His-102 and a Glu residue from an adjacent monomer. A member of this family from Bacillus subtilis, GSP18, has been shown to be expressed in response to several forms of stress. A role in the degradation of small peptides has been suggested. This family is contained in a larger one of the thiamine biosynthesis protein ThiJ and its homologs.; GO: 0016798 hydrolase activity acting on glycosyl bonds.
Probab=24.24 E-value=25 Score=16.11 Aligned_cols=54 Identities=22% Similarity=0.357 Sum_probs=38.5
Q ss_pred HHCCCCHHCCCHHHHHHH--------HHCCCCHHHHHHHHHCCCEEEECCCEECCCCHHHHHHHHHHHCC
Q ss_conf 674343011800232344--------42667046788763057679983813223688999999997512
Q gi|254780448|r 152 EEYPRLQKIGINYFRDFK--------LLGTNKVYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIFP 213 (311)
Q Consensus 152 ~e~~~~~~~~~~~frdf~--------Llg~nk~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~vP 213 (311)
.||-|.---=+.+-|+|. .|..+-+ +-+|. |+-|||+..+.+|++..|++++=.
T Consensus 89 ~e~LR~d~~~~~lvR~f~e~gK~vaaIChgp~l------Li~A~--VlrGkk~T~y~aPei~~d~~nAGa 150 (189)
T TIGR01382 89 PEYLRLDEKVIRLVREFVEKGKPVAAICHGPQL------LISAG--VLRGKKLTAYPAPEIIDDVKNAGA 150 (189)
T ss_pred CCCCCCCHHHHHHHHHHHHCCCEEEEEECCCEE------EEECC--EECCCEEEECCCCCCHHHHHHCCE
T ss_conf 000148768999999984178819998453000------00255--103753753399862155652861
No 21
>PRK11582 flagella biosynthesis protein FliZ; Provisional
Probab=24.19 E-value=40 Score=14.79 Aligned_cols=77 Identities=22% Similarity=0.243 Sum_probs=38.6
Q ss_pred HHHHHHHHHCCCC-HHHHHHHHHCCCEEEECCCEECCCCHHHHHHHHHHHCCCCHHH--------HHHHHHHCCHHHHHH
Q ss_conf 0232344426670-4678876305767998381322368899999999751269746--------555665407466545
Q gi|254780448|r 163 NYFRDFKLLGTNK-VYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIFPKDFEK--------VQLISSYAHEHIFCK 233 (311)
Q Consensus 163 ~~frdf~Llg~nk-~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~vPkd~e~--------~QLISSYAhQ~If~q 233 (311)
-|.+||+---+.- --++.|| |.+ .++||+-|++..-..|=.-.-...=-+.++ ---|+.-+|+..|+-
T Consensus 13 rYLkDfKhsQTHCshC~k~LD--Ris-LV~~GqiinK~~I~~md~liDd~~W~~~Q~~l~aLCRFCs~i~c~~~~~yFDI 89 (179)
T PRK11582 13 RYLKDFKHSQTHCAHCRKLLD--RIT-LVRRGQIVNKIAISRLDTLLDDNGWQKEQKEWAALCRFCGDLHCKTQSDYFDI 89 (179)
T ss_pred HHHHHHHHCCCCHHHHCCHHH--HHE-EEECCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH
T ss_conf 999986451210443265145--630-22357655389987688872288899999999999999888751788760108
Q ss_pred -HHHHHHHHC
Q ss_conf -899998837
Q gi|254780448|r 234 -PFTKDLLNL 242 (311)
Q Consensus 234 -s~~~L~s~h 242 (311)
.|-+-+-++
T Consensus 90 ~gFkQyL~eQ 99 (179)
T PRK11582 90 IGFKQYLFEQ 99 (179)
T ss_pred HHHHHHHHHH
T ss_conf 9999999985
No 22
>pfam10787 YfmQ Uncharacterized protein from bacillus cereus group. This family is conserved in the Bacillus cereus group. Several members are called YfmQ but the function is not known.
Probab=23.32 E-value=55 Score=13.86 Aligned_cols=32 Identities=22% Similarity=0.413 Sum_probs=26.8
Q ss_pred HHHHCCCEEEECCCEECCCCHHHHHHHHHHHCC
Q ss_conf 763057679983813223688999999997512
Q gi|254780448|r 181 LDASRATEFIIDGKKINIDSAQNMLAELNKIFP 213 (311)
Q Consensus 181 LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~vP 213 (311)
|| .+.+++-+||+.+--...-.++++|++++=
T Consensus 40 l~-~~~~tVt~~Gk~Leg~~K~~~I~~FNeAiF 71 (149)
T pfam10787 40 LE-EENTTVTFDGKNLEGEEKSRIIQEFNEAIF 71 (149)
T ss_pred CC-CCCEEEEECCEECCCHHHHHHHHHHHHHHH
T ss_conf 24-542599888964472578799998768776
No 23
>pfam01289 Thiol_cytolysin Thiol-activated cytolysin.
Probab=23.15 E-value=55 Score=13.83 Aligned_cols=85 Identities=25% Similarity=0.421 Sum_probs=49.6
Q ss_pred CHHHHHHHHHCCCEEEECCCEECCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHCCCCCCCC
Q ss_conf 04678876305767998381322368899999999751269746555665407466545899998837231002116872
Q gi|254780448|r 175 KVYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIFPKDFEKVQLISSYAHEHIFCKPFTKDLLNLANKNIYQLSNPR 254 (311)
Q Consensus 175 k~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~vPkd~e~~QLISSYAhQ~If~qs~~~L~s~hPe~~kyq~sns~ 254 (311)
--|+.||+-+.-+-+++-|.- ++-.+.|-+||.. |-.=+-+=..|+.+||.
T Consensus 275 ~ey~dIl~nSSftAvvlGG~A----------~~~~kvvt~~~d~-------------------lr~iIk~na~~s~~nP~ 325 (467)
T pfam01289 275 TEYKDILENSSFKAVILGGDA----------KDHNQVVTGDFDV-------------------IRDVIKDGATFSRKNPG 325 (467)
T ss_pred CHHHHHHHCCEEEEEEECCCC----------HHCCEEECCCHHH-------------------HHHHHHCCCEECCCCCC
T ss_conf 058888646817999978781----------0132455387799-------------------99998627774577998
Q ss_pred E--EEEEEEECCCEEEEEEEE-----CCEEEECCCCCHHHC
Q ss_conf 3--799985357659999960-----210122266034213
Q gi|254780448|r 255 Y--SYQFNTLKDKTISFVAKE-----EGLVTYLNGSLHRNY 288 (311)
Q Consensus 255 y--sY~ineL~dg~vkftAt~-----~t~vq~sD~n~i~~y 288 (311)
| +|+..+|+|-.++.+--+ ++..++.||+..-.|
T Consensus 326 ~PISYtt~FLKDN~iA~v~n~tdYIETt~teY~~Gki~LdH 366 (467)
T pfam01289 326 YPISYTTVFLKDNVIAVVKNNTEYIETTSTAYTDGKINLDH 366 (467)
T ss_pred CCEEEEEEEEECCCEEEEECCCCEEEEEEEEECCCCEEEEC
T ss_conf 62276765430571468844774577643670277278602
No 24
>pfam02520 DUF148 Domain of unknown function DUF148. This domain has no known function nor do any of the proteins that possess it. In one member of this family the aligned region is repeated twice.
Probab=23.09 E-value=39 Score=14.84 Aligned_cols=43 Identities=16% Similarity=0.353 Sum_probs=32.8
Q ss_pred HHHCCCEEEECCCEECCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 6305767998381322368899999999751269746555665
Q gi|254780448|r 182 DASRATEFIIDGKKINIDSAQNMLAELNKIFPKDFEKVQLISS 224 (311)
Q Consensus 182 D~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~vPkd~e~~QLISS 224 (311)
+...--+=|++++-..+....+.++++++..|.++..+.-|+.
T Consensus 65 ~v~~~L~~I~~n~~~T~~q~~~aI~~L~~~~p~ev~~l~~I~~ 107 (114)
T pfam02520 65 SVDAKLSAILDNKDLTRRQKKEAIDALKKQYPQEVSTLFFIRK 107 (114)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999998182236999999999999878405699999999
No 25
>COG4106 Tam Trans-aconitate methyltransferase [General function prediction only]
Probab=22.82 E-value=56 Score=13.79 Aligned_cols=74 Identities=18% Similarity=0.146 Sum_probs=46.9
Q ss_pred HCCCCHHHHHHHHHCCCEEEECCCEECCCCHHHHHHHHHHHCCCCHHHHH-HHHHHC----CHHHHHHHHHHHHHHCCCH
Q ss_conf 26670467887630576799838132236889999999975126974655-566540----7466545899998837231
Q gi|254780448|r 171 LGTNKVYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIFPKDFEKVQ-LISSYA----HEHIFCKPFTKDLLNLANK 245 (311)
Q Consensus 171 lg~nk~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~vPkd~e~~Q-LISSYA----hQ~If~qs~~~L~s~hPe~ 245 (311)
||.|..-.-+.+---+. ...-+||+++||.+-....| |..+-+ =|.++. ---+|+-+..|-+-+||++
T Consensus 39 CGpGnsTelL~~RwP~A------~i~GiDsS~~Mla~Aa~rlp-~~~f~~aDl~~w~p~~~~dllfaNAvlqWlpdH~~l 111 (257)
T COG4106 39 CGPGNSTELLARRWPDA------VITGIDSSPAMLAKAAQRLP-DATFEEADLRTWKPEQPTDLLFANAVLQWLPDHPEL 111 (257)
T ss_pred CCCCHHHHHHHHHCCCC------EEEECCCCHHHHHHHHHHCC-CCCEECCCHHHCCCCCCCCHHHHHHHHHHCCCCHHH
T ss_conf 78877889999868888------67604699999999997489-973210527544998763303344366443640899
Q ss_pred HCCCCC
Q ss_conf 002116
Q gi|254780448|r 246 NIYQLS 251 (311)
Q Consensus 246 ~kyq~s 251 (311)
-.+-++
T Consensus 112 l~rL~~ 117 (257)
T COG4106 112 LPRLVS 117 (257)
T ss_pred HHHHHH
T ss_conf 999998
No 26
>TIGR00512 aIF-2BI_fam translation initiation factor, putative, aIF-2BI family; InterPro: IPR005251 This family contains proteins designated as translation initiation factor 2B subunit 1 (alpha) and 5-methylthioribose-1-phosphate isomerase (MTNA, 5.3.1.23 from EC, ). The delineation of this family is based in part on a discussion and neighbour-joining phylogenetic study , , of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. The archaeal proteins are related to the common ancestor of eIF-2B alpha, beta, and delta rather then specifically to any one of them, and that designation of particular archaeal members as corresponding to eIF-2B alpha or eIF-2B delta is imprecise. It has been suggested that designating the archaeal proteins as translation initiation factors remains unproven. 5-methylthioribose-1-phosphate isomerase (MTNA) participates in the methionine salvage pathway catalysing the isomerisation of 5-methylthioribose-1-phosphate to 5-methylthio ribulose-1-phosphate . The methionine salvage pathway leads to the synthesis of methionine from methylthioadenosine, the end product of the spermidine and spermine anabolism in many species..
Probab=22.59 E-value=33 Score=15.33 Aligned_cols=22 Identities=32% Similarity=0.578 Sum_probs=15.7
Q ss_pred HHCCCCHHHHHHCHHHHHHHHH
Q ss_conf 6315310012200035545442
Q gi|254780448|r 44 LVRGSSIATKIATTGIATVVQE 65 (311)
Q Consensus 44 lvrg~sia~k~~t~g~~~~~~e 65 (311)
.+|+|.++-||||-|.+++||.
T Consensus 211 Ia~~GdvaNKIGTY~lAvlAK~ 232 (306)
T TIGR00512 211 IARDGDVANKIGTYGLAVLAKA 232 (306)
T ss_pred EECCCCEEEHHHHHHHHHHHHC
T ss_conf 1068932400667899999820
No 27
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=21.59 E-value=59 Score=13.63 Aligned_cols=28 Identities=25% Similarity=0.277 Sum_probs=20.1
Q ss_pred HHHHCCCEEEECCCEECCCCHHHHHHHH
Q ss_conf 7630576799838132236889999999
Q gi|254780448|r 181 LDASRATEFIIDGKKINIDSAQNMLAEL 208 (311)
Q Consensus 181 LD~~ra~~FiiNGKKIs~Dsa~~mL~df 208 (311)
+..+---+|+|||+++.-..+.+.|.+.
T Consensus 125 ~gI~gTPt~~Ing~~~~G~~~~~~l~~~ 152 (154)
T cd03023 125 LGITGTPAFIIGDTVIPGAVPADTLKEA 152 (154)
T ss_pred CCCCCCCEEEECCEEECCCCCHHHHHHH
T ss_conf 5997899898999994388999999997
No 28
>pfam11190 DUF2976 Protein of unknown function (DUF2976). This family of proteins has no known function. Some members are annotated as membrane proteins however this cannot be confirmed.
Probab=21.58 E-value=48 Score=14.25 Aligned_cols=24 Identities=33% Similarity=0.711 Sum_probs=16.5
Q ss_pred CCCCHHHHCCCCCCCCHHHHHHHH
Q ss_conf 111077631677442046664002
Q gi|254780448|r 4 VYGTIQEFKKGNYGWGALGIVSDV 27 (311)
Q Consensus 4 ~ygt~~efkkgnygwg~~g~~sd~ 27 (311)
.++||.|...|.-+||-+|..--+
T Consensus 46 ai~ty~ei~~GK~~W~~fg~~viV 69 (87)
T pfam11190 46 ALGTYNEIRDGKKTWGDFGAIVIV 69 (87)
T ss_pred HHHHHHHHHCCHHHHHHCCHHHHH
T ss_conf 997899997261208863137876
No 29
>TIGR02739 TraF type-F conjugative transfer system pilin assembly protein TraF; InterPro: IPR014110 This entry includes TraF; a protein that is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically in the F-type system. TraF has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm . Unlike the related protein TrbB (IPR014109 from INTERPRO), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulphide isomerase by complementation of an Escherichia coli DsbA defect . The protein is believed to be involved in pilin assembly . Even more closely related than TrbB is a clade of genes (IPR014111 from INTERPRO), which do contain the CXXC motif, but it is unclear whether these are involved in type-F conjugation systems per se..
Probab=21.54 E-value=42 Score=14.60 Aligned_cols=38 Identities=24% Similarity=0.312 Sum_probs=26.6
Q ss_pred HHHHHHHCCHHHHHHHHHHHHHHCCCHHCCCCCC-CCEEEEE
Q ss_conf 5556654074665458999988372310021168-7237999
Q gi|254780448|r 219 VQLISSYAHEHIFCKPFTKDLLNLANKNIYQLSN-PRYSYQF 259 (311)
Q Consensus 219 ~QLISSYAhQ~If~qs~~~L~s~hPe~~kyq~sn-s~ysY~i 259 (311)
++.+.-=+ .-|...|-+.++.|||++ |++.+ |++.+.+
T Consensus 101 Q~~~~~~~--~~F~~~~~~~lL~~PeLD-y~l~~GP~~~~a~ 139 (270)
T TIGR02739 101 QQFWTKQA--SQFSMTWQKALLAHPELD-YTLTRGPTSNAAR 139 (270)
T ss_pred HHHHHHHH--HHHHHHHHHHHHCCCCCC-CCCCCCCCHHHHH
T ss_conf 99999988--888999999861588743-2034788527899
No 30
>TIGR03489 cas_csp1 CRISPR-associated protein, Csp1 family. Members of this protein family are Csp1, a CRISPR-associated (cas) gene marker for the Pging subtype of CRISPR/cas system, as found in Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037. This protein belongs to the family of DevR (TIGR01875), a regulator of development in Myxococcus xanthus located in a cas gene region. A different branch of the DevR family, Cst2 (TIGR02585), is a marker for the Tneap subtype of CRISPR/cas system.
Probab=21.16 E-value=42 Score=14.63 Aligned_cols=102 Identities=19% Similarity=0.228 Sum_probs=49.7
Q ss_pred HHHHHCCCHHHCCCCHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCEEEECCCEECCCCHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 77654088667434301180023234442667046788763057679983813223688999999997512697465556
Q gi|254780448|r 143 QAIFQKMPLEEYPRLQKIGINYFRDFKLLGTNKVYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIFPKDFEKVQLI 222 (311)
Q Consensus 143 ~ai~~k~p~~e~~~~~~~~~~~frdf~Llg~nk~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~vPkd~e~~QLI 222 (311)
.+.+|...-.||.--.+...|.|-|.--+|--|-.-.---.+-|+ .+|.- ++-+-++.-...| +|.....
T Consensus 125 d~~~qalat~E~SE~D~mnmnffldI~~vgIsK~f~ye~g~nlGT-~yfkh--~ndeErKrR~~l~-------lEatr~m 194 (292)
T TIGR03489 125 DAKDQALATKEFSEQDKMHMNFFLDISALGISKAFTYEDGFNLGT-KYFKH--ANDDEKKRRAKLF-------LEATKIM 194 (292)
T ss_pred HHHHHHHHCCCCCCCCEEEEEEEEEEEEEEEEECCCCCCCCCCCC-EEEEE--CCCHHHHHHHHHH-------HHHHHHH
T ss_conf 577776531455646535579878766653100103311223672-67761--4848888889999-------9999998
Q ss_pred HHHCCHHHHHHHHHHHHHHCCCHHC------CCCCCCCEEEEEEE
Q ss_conf 6540746654589999883723100------21168723799985
Q gi|254780448|r 223 SSYAHEHIFCKPFTKDLLNLANKNI------YQLSNPRYSYQFNT 261 (311)
Q Consensus 223 SSYAhQ~If~qs~~~L~s~hPe~~k------yq~sns~ysY~ine 261 (311)
+-||||--..+.. -|+++. |+-+-+|| |+++|
T Consensus 195 nDYanQARnav~g------ePe~VlIvFdd~lSrka~r~-yt~~e 232 (292)
T TIGR03489 195 NDYANQARNAVCG------EPEKVLIVFDDRLSRKACRF-YTADE 232 (292)
T ss_pred HHHHHHHHHHHCC------CCCEEEEEECCHHHHHHCEE-ECCCC
T ss_conf 8888886542238------98779999633331112010-20470
No 31
>pfam11477 PM0188 Sialyltransferase PMO188. PMO188 is a sialyltransferase from P.multocida. It transfers sialic acid from cytidine 5'-monophosphonuraminic acid to an acceptor sugar. It has important catalytic residues such as Asp141, His311, Glu338, Ser355 and Ser356.
Probab=21.08 E-value=61 Score=13.56 Aligned_cols=53 Identities=21% Similarity=0.324 Sum_probs=30.5
Q ss_pred HHCCCHHHCCCCHHCCCHHHHHHHHHCCCC-HHHHHHHHHCCCEEEECCCEECCCC
Q ss_conf 540886674343011800232344426670-4678876305767998381322368
Q gi|254780448|r 146 FQKMPLEEYPRLQKIGINYFRDFKLLGTNK-VYKNLLDASRATEFIIDGKKINIDS 200 (311)
Q Consensus 146 ~~k~p~~e~~~~~~~~~~~frdf~Llg~nk-~~q~~LD~~ra~~FiiNGKKIs~Ds 200 (311)
.|+|++..|+++-...+++|-++ +|=+. ..|.-.-++.-..|||-|--..--+
T Consensus 200 ~kqM~Wd~f~~fn~eQk~lfl~i--vgf~~E~~q~q~~~s~~~nFiFtGTttw~g~ 253 (381)
T pfam11477 200 YKQMDWTCYPRFNAEQKQLFLEI--VGFNNELENLQYLLSQHNNFIFTGTTTWNGD 253 (381)
T ss_pred HHCCCCHHHCCCCHHHHHHHHHH--HCCCHHHHHHHHHHCCCCCEEEECCCCCCCC
T ss_conf 32457223201699999999998--5789899999875264775499712345676
No 32
>KOG0102 consensus
Probab=21.08 E-value=61 Score=13.56 Aligned_cols=79 Identities=16% Similarity=0.149 Sum_probs=63.8
Q ss_pred HHHHCCCCHHHHHHHHHCCC----EEEECCCEECCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHCC
Q ss_conf 44426670467887630576----79983813223688999999997512697465556654074665458999988372
Q gi|254780448|r 168 FKLLGTNKVYKNLLDASRAT----EFIIDGKKINIDSAQNMLAELNKIFPKDFEKVQLISSYAHEHIFCKPFTKDLLNLA 243 (311)
Q Consensus 168 f~Llg~nk~~q~~LD~~ra~----~FiiNGKKIs~Dsa~~mL~dfkt~vPkd~e~~QLISSYAhQ~If~qs~~~L~s~hP 243 (311)
|...+.|+.+-.--|-.+++ |....|. +++|-...|..+-+.-+..|-+.+|+|-.----+.|+-.-++++.++|
T Consensus 496 fDIdanGI~~vsA~dk~t~K~qsi~i~~sgg-Ls~~ei~~mV~eaer~~~~d~~~~~~ie~~nka~s~~~~te~~~~~~~ 574 (640)
T KOG0102 496 FDIDANGIGTVSAKDKGTGKSQSITIASSGG-LSKDEIELMVGEAERLASTDKEKREAIETKNKADSIIYDTEKSLKEFE 574 (640)
T ss_pred EEECCCCEEEEEHHHCCCCCCCCEEEEECCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHEECCCHHHHHHHH
T ss_conf 8614775145311010348755469860588-788999999999998776567778876411210002127665523314
Q ss_pred CHHC
Q ss_conf 3100
Q gi|254780448|r 244 NKNI 247 (311)
Q Consensus 244 e~~k 247 (311)
+.+-
T Consensus 575 ~~~~ 578 (640)
T KOG0102 575 EKIP 578 (640)
T ss_pred HHCC
T ss_conf 4375
No 33
>KOG1355 consensus
Probab=20.63 E-value=34 Score=15.20 Aligned_cols=27 Identities=19% Similarity=0.386 Sum_probs=15.2
Q ss_pred EEECCCEEEECCCCCHHHHHHCCCCCC
Q ss_conf 871671254101223265431024520
Q gi|254780448|r 89 IMEGGSTAIKSESVGAKELISASQNSQ 115 (311)
Q Consensus 89 ~~eg~s~~ikses~g~k~~is~~~~~~ 115 (311)
..||...+.-.-..||-.-..|||.+-
T Consensus 249 LVEGanaamLDiDFGTYPfVTSSn~tv 275 (455)
T KOG1355 249 LVEGANAAMLDIDFGTYPFVTSSNCTV 275 (455)
T ss_pred EEECCCCEEEECCCCCCCCCCCCCCCC
T ss_conf 870464203302357665132678764
No 34
>PRK02944 OxaA-like protein precursor; Validated
Probab=20.54 E-value=52 Score=13.99 Aligned_cols=26 Identities=19% Similarity=0.309 Sum_probs=15.7
Q ss_pred HCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 31677442046664002477777877
Q gi|254780448|r 11 FKKGNYGWGALGIVSDVALLAIPAAY 36 (311)
Q Consensus 11 fkkgnygwg~~g~~sd~all~~~~~y 36 (311)
+--|||||+|+-..-=+-++..|...
T Consensus 54 ~~g~~yGlaIIl~TiiVRlillPL~~ 79 (255)
T PRK02944 54 LFGSNYGLAIIVVTLLIRLAILPLMI 79 (255)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 64971999999999999999998899
No 35
>pfam08283 Gemini_AL1_M Geminivirus rep protein central domain. This is the cetral domain of the geminivirus rep proteins.
Probab=20.24 E-value=60 Score=13.58 Aligned_cols=39 Identities=26% Similarity=0.382 Sum_probs=25.1
Q ss_pred EECCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHH
Q ss_conf 322368899999999751269746555665407466545
Q gi|254780448|r 195 KINIDSAQNMLAELNKIFPKDFEKVQLISSYAHEHIFCK 233 (311)
Q Consensus 195 KIs~Dsa~~mL~dfkt~vPkd~e~~QLISSYAhQ~If~q 233 (311)
-|+.-|..+.|+=+|+-+||||-.+---=-|.-..||..
T Consensus 12 alnagsk~eaL~iike~~Pkd~v~q~hnl~~nldriF~~ 50 (106)
T pfam08283 12 AINATSKEEALSIIKEEFPKDWALQLHNLEYNANRLFPD 50 (106)
T ss_pred HHCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCC
T ss_conf 964789999999999847248999976187779985899
No 36
>cd02178 GH16_beta_agarase Beta-agarase is a glycosyl hydrolase family 16 (GH16) member that hydrolyzes the internal beta-1,4-linkage of agarose, producing agaro-oligosaccharides. While beta-agarases are also found in two other families derived from the sequence-based classification of glycosyl hydrolases (GH50, and GH86) the GH16 members are most abundant. This domain adopts a curved beta-sandwich conformation, with a tunnel-shaped active site cavity, referred to as a jellyroll fold.
Probab=20.23 E-value=54 Score=13.92 Aligned_cols=19 Identities=26% Similarity=0.524 Sum_probs=17.1
Q ss_pred EEEECCCEECCCCHHHHHH
Q ss_conf 7998381322368899999
Q gi|254780448|r 188 EFIIDGKKINIDSAQNMLA 206 (311)
Q Consensus 188 ~FiiNGKKIs~Dsa~~mL~ 206 (311)
+|||||+++-.-+.+.|++
T Consensus 197 ~fYiDG~lv~tvs~~~~~d 215 (270)
T cd02178 197 DYYIDGVLVRTVSGPNIID 215 (270)
T ss_pred EEEECCEEEEEECHHHHCC
T ss_conf 9998999976616067247
No 37
>CHL00113 rps4 ribosomal protein S4; Reviewed
Probab=20.21 E-value=58 Score=13.69 Aligned_cols=18 Identities=17% Similarity=0.521 Sum_probs=14.1
Q ss_pred HCCCEEEECCCEECCCCHH
Q ss_conf 0576799838132236889
Q gi|254780448|r 184 SRATEFIIDGKKINIDSAQ 202 (311)
Q Consensus 184 ~ra~~FiiNGKKIs~Dsa~ 202 (311)
+|+. |.+|||+|++-|-.
T Consensus 112 ~HgH-i~VNgkkVnIPSy~ 129 (201)
T CHL00113 112 NHGH-ILVNGRIVDIPSYR 129 (201)
T ss_pred ECCE-EEECCEEECCCCEE
T ss_conf 4662-99899893378758
No 38
>PHA01635 hypothetical protein
Probab=20.08 E-value=57 Score=13.73 Aligned_cols=46 Identities=17% Similarity=0.296 Sum_probs=37.5
Q ss_pred HHHHHHHHHCCCEEEECCCEECCCCHHHHHHHHHHHCCCCHHHHHHHHHHCC
Q ss_conf 4678876305767998381322368899999999751269746555665407
Q gi|254780448|r 176 VYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIFPKDFEKVQLISSYAH 227 (311)
Q Consensus 176 ~~q~~LD~~ra~~FiiNGKKIs~Dsa~~mL~dfkt~vPkd~e~~QLISSYAh 227 (311)
...++.-++||-+..+||+++.+-+- -|-++|+ |+-+.-=+|+|-+
T Consensus 52 ~~~kyVsLlRGA~l~ingq~v~vP~Y-----iFG~AFa-dVYf~ng~S~yi~ 97 (231)
T PHA01635 52 SDRKYVSLLRGAELNINGQQVTVPDY-----IFGNAFA-DVYFANGASTYIN 97 (231)
T ss_pred CCHHEEEEECCEEEEECCCEEECCHH-----HHCHHHH-HHHHHCCHHHHCC
T ss_conf 73310142215089876948850656-----5220567-7765545776525
Done!