Query gi|254780225|ref|YP_003064638.1| peptidyl-tRNA hydrolase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 189
No_of_seqs 138 out of 2149
Neff 6.3
Searched_HMMs 39220
Date Mon May 23 20:54:59 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780225.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd02406 CRS2 Chloroplast RNA s 100.0 0 0 483.4 19.0 187 2-189 3-191 (191)
2 COG0193 Pth Peptidyl-tRNA hydr 100.0 0 0 483.2 18.1 187 1-188 2-190 (190)
3 PRK05426 peptidyl-tRNA hydrola 100.0 0 0 472.1 19.2 186 1-187 2-189 (189)
4 TIGR00447 pth peptidyl-tRNA hy 100.0 0 0 466.9 16.8 185 1-186 1-193 (193)
5 pfam01195 Pept_tRNA_hydro Pept 100.0 0 0 458.4 18.2 182 3-185 1-184 (184)
6 cd00462 PTH Peptidyl-tRNA hydr 100.0 0 0 432.6 16.6 170 3-173 1-171 (171)
7 KOG2255 consensus 100.0 0 0 334.8 11.6 171 2-173 40-213 (224)
8 TIGR00962 atpA ATP synthase F1 62.1 6.4 0.00016 20.3 2.4 25 68-96 248-272 (520)
9 COG0680 HyaD Ni,Fe-hydrogenase 60.3 10 0.00025 19.1 3.1 138 1-173 3-155 (160)
10 TIGR01846 type_I_sec_HlyB type 57.7 8.8 0.00022 19.4 2.5 31 68-100 502-533 (703)
11 cd02166 NMNAT_Archaea This fam 54.4 16 0.0004 17.9 3.3 10 3-12 29-38 (163)
12 PRK01153 nicotinamide-nucleoti 53.8 15 0.00037 18.1 3.1 10 3-12 30-39 (170)
13 cd06062 H2MP_MemB-H2up Endopep 53.0 16 0.00042 17.8 3.2 129 2-167 1-144 (146)
14 pfam06154 YagB_YeeU_YfjZ YagB/ 47.2 25 0.00063 16.8 3.9 32 146-177 35-66 (104)
15 TIGR02362 dhaK1b probable dihy 45.5 15 0.00039 18.0 2.1 33 73-107 115-148 (328)
16 cd06070 H2MP_like-2 Putative [ 45.1 27 0.00068 16.6 8.1 124 3-172 1-139 (140)
17 TIGR02915 PEP_resp_reg putativ 42.9 9.2 0.00024 19.3 0.7 65 109-173 282-356 (451)
18 cd06879 PX_UP1_plant The phosp 41.6 6.8 0.00017 20.1 -0.2 19 120-138 40-58 (138)
19 pfam07352 Phage_Mu_Gam Bacteri 40.8 11 0.00028 18.9 0.8 41 93-133 71-115 (147)
20 KOG3731 consensus 38.7 31 0.0008 16.1 2.8 48 59-106 9-57 (541)
21 PRK10466 hybD hydrogenase 2 ma 38.6 33 0.00085 16.0 3.6 134 2-172 3-152 (164)
22 cd06066 H2MP_NAD-link-bidir En 36.8 32 0.0008 16.1 2.6 26 3-32 1-26 (139)
23 KOG2882 consensus 35.5 16 0.00041 17.8 1.0 36 54-96 218-253 (306)
24 cd00518 H2MP Hydrogenase speci 34.9 32 0.00081 16.1 2.4 88 3-122 1-98 (139)
25 PRK09256 hypothetical protein; 34.7 19 0.00048 17.5 1.2 27 88-114 2-30 (138)
26 TIGR01452 PGP_euk phosphoglyco 32.9 41 0.0011 15.4 3.1 43 51-100 202-246 (288)
27 PRK02858 germination protease; 30.9 24 0.00062 16.8 1.2 79 2-96 111-194 (367)
28 cd06067 H2MP_MemB-H2evol Endop 30.9 43 0.0011 15.3 2.5 90 3-123 1-98 (136)
29 TIGR02471 sucr_syn_bact_C sucr 29.9 36 0.00092 15.8 2.0 25 67-92 163-187 (241)
30 cd00887 MoeA MoeA family. Memb 28.7 38 0.00098 15.6 2.0 73 65-138 193-277 (394)
31 cd00736 bacteriophage_lambda_l 27.1 52 0.0013 14.8 4.0 42 145-186 81-122 (151)
32 PRK03573 transcriptional regul 26.4 54 0.0014 14.7 3.8 36 141-176 109-144 (144)
33 cd06064 H2MP_F420-Reduc Endope 26.0 55 0.0014 14.7 2.7 130 3-167 1-148 (150)
34 PRK12362 germination protease; 25.6 24 0.00062 16.8 0.5 157 2-181 99-310 (324)
35 PRK10264 hydrogenase 1 maturat 24.9 57 0.0015 14.5 3.7 136 2-173 6-157 (195)
36 cd06068 H2MP_like-1 Putative [ 23.5 30 0.00077 16.2 0.6 25 3-31 1-25 (144)
37 TIGR00072 hydrog_prot hydrogen 23.2 42 0.0011 15.4 1.3 143 2-172 4-163 (170)
38 pfam00472 RF-1 RF-1 domain. Th 22.6 36 0.00091 15.8 0.8 23 92-114 6-30 (114)
39 COG1663 LpxK Tetraacyldisaccha 22.1 29 0.00073 16.4 0.3 37 125-161 230-282 (336)
40 TIGR00417 speE spermidine synt 22.1 52 0.0013 14.8 1.6 22 82-118 74-102 (284)
41 COG2607 Predicted ATPase (AAA+ 21.8 53 0.0013 14.8 1.6 29 76-105 131-159 (287)
42 cd02168 NMNAT_Nudix This domai 21.5 67 0.0017 14.1 2.4 21 60-80 71-93 (179)
43 cd06063 H2MP_Cyano-H2up This g 21.5 39 0.001 15.5 0.9 126 2-165 1-143 (146)
44 COG1186 PrfB Protein chain rel 21.3 55 0.0014 14.7 1.6 34 90-131 101-138 (239)
45 pfam03418 Peptidase_A25 Germin 21.0 50 0.0013 14.9 1.3 78 2-96 99-182 (355)
No 1
>cd02406 CRS2 Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of group II introns in the chloroplast. CRS2 forms stable complexes with two CRS2-associated factors, CAF1 and CAF2, which are required for the splicing of distinct subsets of CRS2-dependent introns. CRS2 is closely related to bacterial peptidyl-tRNA hydrolases (PTH).
Probab=100.00 E-value=0 Score=483.38 Aligned_cols=187 Identities=36% Similarity=0.597 Sum_probs=182.1
Q ss_pred EEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCC
Q ss_conf 89998587873660674104899999999982798544432127885147974899982334020033799999940575
Q gi|254780225|r 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKL 81 (189)
Q Consensus 2 ~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i 81 (189)
||||||||||++|++||||||||++|.||+.+++++..+++++.++...+.+.+|+|+||+||||+||.||+++++||+|
T Consensus 3 ~LIvGLGNPG~~Y~~TRHNiGf~vld~la~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~TyMN~SG~~V~~~~~~~ki 82 (191)
T cd02406 3 WLIAGLGNPGNKYKGTRHNVGFEMVDRIAEAEGITMNTIQFKSLLGIGSIGDVPVLLAKPQTYMNYSGESVGPLAAYYKV 82 (191)
T ss_pred EEEEEECCCCCHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECCEEEEEEECCCHHHCCCHHHHHHHHHCCC
T ss_conf 79998089980005495089999999999961989674443757899998998999983870465438879999985689
Q ss_pred CCCCCEEEEEECCCCCCCCEEEECCCCCCCCCHHHHHHHCC-CC-CEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf 66333489840443233823661115888731033333106-87-31366750689877670242437898889999999
Q gi|254780225|r 82 PNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEKC-GK-NYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLL 159 (189)
Q Consensus 82 ~~~~~ilVihDdldL~~G~irlk~~Gg~gGHNGlksI~~~l-g~-~f~RlRIGIG~P~~~~~v~~yVL~~f~~~E~~~i~ 159 (189)
+ +++|+|||||+|||+|++|+|.+||+|||||||||+++| |+ +|+|||||||||+.+.++++|||++|+++|++.++
T Consensus 83 ~-~~~ilVihDDldlp~G~irik~~Gs~gGHNGlkSIi~~L~gt~~f~RlRiGIG~p~~~~~~~~yVL~~F~~~E~~~l~ 161 (191)
T cd02406 83 P-LRHILVIYDDMSLPNGVLRLQPKGGHGRHNGLQSVIEHLDGSREFPRLSIGIGSPPGKMDPRAFLLQKFSSEEREQID 161 (191)
T ss_pred C-HHHEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCHHHHHHHH
T ss_conf 8-789899960367877871012599899989899999981799982789986189988887545426999999999999
Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHCCCC
Q ss_conf 999999999999980998999998633589
Q gi|254780225|r 160 PIIDNIARSLPLLAKREDVSFLNHIVSVRK 189 (189)
Q Consensus 160 ~~i~~~~~~i~~~~~~~~~~~mn~~n~~~k 189 (189)
++++.++++++.++.++++.|||++|+.+|
T Consensus 162 ~~i~~a~~ai~~~~~~g~~~amn~~N~~~k 191 (191)
T cd02406 162 TALEQGVDAVRTLVLKGFNGSAERFNLVQK 191 (191)
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHCCCCC
T ss_conf 999999999999998599999998626589
No 2
>COG0193 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=483.19 Aligned_cols=187 Identities=44% Similarity=0.763 Sum_probs=181.8
Q ss_pred CEEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCC-CCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCC
Q ss_conf 9899985878736606741048999999999827985-444321278851479748999823340200337999999405
Q gi|254780225|r 1 MFIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPA-WKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFY 79 (189)
Q Consensus 1 m~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~-~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~ 79 (189)
|+|||||||||++|+.||||||||++|.||++++.++ +++||.++++++.+++++|+|+||+||||+||++|.++++||
T Consensus 2 ~kLIVGLGNPG~~Y~~TRHNvGf~~vD~La~~~~~~~~~~~kf~~~~~~~~i~g~kv~L~kP~TyMNlSG~~V~~~~~fy 81 (190)
T COG0193 2 MKLIVGLGNPGKKYAKTRHNVGFMVVDLLARRLNLSFKEEKKFNGLVAKGTIEGEKVILLKPTTYMNLSGKAVGALASFY 81 (190)
T ss_pred CEEEEECCCCCHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECCCEEEEECCCCCEECCHHHHHHHHHHH
T ss_conf 37999789996242436413789999999998389975555667546899868947999607622007578999999985
Q ss_pred CCCCCCCEEEEEECCCCCCCCEEEECCCCCCCCCHHHHHHHCCC-CCEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf 75663334898404432338236611158887310333331068-73136675068987767024243789888999999
Q gi|254780225|r 80 KLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEKCG-KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFL 158 (189)
Q Consensus 80 ~i~~~~~ilVihDdldL~~G~irlk~~Gg~gGHNGlksI~~~lg-~~f~RlRIGIG~P~~~~~v~~yVL~~f~~~E~~~i 158 (189)
+|+ +++|+|||||||||+|++|+|.+||+|||||||||+++|| ++|+|||||||||+.+++|++|||++|+++|++++
T Consensus 82 ~i~-~~~ilVvhDdLdl~~G~vrlk~~Gg~gGHNGlKSi~~~lGt~~f~RlRiGIGrP~~~~~v~~~VL~~f~~~E~~~l 160 (190)
T COG0193 82 KIK-PEDILVVHDELDLPLGKVRLKLGGGAGGHNGLKSIIAHLGTNNFYRLRIGIGRPGNGEDVADYVLGKFSKEERELL 160 (190)
T ss_pred CCC-HHHEEEEEECCCCCCCEEEEECCCCCCCCCCHHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHCCCCCHHHHHHH
T ss_conf 899-8898999605678887389974889888455999999849886206998758899888366763589998999999
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHCCC
Q ss_conf 999999999999998099899999863358
Q gi|254780225|r 159 LPIIDNIARSLPLLAKREDVSFLNHIVSVR 188 (189)
Q Consensus 159 ~~~i~~~~~~i~~~~~~~~~~~mn~~n~~~ 188 (189)
+++++.++++++.++.++++.+||++|+.+
T Consensus 161 ~~~~~~a~~~~~~~~~~~~~~~mn~~~~~~ 190 (190)
T COG0193 161 DKAIDKAADALELLLEGDFEKAMNKLNALK 190 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 999999999999999876999999985359
No 3
>PRK05426 peptidyl-tRNA hydrolase; Provisional
Probab=100.00 E-value=0 Score=472.12 Aligned_cols=186 Identities=48% Similarity=0.789 Sum_probs=179.5
Q ss_pred CEEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCC-CCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCC
Q ss_conf 9899985878736606741048999999999827985-444321278851479748999823340200337999999405
Q gi|254780225|r 1 MFIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPA-WKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFY 79 (189)
Q Consensus 1 m~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~-~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~ 79 (189)
|+|||||||||++|++||||||||++|.||+.++.++ ++++++++++++.+.+.+++|+||+||||+||.||+++++||
T Consensus 2 m~LivGLGNPG~~Y~~TRHNvG~~~ld~la~~~~~~~~~~~k~~~~~~~~~~~~~~v~L~kP~tyMN~SG~~V~~~~~~~ 81 (189)
T PRK05426 2 MKLIVGLGNPGPEYANTRHNIGFMVVDELAERLGVSFKKKKKFKGLIAEGRIGGEKVILLKPQTYMNLSGKAVAALASFY 81 (189)
T ss_pred EEEEEEECCCCHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEECCEEEEEEECCCHHHCCHHHHHHHHHHC
T ss_conf 08999808980443749627899999999998099855466552799999989978999968605642078999999984
Q ss_pred CCCCCCCEEEEEECCCCCCCCEEEECCCCCCCCCHHHHHHHCCCC-CEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf 756633348984044323382366111588873103333310687-3136675068987767024243789888999999
Q gi|254780225|r 80 KLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEKCGK-NYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFL 158 (189)
Q Consensus 80 ~i~~~~~ilVihDdldL~~G~irlk~~Gg~gGHNGlksI~~~lg~-~f~RlRIGIG~P~~~~~v~~yVL~~f~~~E~~~i 158 (189)
+|+ +++|+|||||+|||+|++|+|.+||+|||||||||+++||+ +|+|||||||||+.+.++++|||++|+++|++.+
T Consensus 82 ki~-~~~ilVihDDldl~~G~irlk~~Gs~gGHNGlkSI~~~lgt~~f~RlriGIGrP~~~~~~~~yVL~~f~~~E~~~l 160 (189)
T PRK05426 82 KIP-PEDILVIHDDLDLPPGKIRLKKGGGAGGHNGLKSIIAHLGTQDFWRLRIGIGRPGDKEKVVGYVLGKFSKEEQELL 160 (189)
T ss_pred CCC-HHHEEEEEEECCCCCCEEEEECCCCCCCCCCHHHHHHHHCCCCEEEEEEEECCCCCCCCHHHHCCCCCCHHHHHHH
T ss_conf 999-8997999730457578688816998888788899999969875556988708998768553432799899999999
Q ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHCC
Q ss_conf 99999999999999809989999986335
Q gi|254780225|r 159 LPIIDNIARSLPLLAKREDVSFLNHIVSV 187 (189)
Q Consensus 159 ~~~i~~~~~~i~~~~~~~~~~~mn~~n~~ 187 (189)
+++++.++++++.++.++++.|||++|+.
T Consensus 161 ~~~~~~~~~~i~~~i~~~~~~amn~~n~~ 189 (189)
T PRK05426 161 DKAIDKAADAIELLLEGDFEKAMNKLNSK 189 (189)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHCCC
T ss_conf 99999999999999977999999986298
No 4
>TIGR00447 pth peptidyl-tRNA hydrolase; InterPro: IPR001328 Peptidyl-tRNA hydrolase (3.1.1.29 from EC) (PTH) is a bacterial enzyme that cleaves peptidyl-tRNA or N-acyl-aminoacyl-tRNA to yield free peptides or N-acyl-amino acids and tRNA. The natural substrate for this enzyme may be peptidyl-tRNA which drop off the ribosome during protein synthesis , . Bacterial PTH has been found to be evolutionary related to a yeast protein .; GO: 0004045 aminoacyl-tRNA hydrolase activity, 0006412 translation.
Probab=100.00 E-value=0 Score=466.91 Aligned_cols=185 Identities=43% Similarity=0.736 Sum_probs=176.4
Q ss_pred CEEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCC-CC--CCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHH
Q ss_conf 98999858787366067410489999999998279854-44--3212788514797489998233402003379999994
Q gi|254780225|r 1 MFIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAW-KK--KFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMN 77 (189)
Q Consensus 1 m~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~-~~--k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~ 77 (189)
|.|||||||||++|+.||||||||+||.||+.+.+++. ++ ++.+.....-+.+++++|+||+||||+||++|.++++
T Consensus 1 ~~LivGLGNPg~~Y~~TRHN~Gf~~lD~L~~~~~~~l~~~~Pv~f~G~~~~~l~~~~~v~L~kP~TYMNlSG~~V~~~~~ 80 (193)
T TIGR00447 1 MKLIVGLGNPGKKYAETRHNAGFMVLDRLASRLGLSLRTEKPVKFLGKTERGLISGKKVILLKPLTYMNLSGEAVKALAD 80 (193)
T ss_pred CEEEEEECCCCHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCEEEEECCCCCCCCHHHHHHHHHH
T ss_conf 90688505885201046340368899999998388745368866788602376514258974697410011789999998
Q ss_pred CCCCCCCCCEEEEEECCCCCCCCEEEECCCCCC-CCCHHHHHHHCC-CC-CEEEEEECCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf 057566333489840443233823661115888-731033333106-87-313667506898776702424378988899
Q gi|254780225|r 78 FYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDA-GHNGLKSISEKC-GK-NYKRLRIGIGRPPDTAHIIRHVLGNFSSPE 154 (189)
Q Consensus 78 ~~~i~~~~~ilVihDdldL~~G~irlk~~Gg~g-GHNGlksI~~~l-g~-~f~RlRIGIG~P~~~~~v~~yVL~~f~~~E 154 (189)
+|+++ +++++|||||||||+|++|||.+||++ ||||||||+++| |+ +|.|||||||+|..+..+.+||||+|+++|
T Consensus 81 ~y~~~-~~~~lVvhDeLdLPlG~~rLk~~G~~grgHNGlKS~~~~LGg~~~F~RLRiGIg~~~~~~~~~~~VLs~F~~~E 159 (193)
T TIGR00447 81 FYKIK-PAELLVVHDELDLPLGKVRLKQGGGAGRGHNGLKSIISHLGGTSNFNRLRIGIGSPNGSNKVIEFVLSKFSKSE 159 (193)
T ss_pred HHCCC-CCCEEEEEECCCCCCCEEEEECCCCCCCCCCHHHHHHHHCCCCCCCCEEEEEECCCCCCCEEEEEECCCCCHHH
T ss_conf 62678-34257888525689674776168889987433788998747889865357873568875113234438877114
Q ss_pred HHHHHHHHHHHHHHHHHHHCCC--HHHHHHHHHC
Q ss_conf 9999999999999999998099--8999998633
Q gi|254780225|r 155 RYFLLPIIDNIARSLPLLAKRE--DVSFLNHIVS 186 (189)
Q Consensus 155 ~~~i~~~i~~~~~~i~~~~~~~--~~~~mn~~n~ 186 (189)
++.+|++++.+.++++.++..+ +.++||+||+
T Consensus 160 ~~~~E~a~d~a~~~~~~~~~eg~~~~~~~~~~~~ 193 (193)
T TIGR00447 160 LPLLEKALDKATEALKMSFSEGADFLKAMNRFNS 193 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCC
T ss_conf 5689999889999999871186899999998519
No 5
>pfam01195 Pept_tRNA_hydro Peptidyl-tRNA hydrolase.
Probab=100.00 E-value=0 Score=458.37 Aligned_cols=182 Identities=47% Similarity=0.791 Sum_probs=175.6
Q ss_pred EEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCC-CCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCC
Q ss_conf 999858787366067410489999999998279854-4432127885147974899982334020033799999940575
Q gi|254780225|r 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAW-KKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKL 81 (189)
Q Consensus 3 livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~-~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i 81 (189)
|||||||||++|++||||||||++|.||+.+++++. ++++.+.++...+++.+++|+||+||||+||+||++++++|+|
T Consensus 1 LIvGLGNPG~~Y~~TRHNiG~~~ld~la~~~~~~~~~~k~~~~~~~~~~~~~~~v~l~kp~tfMN~SG~~v~~~~~~~~i 80 (184)
T pfam01195 1 LIVGLGNPGPKYENTRHNVGFMVIDRLAERLGVSLKKKKKFKGLIAKGRINGEKVLLLKPQTYMNLSGEAVRAIARFYKI 80 (184)
T ss_pred CEEEECCCCHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEECCEEEEEEECCCHHHCCHHHHHHHHHHHCC
T ss_conf 98981888144375963789999999999809996646664479999986995899995870564328999999999099
Q ss_pred CCCCCEEEEEECCCCCCCCEEEECCCCCCCCCHHHHHHHCCC-CCEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 663334898404432338236611158887310333331068-7313667506898776702424378988899999999
Q gi|254780225|r 82 PNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEKCG-KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLP 160 (189)
Q Consensus 82 ~~~~~ilVihDdldL~~G~irlk~~Gg~gGHNGlksI~~~lg-~~f~RlRIGIG~P~~~~~v~~yVL~~f~~~E~~~i~~ 160 (189)
+ +++++|||||+|||+|++|+|.+||+|||||||||+++|| ++|+|||||||||+.+.++++|||++|+++|++.+++
T Consensus 81 ~-~~~ilVihDDldl~~G~irlk~~G~~gGHNGlkSIi~~lgt~~f~RlrIGIGrP~~~~~v~~yVL~~f~~~E~~~l~~ 159 (184)
T pfam01195 81 P-PEDILVVHDDLDLPLGKLRLKKGGGAGGHNGLKSIISHLGTNDFKRLRIGIGRPPDKNDVADYVLSKFSPEELELLDK 159 (184)
T ss_pred C-HHHEEEEEECCCCCCCCEEECCCCCCCCCCCHHHHHHHHCCCCEEEEEEECCCCCCCCCHHHHCCCCCCHHHHHHHHH
T ss_conf 9-899799862465625785256799898978888999983977634799862889887866354289999999999999
Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9999999999998099899999863
Q gi|254780225|r 161 IIDNIARSLPLLAKREDVSFLNHIV 185 (189)
Q Consensus 161 ~i~~~~~~i~~~~~~~~~~~mn~~n 185 (189)
+++.++++++.+++++++.|||++|
T Consensus 160 ~i~~~~~~i~~~i~~~~~~amn~~n 184 (184)
T pfam01195 160 AIEKAADALEDLIEGGFDKAMNRFN 184 (184)
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHC
T ss_conf 9999999999999779999998659
No 6
>cd00462 PTH Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through abortion of translation and is essential for cell viability.This group also contains chloroplast RNA splicing 2 (CRS2), which is closely related nuclear-encoded protein required for the splicing of nine group II introns in chloroplasts.
Probab=100.00 E-value=0 Score=432.59 Aligned_cols=170 Identities=48% Similarity=0.821 Sum_probs=163.9
Q ss_pred EEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCCC
Q ss_conf 99985878736606741048999999999827985444321278851479748999823340200337999999405756
Q gi|254780225|r 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKLP 82 (189)
Q Consensus 3 livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i~ 82 (189)
|||||||||++|++||||||||++|.|++.+++++.++++++.++++.+.+.+++|+||+||||+||.+|++++++|+++
T Consensus 1 LivGLGNPG~~Y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kp~tyMN~SG~~v~~~~~~~~i~ 80 (171)
T cd00462 1 LIVGLGNPGPKYENTRHNVGFMVLDALAERYGVSFKKKKKKGLVGEGRIGGEKVLLLKPQTYMNLSGEAVAALANFYKIP 80 (171)
T ss_pred CEEEECCCCHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEECCEEEEEEECCHHHHCCHHHHHHHHHHCCCC
T ss_conf 98992888244374952689999999999829897766774799999989989999819606652079999999974699
Q ss_pred CCCCEEEEEECCCCCCCCEEEECCCCCCCCCHHHHHHHCCCC-CEEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 633348984044323382366111588873103333310687-3136675068987767024243789888999999999
Q gi|254780225|r 83 NLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEKCGK-NYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPI 161 (189)
Q Consensus 83 ~~~~ilVihDdldL~~G~irlk~~Gg~gGHNGlksI~~~lg~-~f~RlRIGIG~P~~~~~v~~yVL~~f~~~E~~~i~~~ 161 (189)
+++++|||||+|||+|++|+|.+||+|||||||||+++||+ +|+|||||||||+.+.++++|||++|+++|++.|+++
T Consensus 81 -~~~llVihDdldl~~G~irik~~G~~gGHNGlkSIi~~lg~~~f~RlrIGIG~p~~~~~v~~yVL~~f~~~E~~~l~~~ 159 (171)
T cd00462 81 -PEDILVIHDDLDLPLGKIRLKKGGGSGGHNGLKSIIAHLGTEDFPRLRIGIGRPPNKMDVADYVLSKFSKEERELLEEA 159 (171)
T ss_pred -HHHEEEEEEECCCCCCEEEEECCCCCCCCCCHHHHHHHHCCCCEEEEEEEECCCCCCCCHHHHCCCCCCHHHHHHHHHH
T ss_conf -8898998730557788088707999998899899999859873688998858998888662113899899999999999
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999999999998
Q gi|254780225|r 162 IDNIARSLPLLA 173 (189)
Q Consensus 162 i~~~~~~i~~~~ 173 (189)
++.++++++.++
T Consensus 160 ~~~~~~~~~~~i 171 (171)
T cd00462 160 IEKAADALEDIL 171 (171)
T ss_pred HHHHHHHHHHHC
T ss_conf 999999999869
No 7
>KOG2255 consensus
Probab=100.00 E-value=0 Score=334.81 Aligned_cols=171 Identities=36% Similarity=0.671 Sum_probs=154.9
Q ss_pred EEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCC
Q ss_conf 89998587873660674104899999999982798544432127885147974899982334020033799999940575
Q gi|254780225|r 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKL 81 (189)
Q Consensus 2 ~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i 81 (189)
|+|+||||||++|..|||||||.++|.||.+.+++......++..+-+.+++..+++++|++|||.||++|.+++..|+|
T Consensus 40 wli~GLGNPg~~y~gTRHnvG~~Ml~~larrlgv~~nt~s~~a~~~l~~v~d~~~~llrp~qymN~SgesV~kva~~y~i 119 (224)
T KOG2255 40 WLIVGLGNPGSKYVGTRHNVGFEMLDMLARRLGVPMNTISSKALEGLGLVGDVPILLLRPQQYMNFSGESVGKVAALYKI 119 (224)
T ss_pred EEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCEEEEEECCHHHHCCCCCHHHHHHHHHCC
T ss_conf 38995689865456630156899999999873776566574113652350323367607076625464103556875343
Q ss_pred CCCCCEEEEEECCCCCCCCEEEECCCCCCCCCHHHHHHHCCC-C-CEEEEEECCCCCCCCCCCCCCCCCCCCHHHHH-HH
Q ss_conf 663334898404432338236611158887310333331068-7-31366750689877670242437898889999-99
Q gi|254780225|r 82 PNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISEKCG-K-NYKRLRIGIGRPPDTAHIIRHVLGNFSSPERY-FL 158 (189)
Q Consensus 82 ~~~~~ilVihDdldL~~G~irlk~~Gg~gGHNGlksI~~~lg-~-~f~RlRIGIG~P~~~~~v~~yVL~~f~~~E~~-~i 158 (189)
+ ..+++||||||++|+|++|+|++||++||||+||++++++ . .|+||+||||||+..+++.+|||++|++.|++ .|
T Consensus 120 ~-~~~ivvIhDEl~l~~Gkl~Lrp~gs~rgHNGvrs~~~~l~g~~~fpRL~iGIGrppg~~d~~a~vLskfsp~e~ke~L 198 (224)
T KOG2255 120 P-LRHIVVIHDELELPLGKLRLRPGGSHRGHNGVRSVFNCLNGRRSFPRLSIGIGRPPGNEDVKAFVLSKFSPAEQKELL 198 (224)
T ss_pred H-HEEEEEEECCCCCCCCEEEECCCCCCCCCCCHHHHHHHCCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCHHHHHHHH
T ss_conf 0-105899951125757648854478745553589998643688666115542389998204668988724824557888
Q ss_pred HHHHHHHHHHHHHHH
Q ss_conf 999999999999998
Q gi|254780225|r 159 LPIIDNIARSLPLLA 173 (189)
Q Consensus 159 ~~~i~~~~~~i~~~~ 173 (189)
++.++.+...+..-+
T Consensus 199 et~l~~~~~lil~~l 213 (224)
T KOG2255 199 ETLLEHVKTLILQGL 213 (224)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 878766179999999
No 8
>TIGR00962 atpA ATP synthase F1, alpha subunit; InterPro: IPR005294 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , . F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents the alpha subunit found in the F1 complex of F-ATPases. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha-subunit contains a highly conserved adenine-specific non-catalytic nucleotide-binding domain, with a conserved amino acid sequence of Gly-X-X-X-X-Gly-Lys. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself is driven by the movement of protons through the F0 complex C subunit . More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0016820 hydrolase activity acting on acid anhydrides catalyzing transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0016469 proton-transporting two-sector ATPase complex.
Probab=62.07 E-value=6.4 Score=20.26 Aligned_cols=25 Identities=28% Similarity=0.363 Sum_probs=17.8
Q ss_pred CCHHHHHHHHCCCCCCCCCEEEEEECCCC
Q ss_conf 33799999940575663334898404432
Q gi|254780225|r 68 SGQSLLEVMNFYKLPNLENYLVIHDDLDL 96 (189)
Q Consensus 68 SG~sv~~~~~~~~i~~~~~ilVihDdldL 96 (189)
||-++..++.+.. .+.|||||||.=
T Consensus 248 ~G~tmaEyF~d~G----khaLIiYDDLSK 272 (520)
T TIGR00962 248 TGCTMAEYFRDNG----KHALIIYDDLSK 272 (520)
T ss_pred HHHHHHHHHHHCC----CEEEEEEECCHH
T ss_conf 8999999998659----737999747407
No 9
>COG0680 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]
Probab=60.27 E-value=10 Score=19.12 Aligned_cols=138 Identities=16% Similarity=0.177 Sum_probs=77.4
Q ss_pred CEEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEEC-CCHHHHCCHHHHHHHHCC
Q ss_conf 9899985878736606741048999999999827985444321278851479748999823-340200337999999405
Q gi|254780225|r 1 MFIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKP-QTFMNLSGQSLLEVMNFY 79 (189)
Q Consensus 1 m~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP-~tyMN~SG~sv~~~~~~~ 79 (189)
|++|+|+|||= ..=--+|-++...|.+.+.... +|.++.- +--+++. ..+
T Consensus 3 ~ilIlG~GN~L----~~DDG~Gv~vae~L~~~~~~~~-----------------~v~vid~Gt~~~~l~--------~~l 53 (160)
T COG0680 3 RILILGVGNIL----MGDDGFGVRVAEKLKKRYKPPE-----------------NVEVIDGGTAGPNLL--------GLL 53 (160)
T ss_pred EEEEEEECCCC----CCCCCCCHHHHHHHHHHCCCCC-----------------CEEEEECCCCCHHHH--------HHH
T ss_conf 58999608844----1667403999999998457777-----------------738997687708899--------985
Q ss_pred CCCCCCCEEEEEECCC--CCCCCEEEEC------CCCCC---CCCH-HHHHHHCCCC--CEEEEEECCCCCCCCCCCCCC
Q ss_conf 7566333489840443--2338236611------15888---7310-3333310687--313667506898776702424
Q gi|254780225|r 80 KLPNLENYLVIHDDLD--LDFGTLRLKT------GGGDA---GHNG-LKSISEKCGK--NYKRLRIGIGRPPDTAHIIRH 145 (189)
Q Consensus 80 ~i~~~~~ilVihDdld--L~~G~irlk~------~Gg~g---GHNG-lksI~~~lg~--~f~RlRIGIG~P~~~~~v~~y 145 (189)
.+.+. ++|-|=.+ ..+|++++=. ...+. .|+. +...+..+-. ++...=+|+.-+....+..
T Consensus 54 --~~~d~-vIIVDav~~g~epG~v~~i~~e~i~~~~~~~~~s~H~~~~~~~L~~~~~~~~~~~~~~~~~v~~~~~~~~-- 128 (160)
T COG0680 54 --AGYDP-VIIVDAVLFGLEPGEVRIIDPEEIPAYSSASKDSAHELPLSELLALLKELGGLPVLILGVQVPIVSLPEF-- 128 (160)
T ss_pred --CCCCC-EEEEEEEECCCCCCEEEEECHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEEEECEECCCCC--
T ss_conf --27880-8999833248998669992656623222347786566789999999998638850699996020023100--
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3789888999999999999999999998
Q gi|254780225|r 146 VLGNFSSPERYFLLPIIDNIARSLPLLA 173 (189)
Q Consensus 146 VL~~f~~~E~~~i~~~i~~~~~~i~~~~ 173 (189)
...+|++=+..++.+++.+.+.+..+.
T Consensus 129 -~~~lS~ev~~a~~~av~~i~~~l~~~~ 155 (160)
T COG0680 129 -GGGLSPEVEEAVDKAVERILEELREWG 155 (160)
T ss_pred -CCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf -345799999999999999999998534
No 10
>TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132 Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane.
Probab=57.65 E-value=8.8 Score=19.45 Aligned_cols=31 Identities=32% Similarity=0.478 Sum_probs=24.6
Q ss_pred CCHH-HHHHHHCCCCCCCCCEEEEEECCCCCCCC
Q ss_conf 3379-99999405756633348984044323382
Q gi|254780225|r 68 SGQS-LLEVMNFYKLPNLENYLVIHDDLDLDFGT 100 (189)
Q Consensus 68 SG~s-v~~~~~~~~i~~~~~ilVihDdldL~~G~ 100 (189)
||+| +.++++-..+|+.-++|| |+.||..-.
T Consensus 502 SGKSTLTKL~QRLYtP~~GqVLV--DG~DLA~~D 533 (703)
T TIGR01846 502 SGKSTLTKLLQRLYTPEHGQVLV--DGVDLAIAD 533 (703)
T ss_pred CCHHHHHHHHHHHCCCCCCEEEE--CCCCCCCCC
T ss_conf 86789999988614888874777--030001018
No 11
>cd02166 NMNAT_Archaea This family of archaeal proteins exhibits nicotinamide-nucleotide adenylyltransferase (NMNAT) activity utilizing the salvage pathway to synthesize NAD. In some cases, the enzyme was tested and found also to have the activity of nicotinate-nucleotide adenylyltransferase an enzyme of NAD de novo biosynthesis, although with a higher Km. In some archaeal species, a number of proteins which are uncharacterized with respect to activity, are also present.
Probab=54.37 E-value=16 Score=17.95 Aligned_cols=10 Identities=20% Similarity=0.723 Sum_probs=5.7
Q ss_pred EEEECCCCCH
Q ss_conf 9998587873
Q gi|254780225|r 3 IVAGLGNPGH 12 (189)
Q Consensus 3 livGLGNPG~ 12 (189)
+|||+|++..
T Consensus 29 ~ii~igs~~~ 38 (163)
T cd02166 29 LIIGIGSAQE 38 (163)
T ss_pred EEEEECCCCC
T ss_conf 7999777866
No 12
>PRK01153 nicotinamide-nucleotide adenylyltransferase; Provisional
Probab=53.84 E-value=15 Score=18.14 Aligned_cols=10 Identities=20% Similarity=0.723 Sum_probs=6.0
Q ss_pred EEEECCCCCH
Q ss_conf 9998587873
Q gi|254780225|r 3 IVAGLGNPGH 12 (189)
Q Consensus 3 livGLGNPG~ 12 (189)
+|||+|.+..
T Consensus 30 vii~Igsa~~ 39 (170)
T PRK01153 30 LIIGIGSAQE 39 (170)
T ss_pred EEEEECCCCC
T ss_conf 5999556655
No 13
>cd06062 H2MP_MemB-H2up Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel metallocenter. Hydrogenase maturation endopeptidase (HybD) cleaves a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2 (hyb operon) in E. coli. This cleavage is nickel dependent. A variety of endopeptidases belong to this group that are similar in function and sequence homology. They include such proteins as HynC, HoxM, and HupD.
Probab=53.01 E-value=16 Score=17.81 Aligned_cols=129 Identities=24% Similarity=0.307 Sum_probs=62.6
Q ss_pred EEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCC
Q ss_conf 89998587873660674104899999999982798544432127885147974899982334020033799999940575
Q gi|254780225|r 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKL 81 (189)
Q Consensus 2 ~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i 81 (189)
.||+|+|||= ..=--+|..+++.|.+++..+. .|.++---| +|..+...++
T Consensus 1 IlV~GiGN~l----~gDDG~G~~v~~~L~~~~~~~~-----------------~v~~id~gt----~g~~l~~~l~---- 51 (146)
T cd06062 1 ILVLGIGNIL----LADEGIGVHAVERLEENYSFPE-----------------NVELIDGGT----LGLELLPYIE---- 51 (146)
T ss_pred CEEEEECCHH----HCCCCHHHHHHHHHHHHCCCCC-----------------CEEEEECCC----CHHHHHHHHH----
T ss_conf 9999938512----0438189999999997569999-----------------859998898----7899999981----
Q ss_pred CCCCCEEEEEE--CCCCCCCCEEEECC--------CCCCCCC-HHHHHHH---CCCCCEEEEEE-CCCCCCCCCCCCCCC
Q ss_conf 66333489840--44323382366111--------5888731-0333331---06873136675-068987767024243
Q gi|254780225|r 82 PNLENYLVIHD--DLDLDFGTLRLKTG--------GGDAGHN-GLKSISE---KCGKNYKRLRI-GIGRPPDTAHIIRHV 146 (189)
Q Consensus 82 ~~~~~ilVihD--dldL~~G~irlk~~--------Gg~gGHN-GlksI~~---~lg~~f~RlRI-GIG~P~~~~~v~~yV 146 (189)
..+. +|+-| +...++|+++.-.. .+...|. ++.++.. .++..-.++.+ ||- | ... +|
T Consensus 52 -~~d~-vIiVDA~~~g~~PG~i~~~~~~~~~~~~~~~~s~H~~~l~~~L~~~~~~~~~~~~v~ligie-~-~~~---~~- 123 (146)
T cd06062 52 -EADR-LIIVDAVDAGGPPGTVYRFEGEDVPAFLSAKLSAHQVGLLEVLALAELLGDLPPEIVLIGVQ-P-ESI---EW- 123 (146)
T ss_pred -CCCE-EEEEEECCCCCCCCEEEEECHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEEE-E-CCC---CC-
T ss_conf -8998-99998277799997289964355320026776855389999999999808999808999987-6-104---36-
Q ss_pred CCCCCHHHHHHHHHHHHHHHH
Q ss_conf 789888999999999999999
Q gi|254780225|r 147 LGNFSSPERYFLLPIIDNIAR 167 (189)
Q Consensus 147 L~~f~~~E~~~i~~~i~~~~~ 167 (189)
=...|++=+..++.+++.+.+
T Consensus 124 g~~LS~~V~~av~~~v~~i~~ 144 (146)
T cd06062 124 GLELSPEVAAALPTAIEAVLA 144 (146)
T ss_pred CCCCCHHHHHHHHHHHHHHHH
T ss_conf 999899999989999999996
No 14
>pfam06154 YagB_YeeU_YfjZ YagB/YeeU/YfjZ family. This family of proteins includes three proteins from E. coli YagB, YeeU and YfjZ. The function of these proteins is unknown. They are about 120 amino acids in length.
Probab=47.15 E-value=25 Score=16.76 Aligned_cols=32 Identities=19% Similarity=0.349 Sum_probs=28.0
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf 37898889999999999999999999980998
Q gi|254780225|r 146 VLGNFSSPERYFLLPIIDNIARSLPLLAKRED 177 (189)
Q Consensus 146 VL~~f~~~E~~~i~~~i~~~~~~i~~~~~~~~ 177 (189)
+-+.|+++|...+++++..+.+.++..+..+.
T Consensus 35 i~G~Fs~~~~~~Ld~aFP~~i~qlE~ml~sGe 66 (104)
T pfam06154 35 ITGTFSDAQKRHLDEAFPHFIKQLELMLLSGE 66 (104)
T ss_pred CEEECCHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 34626999998999999999999999864599
No 15
>TIGR02362 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit; InterPro: IPR012735 Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated 2.7.1.29 from EC. By contract, Escherichia coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex..
Probab=45.47 E-value=15 Score=17.99 Aligned_cols=33 Identities=18% Similarity=0.509 Sum_probs=25.6
Q ss_pred HHHHHCCCCCCCCCEEEEEECCCCCCCC-EEEECCC
Q ss_conf 9999405756633348984044323382-3661115
Q gi|254780225|r 73 LEVMNFYKLPNLENYLVIHDDLDLDFGT-LRLKTGG 107 (189)
Q Consensus 73 ~~~~~~~~i~~~~~ilVihDdldL~~G~-irlk~~G 107 (189)
...++.... +. .++|+|||+..+.-+ ++.|..|
T Consensus 115 ~~qar~EG~-~~-~~~iv~DDiSVe~~~~f~~R~RG 148 (328)
T TIGR02362 115 IEQARQEGR-DI-KYIIVHDDISVESESSFKKRRRG 148 (328)
T ss_pred HHHHHHCCC-CE-EEEEECCCCCCCCHHHHHHCCCC
T ss_conf 999986389-50-37997275331764556330356
No 16
>cd06070 H2MP_like-2 Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.
Probab=45.07 E-value=27 Score=16.56 Aligned_cols=124 Identities=15% Similarity=0.218 Sum_probs=60.0
Q ss_pred EEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCCC
Q ss_conf 99985878736606741048999999999827985444321278851479748999823340200337999999405756
Q gi|254780225|r 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKLP 82 (189)
Q Consensus 3 livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i~ 82 (189)
||+|+|||= ..=--+|-.+++.|.+. +++ ++---| .|.. ++.+. .
T Consensus 1 LVlGiGN~l----~gDDGvG~~vv~~L~~~-~v~---------------------viD~Gt----~g~~---l~~~l--~ 45 (140)
T cd06070 1 LIIGVGNRL----YGDDGFGSCLAEALEQC-GAP---------------------VFDGGL----DGFG---LLSHL--E 45 (140)
T ss_pred CEEEECCCC----CCCCCHHHHHHHHHHHC-CCE---------------------EEEECC----CHHH---HHHHH--H
T ss_conf 989978600----25386899999999863-985---------------------999258----5899---99998--2
Q ss_pred CCCCEEEEEE--CCCCCCCCEEEECCC----------CCCCCCHHHHHHHCCC-CC-EEEEE-ECCCCCCCCCCCCCCCC
Q ss_conf 6333489840--443233823661115----------8887310333331068-73-13667-50689877670242437
Q gi|254780225|r 83 NLENYLVIHD--DLDLDFGTLRLKTGG----------GDAGHNGLKSISEKCG-KN-YKRLR-IGIGRPPDTAHIIRHVL 147 (189)
Q Consensus 83 ~~~~ilVihD--dldL~~G~irlk~~G----------g~gGHNGlksI~~~lg-~~-f~RlR-IGIG~P~~~~~v~~yVL 147 (189)
..+.++ +-| +.+.++|.+++.... .+.-+-|+..+...+. .+ -++.. |||- | ..-+..
T Consensus 46 ~~d~vI-iVDAv~~g~~pG~i~~~~~~~~~~~~~~~~~s~H~~~l~~~l~~~~~~g~~p~~~liGi~-p-~~~~~g---- 118 (140)
T cd06070 46 NYDIVI-FIDVAVIDEDVGVFKITPEPASVAEQISFETDAHRLGPAHLLLLLKSSGRRPKAYIVGVK-P-ESIEFA---- 118 (140)
T ss_pred CCCEEE-EEEEECCCCCCCEEEEEECCCCHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEE-E-EECCCC----
T ss_conf 799899-995111689982799985653022322666788889999999999973999828999976-8-743358----
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8988899999999999999999999
Q gi|254780225|r 148 GNFSSPERYFLLPIIDNIARSLPLL 172 (189)
Q Consensus 148 ~~f~~~E~~~i~~~i~~~~~~i~~~ 172 (189)
...|++=+..+ +++++.++.+
T Consensus 119 ~~LS~~v~~av----~~~~e~i~~~ 139 (140)
T cd06070 119 RGLSEAVIARA----EKALEELKKL 139 (140)
T ss_pred CCCCHHHHHHH----HHHHHHHHHH
T ss_conf 99999999999----9999999975
No 17
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator; InterPro: IPR014264 Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC (see Q06065 from SWISSPROT). These proteins have a Fis family DNA binding sequence, a response regulator receiver domain, and sigma-54 interaction domain. They are found strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria, where members of IPR014265 from INTERPRO and IPR014266 from INTERPRO also occur..
Probab=42.87 E-value=9.2 Score=19.32 Aligned_cols=65 Identities=22% Similarity=0.260 Sum_probs=51.3
Q ss_pred CCCCCHHHHHHHCCC--CC-EEEEE-ECCCCCCCCCC------CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 887310333331068--73-13667-50689877670------24243789888999999999999999999998
Q gi|254780225|r 109 DAGHNGLKSISEKCG--KN-YKRLR-IGIGRPPDTAH------IIRHVLGNFSSPERYFLLPIIDNIARSLPLLA 173 (189)
Q Consensus 109 ~gGHNGlksI~~~lg--~~-f~RlR-IGIG~P~~~~~------v~~yVL~~f~~~E~~~i~~~i~~~~~~i~~~~ 173 (189)
++-|-=|++.|+.=. .| ||||- |-|-=||-++. ++++.|.+|+.+++......-+.+.++|+..-
T Consensus 282 CATnqdL~~~i~eg~FREDLfYRl~Eisi~iPPLR~R~gDa~lLA~~Fl~rf~~~~k~~~~~F~~DA~~ale~h~ 356 (451)
T TIGR02915 282 CATNQDLKKMIAEGTFREDLFYRLAEISITIPPLRDRDGDAVLLANAFLERFARELKRKAKGFTDDALRALEAHK 356 (451)
T ss_pred ECCCHHHHHHHHCCCCCCCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCC
T ss_conf 032246899985489720001346667862588998601899999999998878733021660699999976069
No 18
>cd06879 PX_UP1_plant The phosphoinositide binding Phox Homology domain of uncharacterized plant proteins. The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to PI-enriched membranes. Members in this subfamily are uncharacterized fungal proteins containing a PX domain. PX domain harboring proteins have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction.
Probab=41.61 E-value=6.8 Score=20.13 Aligned_cols=19 Identities=16% Similarity=0.527 Sum_probs=13.7
Q ss_pred HCCCCCEEEEEECCCCCCC
Q ss_conf 1068731366750689877
Q gi|254780225|r 120 EKCGKNYKRLRIGIGRPPD 138 (189)
Q Consensus 120 ~~lg~~f~RlRIGIG~P~~ 138 (189)
..++.+|+|+-+||..|..
T Consensus 40 n~~~~~fyrvqvgiqSPeg 58 (138)
T cd06879 40 NNAVDKFYRVQVGVQSPEG 58 (138)
T ss_pred CCCCCCEEEEEEECCCCCC
T ss_conf 2233316889984358752
No 19
>pfam07352 Phage_Mu_Gam Bacteriophage Mu Gam like protein. This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo.
Probab=40.79 E-value=11 Score=18.86 Aligned_cols=41 Identities=24% Similarity=0.334 Sum_probs=29.2
Q ss_pred CCCCCCCCEEEECCCCCCCCCHHHHHHHCCC----CCEEEEEECC
Q ss_conf 4432338236611158887310333331068----7313667506
Q gi|254780225|r 93 DLDLDFGTLRLKTGGGDAGHNGLKSISEKCG----KNYKRLRIGI 133 (189)
Q Consensus 93 dldL~~G~irlk~~Gg~gGHNGlksI~~~lg----~~f~RlRIGI 133 (189)
-+++|+|++..|.+...--..+..++++.|- ++|.|..-=|
T Consensus 71 t~~~~~G~v~~R~~~~~~~~~~~~~vle~Lk~~gl~~~Ir~kEev 115 (147)
T pfam07352 71 TLKLPYGTVGWRTRPPVVKVRGVESVLEALKSNGLTRFIRTKEEI 115 (147)
T ss_pred EEECCCEEEEEEECCCCCCCCCHHHHHHHHHHCCCHHHHHHHCCC
T ss_conf 777687148645379856656899999999986967552323124
No 20
>KOG3731 consensus
Probab=38.71 E-value=31 Score=16.13 Aligned_cols=48 Identities=19% Similarity=0.080 Sum_probs=24.2
Q ss_pred EECCCHHHHCCHHHHH-HHHCCCCCCCCCEEEEEECCCCCCCCEEEECC
Q ss_conf 8233402003379999-99405756633348984044323382366111
Q gi|254780225|r 59 IKPQTFMNLSGQSLLE-VMNFYKLPNLENYLVIHDDLDLDFGTLRLKTG 106 (189)
Q Consensus 59 ~kP~tyMN~SG~sv~~-~~~~~~i~~~~~ilVihDdldL~~G~irlk~~ 106 (189)
+-+.|||=.+.-...- .-..-.+-+|..|+|+.||.|.++|.+-+++.
T Consensus 9 ~~~it~~L~l~~~~~v~~~~~a~~~~PNvIlvLTDDqD~eLGsm~vm~k 57 (541)
T KOG3731 9 GSMITLMLLLNLWKYVALSDGAGRLPPNVILVLTDDQDVELGSMAVMFK 57 (541)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCHHCCCCCCCCH
T ss_conf 3168999887666775502445778987799970686410046210536
No 21
>PRK10466 hybD hydrogenase 2 maturation endopeptidase; Provisional
Probab=38.64 E-value=33 Score=15.96 Aligned_cols=134 Identities=16% Similarity=0.280 Sum_probs=72.9
Q ss_pred EEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCC
Q ss_conf 89998587873660674104899999999982798544432127885147974899982334020033799999940575
Q gi|254780225|r 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKL 81 (189)
Q Consensus 2 ~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i 81 (189)
.||+|+|||= ..=--+|-.++.+|.+++..+.. |.++- .|..-..++.++.
T Consensus 3 ilVlGiGN~l----~~DDGvG~~vv~~L~~~~~~p~~-----------------V~~iD-------~Gt~g~~Ll~~l~- 53 (164)
T PRK10466 3 ILVLGVGNIL----LTDEAIGVRIVEALEQRYILPDY-----------------VEILD-------GGTAGMELLGDMA- 53 (164)
T ss_pred EEEEEECCHH----CCCCCHHHHHHHHHHHHCCCCCC-----------------EEEEE-------CCCCHHHHHHHHC-
T ss_conf 9999768531----15472899999999975699998-----------------19998-------7885899999973-
Q ss_pred CCCCCEEEEEECC---CCCCCCEEEEC--------CC-CCCCCCHHHHHHHCCC--CCEE-EEEE-CCCCCCCCCCCCCC
Q ss_conf 6633348984044---32338236611--------15-8887310333331068--7313-6675-06898776702424
Q gi|254780225|r 82 PNLENYLVIHDDL---DLDFGTLRLKT--------GG-GDAGHNGLKSISEKCG--KNYK-RLRI-GIGRPPDTAHIIRH 145 (189)
Q Consensus 82 ~~~~~ilVihDdl---dL~~G~irlk~--------~G-g~gGHNGlksI~~~lg--~~f~-RlRI-GIG~P~~~~~v~~y 145 (189)
..+ .+++-|-+ +-++|+++.-. .. -+.-.-|+.++...+- .+++ ++.| ||- |.+- ++
T Consensus 54 -~~d-~vIivDAv~~~~~~PG~v~~~~~e~~~~~~~~~~S~H~~~l~~~L~~~~~~g~~P~~i~iiGie-p~~~----~~ 126 (164)
T PRK10466 54 -NRD-HLIIADAIVSKKNAPGTIMVLRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVI-PESL----EP 126 (164)
T ss_pred -CCC-EEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEE-EEEC----CC
T ss_conf -898-7999997225899994899965430530015675800147999999999759999879999999-7034----58
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 378988899999999999999999999
Q gi|254780225|r 146 VLGNFSSPERYFLLPIIDNIARSLPLL 172 (189)
Q Consensus 146 VL~~f~~~E~~~i~~~i~~~~~~i~~~ 172 (189)
= ...|++=+..++.+++.+.+.|+.+
T Consensus 127 g-~~LSp~V~~av~~~v~~i~~~L~~~ 152 (164)
T PRK10466 127 H-IGLTPTVEAMIEPALEQVLAALRES 152 (164)
T ss_pred C-CCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9-9989999999999999999999984
No 22
>cd06066 H2MP_NAD-link-bidir Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit assembly. These bidirectional hydrogenases are heteropentamers encoded by the hox (hydrogen oxidation) genes, in which complex HoxEFU shows the diaphorase activity, and HoxYH constitutes the NiFe-hydrogenase.
Probab=36.79 E-value=32 Score=16.11 Aligned_cols=26 Identities=31% Similarity=0.598 Sum_probs=20.4
Q ss_pred EEEECCCCCHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 999858787366067410489999999998
Q gi|254780225|r 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHSF 32 (189)
Q Consensus 3 livGLGNPG~~y~~TRHNvG~~~ld~l~~~ 32 (189)
||+|+|||= ..=--+|-.+++.|.+.
T Consensus 1 LVlGiGN~l----~gDDgvG~~v~~~L~~~ 26 (139)
T cd06066 1 LVIGYGNPL----RGDDGLGPAVAERIEEW 26 (139)
T ss_pred CEEEECCCC----CCCCCHHHHHHHHHHHH
T ss_conf 989968866----57480899999999723
No 23
>KOG2882 consensus
Probab=35.52 E-value=16 Score=17.85 Aligned_cols=36 Identities=25% Similarity=0.367 Sum_probs=19.1
Q ss_pred EEEEEEECCCHHHHCCHHHHHHHHCCCCCCCCCEEEEEECCCC
Q ss_conf 4899982334020033799999940575663334898404432
Q gi|254780225|r 54 LRTILIKPQTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDL 96 (189)
Q Consensus 54 ~~v~l~kP~tyMN~SG~sv~~~~~~~~i~~~~~ilVihDdldL 96 (189)
+++++-||.++|=++ +.+.++| ++++.+.|=|-||-
T Consensus 218 ~P~v~GKP~~~m~~~------l~~~~~i-~psRt~mvGDRL~T 253 (306)
T KOG2882 218 QPIVLGKPSTFMFEY------LLEKFNI-DPSRTCMVGDRLDT 253 (306)
T ss_pred CCEECCCCCHHHHHH------HHHHCCC-CCCEEEEECCCCHH
T ss_conf 881058988899999------9997188-95338897663202
No 24
>cd00518 H2MP Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE, the large subunit of hydrogenase 3. This cleavage is nickel dependent. This CD also includes such hydrogenase-processing proteins as HydD, HupW, and HoxW, as well as, proteins of the F420-reducing hydrogenase of methanogens (e.g., FrcD). Also included, is the Pyrococcus furiosus FrxA protein, a bifunctional endopeptidase/ sulfhydrogenase found in NADP-reducing hyperthermophiles.The Pyrococcus FrxA is not related to those found in Helicobacter pylori.
Probab=34.91 E-value=32 Score=16.09 Aligned_cols=88 Identities=22% Similarity=0.284 Sum_probs=45.8
Q ss_pred EEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCCC
Q ss_conf 99985878736606741048999999999827985444321278851479748999823340200337999999405756
Q gi|254780225|r 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKLP 82 (189)
Q Consensus 3 livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i~ 82 (189)
+|+|+|||= ..=--+|..+++.|.+.... ..+.++-- |...-.++.+..
T Consensus 1 lViGiGN~l----~gDDG~G~~v~~~L~~~~~~------------------~~v~v~d~-------g~~~~~l~~~l~-- 49 (139)
T cd00518 1 LVLGIGNPL----RGDDGFGPAVAERLEERYLP------------------PGVEVIDG-------GTLGLELLDLLE-- 49 (139)
T ss_pred CEEEECCCC----CCCCCHHHHHHHHHHHCCCC------------------CCEEEEEC-------CCCHHHHHHHHH--
T ss_conf 999968843----25280899999999833799------------------98799989-------986799999982--
Q ss_pred CCCCEEEEEECCC--CCCCCEEEECC------CC--CCCCCHHHHHHHCC
Q ss_conf 6333489840443--23382366111------58--88731033333106
Q gi|254780225|r 83 NLENYLVIHDDLD--LDFGTLRLKTG------GG--DAGHNGLKSISEKC 122 (189)
Q Consensus 83 ~~~~ilVihDdld--L~~G~irlk~~------Gg--~gGHNGlksI~~~l 122 (189)
.. +.+|+-|=.+ .++|+++.-.. .. +.-+-|+.++...+
T Consensus 50 ~~-d~vI~VDA~~~g~~pG~i~~~~~~~~~~~~~~~s~H~~~~~~~L~~~ 98 (139)
T cd00518 50 GA-DRVIIVDAVDSGGEPGTVRRLEPEELPAYLSALSTHQLGLAELLALL 98 (139)
T ss_pred CC-CEEEEEEECCCCCCCCEEEEECHHHHHCCCCCCCCCCCCHHHHHHHH
T ss_conf 89-98999986878999947999651562012577787779999999999
No 25
>PRK09256 hypothetical protein; Provisional
Probab=34.69 E-value=19 Score=17.46 Aligned_cols=27 Identities=26% Similarity=0.304 Sum_probs=20.2
Q ss_pred EEEEECCCCCCCCEEEEC--CCCCCCCCH
Q ss_conf 898404432338236611--158887310
Q gi|254780225|r 88 LVIHDDLDLDFGTLRLKT--GGGDAGHNG 114 (189)
Q Consensus 88 lVihDdldL~~G~irlk~--~Gg~gGHNG 114 (189)
|.|-+.+.+|.-.+.+++ ++|.||+|=
T Consensus 2 i~i~~~i~Ip~~el~~~f~RSsGPGGQnV 30 (138)
T PRK09256 2 LRITRRLVIPENELEWRFIRASGPGGQNV 30 (138)
T ss_pred EEECCCEEECHHHCEEEEEECCCCCCCCC
T ss_conf 47368737876990777777579987642
No 26
>TIGR01452 PGP_euk phosphoglycolate/pyridoxal phosphate phosphatase family; InterPro: IPR006349 This family of sequences represent 2-phosphoglycolate phosphatase which is limited to the eukaryotic lineage. PGP is an essential enzyme in the glycolate salvage pathway in higher organisms (photorespiration in plants). Phosphoglycolate results from the oxidase activity of RubisCO in the Calvin cycle when concentrations of carbon dioxide are low relative to oxygen. In mammals, PGP is found in many tissues, notably in red blood cells where P-glycolate is and important activator of the hydrolysis of 2,3-bisphosphoglycerate, a major modifier of the oxygen affinity of hemoglobin. The PGPase enzyme described here is a member of the Haloacid dehalogenase superfamily of hydrolase enzymes. Unlike the bacterial PGP equivalog (IPR006346 from INTERPRO), which is a member of class (subfamily) I, this enzyme is a member of class (subfamily) II . These two enzymes have almost certainly arisen from convergent evolution (although these two ancestors may themselves have diverged from a more distant HAD superfamily progenitor). One of the sequences in the group comes from Chlamydomonas reinhardtii, a photosynthetic alga. The enzyme has been purified and characterised and these data are fully consistent with the assignment of function as a PGPase involved in photorespiration . Another, from Homo sapiens, is supported as a member of the family indirectly. Biochemical characterization of partially purified PGP's from various tissues including red blood cells have been performed while one gene for PGP has been localized to chromosome 16p13.3 . The Homo sapiens sequence maps to chromosome 22. There is indeed a related gene on chromosome 16 (and it is expressed, since EST's are found) which shows 46 0dentity and 59603b08ositives by BLAST2 (E=1e-66). Presumably, these two genes are isoforms and have the same catalytic function while being expressed in different tissues and may be differently regulated. The sequence from Caenorhabditis elegans, is only supported by sequence similarity. This family is closely related to a family of bacterial sequences including the Escherichia coli NagD and Bacillus subtilus AraL genes which are characterised by the ability to hydrolyze para-nitrophenylphosphate (pNPPases or NPPases). The Chlamydomonas reinhardtii PGPase does not catalyze this reaction and so presumably these two groups have different functions and substrate specificities. Many of the genes in this family have been annotated as pNPPases due to this association.; GO: 0016791 phosphoric monoester hydrolase activity, 0008152 metabolic process.
Probab=32.89 E-value=41 Score=15.40 Aligned_cols=43 Identities=19% Similarity=0.317 Sum_probs=33.5
Q ss_pred CCCEEEEEEECCCHHHHCCHHHHHHHHCCCCCCCCCEEEEEECCC--CCCCC
Q ss_conf 797489998233402003379999994057566333489840443--23382
Q gi|254780225|r 51 LDGLRTILIKPQTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLD--LDFGT 100 (189)
Q Consensus 51 ~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i~~~~~ilVihDdld--L~~G~ 100 (189)
..-+.++.=||.+|| ...+.+.+.| +|++++-|=|=+| +-||+
T Consensus 202 sgR~plvVGKPs~~m------f~~I~~~~~i-~P~r~~MvGDRl~TDi~FG~ 246 (288)
T TIGR01452 202 SGREPLVVGKPSDYM------FEYIKEKLSI-DPARTLMVGDRLETDILFGK 246 (288)
T ss_pred CCCCCEEECCCCHHH------HHHHHHHHCC-CCCCEEEECCCCHHHHHHCC
T ss_conf 687243655898478------9998875178-80126775177202245321
No 27
>PRK02858 germination protease; Provisional
Probab=30.93 E-value=24 Score=16.79 Aligned_cols=79 Identities=15% Similarity=0.209 Sum_probs=44.0
Q ss_pred EEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCC-CCCCCCCCEEEEEECCCCEEEEEEEC----CCHHHHCCHHHHHHH
Q ss_conf 8999858787366067410489999999998279-85444321278851479748999823----340200337999999
Q gi|254780225|r 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFF-PAWKKKFHAEISEGQLDGLRTILIKP----QTFMNLSGQSLLEVM 76 (189)
Q Consensus 2 ~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~-~~~~~k~~~~~~~~~~~~~~v~l~kP----~tyMN~SG~sv~~~~ 76 (189)
.|+|||||. .-|--..|-.+++.+.-...+ ........ . +-.+|--+-| +|-| +++.-|+.++
T Consensus 111 vLVVGLGN~----~vTPDALGP~vv~~l~VTRHL~~~~p~~~~----~---g~r~VsaiaPGVmg~TGi-ET~EIIkgIV 178 (367)
T PRK02858 111 CLIVGLGNW----NVTPDALGPIVVENVLVTRHLFQLQPESVE----E---GFRPVSAIAPGVMGITGI-ETSDIIYGII 178 (367)
T ss_pred EEEEECCCC----CCCCCCCCHHHHHCEEEEHHHHHHCCHHHC----C---CCCEEEEECCCCCCCCCC-CHHHHHHHHH
T ss_conf 899967887----778655262422014113436553714340----5---763024775774304440-3999999998
Q ss_pred HCCCCCCCCCEEEEEECCCC
Q ss_conf 40575663334898404432
Q gi|254780225|r 77 NFYKLPNLENYLVIHDDLDL 96 (189)
Q Consensus 77 ~~~~i~~~~~ilVihDdldL 96 (189)
...| | +++|+-|-|.-
T Consensus 179 ek~k---P-D~VIaIDALAa 194 (367)
T PRK02858 179 EKTK---P-DFVIAIDALAA 194 (367)
T ss_pred HHHC---C-CEEEEEHHHHC
T ss_conf 7508---9-88999603122
No 28
>cd06067 H2MP_MemB-H2evol Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase 3 from E coli, the maturation of the large subunit (HycE) requires the cleavage of a C-terminal peptide by the endopeptidase HycI, before the final formation of the [NiFe] metallocenter. HycI protease is a monomer and lacks characteristic signature motifs of serine, zinc, cysteine, or acid proteases and thus its cleavage reaction is not inhibited by conventional inhibitors of serine and metalloproteases. Such hydrogenases as those from Methanosarcina barkeri (EchCE) and Rhodospirillum rubrum (CooLH) also belong to this group of membrane-bound hydrogen evolving hydrogenase. Sequence comparison of the large subunits from related hydrogenase indicates that in contrast to EchE (358 amino acids) and CooH (361 amino acids), the large subunit HycE (569 amino acids) contains an extra carboxy-terminal stretch of 32 amino acids that is cleaved during the maturation process. In
Probab=30.88 E-value=43 Score=15.30 Aligned_cols=90 Identities=17% Similarity=0.193 Sum_probs=48.0
Q ss_pred EEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCCC
Q ss_conf 99985878736606741048999999999827985444321278851479748999823340200337999999405756
Q gi|254780225|r 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKLP 82 (189)
Q Consensus 3 livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i~ 82 (189)
||+|+|||= ..=--+|-.+++.|.+... . .+.++.--| .|..+...++.++
T Consensus 1 LVlGiGN~l----~gDDgvG~~v~~~L~~~~~-----~--------------~v~vid~gt----~~~~~~~~~~~~~-- 51 (136)
T cd06067 1 VLLGVGNEL----RGDDGAGPLLAEKLEDLPN-----P--------------NWLVIDGGT----VPENFTGKIREEK-- 51 (136)
T ss_pred CEEEECCCC----CCCCCHHHHHHHHHHHHCC-----C--------------CEEEEECCC----CHHHHHHHHHHCC--
T ss_conf 989968844----0438399999999962468-----9--------------859998898----7799999997418--
Q ss_pred CCCCEEEEEECC--CCCCCCEEEECC-----CCCCCCC-HHHHHHHCCC
Q ss_conf 633348984044--323382366111-----5888731-0333331068
Q gi|254780225|r 83 NLENYLVIHDDL--DLDFGTLRLKTG-----GGDAGHN-GLKSISEKCG 123 (189)
Q Consensus 83 ~~~~ilVihDdl--dL~~G~irlk~~-----Gg~gGHN-GlksI~~~lg 123 (189)
++ .+++-|=. +.++|+++.-.. ....-|. |++.+.+.+.
T Consensus 52 -~d-~vIivDAv~~g~~PG~i~~~~~~~~~~~~~S~H~~~l~~~l~~l~ 98 (136)
T cd06067 52 -PD-LIVIVDAADMGLEPGEIRIIDPEEIAEYFFSTHTLPLSILIDYLR 98 (136)
T ss_pred -CC-EEEEEECCCCCCCCCEEEEECHHHCCCCCCCCCCCCHHHHHHHHH
T ss_conf -98-899996101699996799975688050477876389999999987
No 29
>TIGR02471 sucr_syn_bact_C sucrose phosphate synthase, sucrose phosphatase-like domain; InterPro: IPR012821 Sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP) are the last two enzymes of sucrose biosynthesis. In cyanobacteria and plants, the C-terminal region of most or all versions of SPS has a domain homologous to the known SPP. This domain may serve a binding or regulatory rather than catalytic function. Sequences in this family are bacterial C-terminal regions found in all but two of the putative bacterial sucrose phosphate synthases described by IPR012822 from INTERPRO..
Probab=29.91 E-value=36 Score=15.76 Aligned_cols=25 Identities=36% Similarity=0.425 Sum_probs=20.5
Q ss_pred HCCHHHHHHHHCCCCCCCCCEEEEEE
Q ss_conf 03379999994057566333489840
Q gi|254780225|r 67 LSGQSLLEVMNFYKLPNLENYLVIHD 92 (189)
Q Consensus 67 ~SG~sv~~~~~~~~i~~~~~ilVihD 92 (189)
-+|.||+.++-.+.+| +|++||+=|
T Consensus 163 S~~~A~Ryls~~wGlp-Le~~Lvag~ 187 (241)
T TIGR02471 163 SKGLALRYLSYRWGLP-LEQLLVAGD 187 (241)
T ss_pred CCHHHHHHHHHHHCCC-HHHEEEEEC
T ss_conf 7048999999982797-458145406
No 30
>cd00887 MoeA MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MoeA, together with MoaB, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes.
Probab=28.74 E-value=38 Score=15.59 Aligned_cols=73 Identities=15% Similarity=0.271 Sum_probs=51.8
Q ss_pred HHHCCHHHHHHHHCCCCCCCCCEEEEEECCCCCC---------CCEEEECCCCCCCCCH-HHHHHHCCC-C-CEEEEEEC
Q ss_conf 2003379999994057566333489840443233---------8236611158887310-333331068-7-31366750
Q gi|254780225|r 65 MNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDF---------GTLRLKTGGGDAGHNG-LKSISEKCG-K-NYKRLRIG 132 (189)
Q Consensus 65 MN~SG~sv~~~~~~~~i~~~~~ilVihDdldL~~---------G~irlk~~Gg~gGHNG-lksI~~~lg-~-~f~RlRIG 132 (189)
.|-.+..+.++++.+.. ....+-++-||.+.=- -.+=+-.||.+.|..- ++++++.+| + -|+|+.+-
T Consensus 193 ~dsN~~~L~a~l~~~G~-~~~~~~~v~Dd~~~l~~~l~~a~~~~DiiIttGG~S~G~~D~v~~~l~~lg~~~~f~~v~ik 271 (394)
T cd00887 193 YDSNSYMLAALLRELGA-EVVDLGIVPDDPEALREALEEALEEADVVITSGGVSVGDYDFVKEVLEELGGEVLFHGVAMK 271 (394)
T ss_pred EECCHHHHHHHHHHCCC-EEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCHHHHHHHHCCCEEEEEEEECC
T ss_conf 73579999999997899-89996731899999999999764309999992774268763399999977998999774135
Q ss_pred CCCCCC
Q ss_conf 689877
Q gi|254780225|r 133 IGRPPD 138 (189)
Q Consensus 133 IG~P~~ 138 (189)
=|+|..
T Consensus 272 PGkp~~ 277 (394)
T cd00887 272 PGKPLA 277 (394)
T ss_pred CCCCEE
T ss_conf 776228
No 31
>cd00736 bacteriophage_lambda_lysozyme The lysozyme from bacteriophage lambda hydrolyses the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), as do other lysozymes. But unlike other lysozymes, bacteriophage lambda does not produce a reducing end upon cleavage of the peptidoglycan but rather uses the 6-OH of the same MurNAc residue to produce a 1,6-anhydromuramic acid terminal residue and is therefore a lytic transglycosylase. An identical 1,6-anhydro bond is formed in bacterial peptidoglycans by the action of the lytic transglycosylases of E. coli. However, they differ structurally.
Probab=27.06 E-value=52 Score=14.79 Aligned_cols=42 Identities=12% Similarity=0.039 Sum_probs=31.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHC
Q ss_conf 437898889999999999999999999980998999998633
Q gi|254780225|r 145 HVLGNFSSPERYFLLPIIDNIARSLPLLAKREDVSFLNHIVS 186 (189)
Q Consensus 145 yVL~~f~~~E~~~i~~~i~~~~~~i~~~~~~~~~~~mn~~n~ 186 (189)
+=|.+|+|+-++.+--.+-.-..+++.+..+.+..+++++..
T Consensus 81 l~l~dF~P~~QD~~Al~li~~rgal~~i~~G~~~~ai~kl~~ 122 (151)
T cd00736 81 YGLYDFSPESQDLVAYQLIRERGALPDILAGRIEQAIAKLSN 122 (151)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHCC
T ss_conf 499999927899999999997286687876689999998421
No 32
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=26.37 E-value=54 Score=14.72 Aligned_cols=36 Identities=19% Similarity=0.236 Sum_probs=29.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 024243789888999999999999999999998099
Q gi|254780225|r 141 HIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKRE 176 (189)
Q Consensus 141 ~v~~yVL~~f~~~E~~~i~~~i~~~~~~i~~~~~~~ 176 (189)
...+-+++.|+++|++.+..+++.+.+++..+-.+|
T Consensus 109 ~~~~~~~~~ls~eE~~~l~~~L~ki~~Nl~~l~~~~ 144 (144)
T PRK03573 109 KTRAEILHGISSEEIEQLIKLIAKLEHNIIELQSKG 144 (144)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 999999819999999999999999999999998485
No 33
>cd06064 H2MP_F420-Reduc Endopeptidases belonging to F420-reducing hydrogenases group. These hydrogenases from methanogens are encoded by the fru, frc, or frh genes. Sequence comparison indicates that fruD and frcD gene products from Methanococcus voltae are similar to HycI protease of Escherichia coli and are putatively involved in the C-terminal processing of large subunits (FruA and FrcA respectively). FrhD (F420 reducing hydrogenase delta subunit) enzyme belongs to the gene cluster of 8-hydroxy-5-deazaflavin (F420) reducing hydrogenase (FRH) from the thermophilic methanogen Methanobacterium thermoautotrophicum delta H. FrhD subunit is putatively involved in the processing of the coenzyme F420 hydrogenase-processing. It is similar to those frhD genes found in Methanomicrobia and Methanobacteria. It is different from the FrhD conserved domain found in methyl viologen-reducing hydrogenase and F420-non-reducing hydrogenase iron-sulfur subunit D.
Probab=26.00 E-value=55 Score=14.67 Aligned_cols=130 Identities=18% Similarity=0.240 Sum_probs=59.8
Q ss_pred EEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHH----HHHHHC
Q ss_conf 9998587873660674104899999999982798544432127885147974899982334020033799----999940
Q gi|254780225|r 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSL----LEVMNF 78 (189)
Q Consensus 3 livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv----~~~~~~ 78 (189)
||+|+|||= ..=--+|-.++..|.+....+. .+.++ ..|.+. -.++.+
T Consensus 1 lVlGiGN~L----~~DDG~G~~vv~~L~~~~~~p~-----------------~v~vi-------d~Gt~g~~~~~~l~~~ 52 (150)
T cd06064 1 LVVGCGNIL----FGDDGFGPAVIEELEKLELLPD-----------------NVQVI-------DAGTGAPHLLFTLLDE 52 (150)
T ss_pred CEEEECCCC----CCCCCHHHHHHHHHHHCCCCCC-----------------CEEEE-------ECCCCHHHHHHHHHHH
T ss_conf 989968602----4248599999999985179999-----------------87999-------8677508888887655
Q ss_pred CCCCCCCCEEEEEE--CCCCCCCCEEEECC--------CCCCCC-CHHHHHHHCCCCCEE-EE-EECCCCCCCCCCCCCC
Q ss_conf 57566333489840--44323382366111--------588873-103333310687313-66-7506898776702424
Q gi|254780225|r 79 YKLPNLENYLVIHD--DLDLDFGTLRLKTG--------GGDAGH-NGLKSISEKCGKNYK-RL-RIGIGRPPDTAHIIRH 145 (189)
Q Consensus 79 ~~i~~~~~ilVihD--dldL~~G~irlk~~--------Gg~gGH-NGlksI~~~lg~~f~-Rl-RIGIG~P~~~~~v~~y 145 (189)
.. .++.+++ -| +.+.++|+++.-.. ....-| =|+..++..+...+. ++ =+||- |. +++.+
T Consensus 53 ~~--~~d~vIi-VDAv~~g~~PGti~~~~~~el~~~~~~~~S~H~~~l~~~l~~l~~~~~~~i~iiGie-p~---~i~~~ 125 (150)
T cd06064 53 ES--KPKKIII-VDAIDFGLEPGTLKKISVDELPPGKYYDFDAHSWPLADPLHELKDKYGIEIVVIGCQ-PK---RVPEP 125 (150)
T ss_pred HC--CCCEEEE-EECCCCCCCCCEEEEECHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCEEEEEEEE-EE---EECCC
T ss_conf 31--7887999-961137999967999765765544477757767889999999860289849999988-75---76268
Q ss_pred CCC-CCCHHHHHHHHHHHHHHHH
Q ss_conf 378-9888999999999999999
Q gi|254780225|r 146 VLG-NFSSPERYFLLPIIDNIAR 167 (189)
Q Consensus 146 VL~-~f~~~E~~~i~~~i~~~~~ 167 (189)
=++ ..|++=++.++++++.+.+
T Consensus 126 ~~~~gLS~~V~~av~~~v~~i~~ 148 (150)
T cd06064 126 DVEPGLSEEVEKAVPKAVEIILE 148 (150)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 87887699999989999999997
No 34
>PRK12362 germination protease; Provisional
Probab=25.59 E-value=24 Score=16.78 Aligned_cols=157 Identities=19% Similarity=0.244 Sum_probs=77.5
Q ss_pred EEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCC-CCCCCEEEEEECCCC-EEEEEEEC----CCHHHHCCHHHHHH
Q ss_conf 8999858787366067410489999999998279854-443212788514797-48999823----34020033799999
Q gi|254780225|r 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAW-KKKFHAEISEGQLDG-LRTILIKP----QTFMNLSGQSLLEV 75 (189)
Q Consensus 2 ~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~-~~k~~~~~~~~~~~~-~~v~l~kP----~tyMN~SG~sv~~~ 75 (189)
.|+|||||.- -|--..|-.+++.+.-...+... .... -++ .+|--+-| +|-| +++.-|+.+
T Consensus 99 vLVVGLGN~~----vTPDALGP~vv~~l~VTRHl~~~~p~~~--------~~g~r~VsaiaPGVmg~TGi-ET~EIIkgi 165 (324)
T PRK12362 99 VLVVGLGNWN----VTPDALGPKVVSKIMVTRHLKEYVPEQI--------DEGVRPVSAISPGVLGITGI-ETAEIIKGI 165 (324)
T ss_pred EEEEECCCCC----CCCCCCCHHEECCEEEEHHHHHHCCHHH--------CCCCCEEEEECCCCCCCCCC-CHHHHHHHH
T ss_conf 8999678877----7865637120002510253676563544--------27873146885875404430-399999999
Q ss_pred HHCCCCCCCCCEEEEEECCCCCC-----CCEEEE-----CCCCCCCCCHHHHHHH-CCCCCEEEEEECCCCCCCC-----
Q ss_conf 94057566333489840443233-----823661-----1158887310333331-0687313667506898776-----
Q gi|254780225|r 76 MNFYKLPNLENYLVIHDDLDLDF-----GTLRLK-----TGGGDAGHNGLKSISE-KCGKNYKRLRIGIGRPPDT----- 139 (189)
Q Consensus 76 ~~~~~i~~~~~ilVihDdldL~~-----G~irlk-----~~Gg~gGHNGlksI~~-~lg~~f~RlRIGIG~P~~~----- 139 (189)
+...| | +++|.-|-|.-.- -+|.+. +|.|=|-| -+.|.+ .|| -+=+-| |=|---
T Consensus 166 v~k~k---P-d~VIaIDALAaRs~~Rln~TIQIsDTGI~PGSGVGN~--R~~l~~etLG--VPVIAI--GVPTVVdAatI 235 (324)
T PRK12362 166 VEKIK---P-DLVIAIDALASRKVERVNTTIQISDTGISPGSGVGNK--RMGLNEETLG--VPVIAI--GVPTVVDAATI 235 (324)
T ss_pred HHHHC---C-CEEEEEHHHHCCCHHHCCCEEEECCCCCCCCCCCCCC--CCCCCHHHCC--CCEEEE--CCCEEECHHHH
T ss_conf 87508---9-8999960211376665367588657785899886754--4426987829--988996--58816522999
Q ss_pred -CCCCCC-----------------CCCCCCHHHHHHH-H--------------HHHHHHHHHHHHHHCCCHHHHH
Q ss_conf -702424-----------------3789888999999-9--------------9999999999999809989999
Q gi|254780225|r 140 -AHIIRH-----------------VLGNFSSPERYFL-L--------------PIIDNIARSLPLLAKREDVSFL 181 (189)
Q Consensus 140 -~~v~~y-----------------VL~~f~~~E~~~i-~--------------~~i~~~~~~i~~~~~~~~~~~m 181 (189)
.+..++ +|+.++++|++.+ . +-++..++.+..++.++.+.|.
T Consensus 236 ~~Dti~~~~~~~~~~~~~~~~~~~~~~~l~~~ek~~li~evL~P~~~~l~VTPKeID~~i~~~s~iIs~giN~AL 310 (324)
T PRK12362 236 ANDTIDMVLDELIKQSESGSEFYNMLKSIDQEEKQNLIKEVLSPYVGNLMVTPKEIDMLIENLSKIIANGINIAL 310 (324)
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHCCCHHHHHHHHHHHHCCCCCCCEECCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 899999999998640212202777761469899999999974835896467757489999999999998999986
No 35
>PRK10264 hydrogenase 1 maturation protease; Provisional
Probab=24.87 E-value=57 Score=14.55 Aligned_cols=136 Identities=19% Similarity=0.273 Sum_probs=79.9
Q ss_pred EEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCC
Q ss_conf 89998587873660674104899999999982798544432127885147974899982334020033799999940575
Q gi|254780225|r 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKL 81 (189)
Q Consensus 2 ~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i 81 (189)
.||.|+||+ -.+---+|-.++.+|.+++.++.. |.++-=-| .|-. ++.+.
T Consensus 6 IlVLGiGNi----L~~DEG~GV~~v~~L~~~~~~p~~-----------------V~liDGGT----~G~~---Ll~~l-- 55 (195)
T PRK10264 6 VVVMGLGNL----LWADEGFGVRVAERLYAHYHWPEE-----------------VEIVDGGT----QGLN---LLGYV-- 55 (195)
T ss_pred EEEEECCCC----CCCCCCHHHHHHHHHHHHCCCCCC-----------------CEEEECCC----CHHH---HHHHH--
T ss_conf 899912731----123573899999999985689988-----------------28984453----1999---99998--
Q ss_pred CCCCCEEEEEE--CCCCCCCCEEEEC----------CCCCCCCCHHHHHHHCCC--CCEE-EE-EECCCCCCCCCCCCCC
Q ss_conf 66333489840--4432338236611----------158887310333331068--7313-66-7506898776702424
Q gi|254780225|r 82 PNLENYLVIHD--DLDLDFGTLRLKT----------GGGDAGHNGLKSISEKCG--KNYK-RL-RIGIGRPPDTAHIIRH 145 (189)
Q Consensus 82 ~~~~~ilVihD--dldL~~G~irlk~----------~Gg~gGHNGlksI~~~lg--~~f~-Rl-RIGIG~P~~~~~v~~y 145 (189)
...+.+ +|.| |...++|+++.-. .+-+.-+-|+..+..... .+.+ |+ =||| -|. ++.+|
T Consensus 56 e~~d~L-IvvDAV~~g~~PGtv~~~~~devp~~~~~~kmS~Hqvgl~evL~~a~L~G~~P~~~~LiGv-qP~---~le~~ 130 (195)
T PRK10264 56 ESASHL-LILDAIDYGLEPGTLRTYAGERIPAYLSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGL-QPA---MLDDY 130 (195)
T ss_pred HCCCEE-EEEECCCCCCCCCEEEEEECCCCCHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEECC-CCC---EEECC
T ss_conf 429979-9984653799997599971430421217577786404799999999954999874999843-102---33057
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3789888999999999999999999998
Q gi|254780225|r 146 VLGNFSSPERYFLLPIIDNIARSLPLLA 173 (189)
Q Consensus 146 VL~~f~~~E~~~i~~~i~~~~~~i~~~~ 173 (189)
= ..-++.=+..++.+++.+.+.+..|-
T Consensus 131 g-~~Ltp~V~a~ip~av~~~l~~L~~wG 157 (195)
T PRK10264 131 G-GSLSELAREQLPAAEQAALAQLAAWG 157 (195)
T ss_pred C-CCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 8-98898999866999999999999809
No 36
>cd06068 H2MP_like-1 Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.
Probab=23.52 E-value=30 Score=16.24 Aligned_cols=25 Identities=28% Similarity=0.412 Sum_probs=18.5
Q ss_pred EEEECCCCCHHHHCCCCCHHHHHHHHHHH
Q ss_conf 99985878736606741048999999999
Q gi|254780225|r 3 IVAGLGNPGHEYCENRHNIGFMCIDRIHS 31 (189)
Q Consensus 3 livGLGNPG~~y~~TRHNvG~~~ld~l~~ 31 (189)
||+|+|||= ..=--+|..++++|.+
T Consensus 1 LVlGiGN~l----~gDDGvG~~v~~~L~~ 25 (144)
T cd06068 1 LVAGVGNIF----LGDDGFGVEVARRLRP 25 (144)
T ss_pred CEEEECCCC----CCCCCHHHHHHHHHHC
T ss_conf 989858720----0548089999999855
No 37
>TIGR00072 hydrog_prot hydrogenase maturation protease; InterPro: IPR000671 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised . More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin and archaean preflagellin have been described , . Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. Metalloproteases are the most diverse of the four main types of protease, with more than 30 families identified to date . In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as abXHEbbHbc, where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor undergoes a complex post-translational maturation process that requires a number of accessory proteins , , . At one step of this process, after nickel incorporation, each hydrogenase isoenzyme is processed by proteolytic cleavage at the C-terminal end by the corresponding hydrogenase maturation endopeptidase . For example, Escherichia coli HycI is involved in processing of pre-HycE (the large subunit of hydrogenase 3) , ; HybD is involved in processing of pre-HybC (the large subunit of hydrogenase 2) ; and HyaD is assumed to be involved in processing of the large subunit of hydrogenase 1. This group represents metallopeptidases of the MEROPS peptidase family A31 (HybD endopeptidase family, clan AE). The cleavage site is after a His or an Arg, liberating a short peptide , . This cleavage occurs only in the presence of nickel, and the endopeptidase probably uses the metal in the large subunit of [NiFe]-hydrogenases as a recognition motif . There is no direct evidence for the active site or substrate-binding site, but there are predictions based on an available structure . Nomenclature note: the following names are used in different organisms for members of this group: HycI, HybD, HyaD, HoxM, HoxW, HupD, HynC, HupM, VhoD, VhtD . Gene/protein names are sometimes used interchangeably to designate various "hydrogenase cluster" proteins unrelated to each other in various organisms. For example, the following names are used for members of this group, but also for unrelated proteins: HupD is used in Azotobacter chroococcum and Anabaena sp. to designate an unrelated hydrogenase maturation factor; HydD is used to designate hydrogenase structural genes in Thermococcus litoralis, Pyrococcus abyssi, and other species.; GO: 0008047 enzyme activator activity, 0008233 peptidase activity.
Probab=23.23 E-value=42 Score=15.37 Aligned_cols=143 Identities=17% Similarity=0.225 Sum_probs=87.6
Q ss_pred EEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCC
Q ss_conf 89998587873660674104899999999982798544432127885147974899982334020033799999940575
Q gi|254780225|r 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKL 81 (189)
Q Consensus 2 ~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i 81 (189)
.||+|.||| -..==-+|-.++..|.+.+..+... + ++.++--=| .|.-....+..+.
T Consensus 4 ilvlG~GN~----L~gDDG~G~~v~e~l~~~~~~p~~~-~-------------nv~~iDgGt----~g~~l~~~l~~~~- 60 (170)
T TIGR00072 4 ILVLGVGNI----LFGDDGFGVRVAEKLKKRFELPENI-K-------------NVEVIDGGT----GGLDLLGLLEEAD- 60 (170)
T ss_pred EEEEEECCC----CCCCCCCCHHHHHHHHHHHCCCCCC-C-------------EEEEEECCC----CCHHHHHHHHHCC-
T ss_conf 789975483----3056765788999999974066668-7-------------289980665----7866788774158-
Q ss_pred CCCCCEEEE-EECCC-CCCCCEEEEC-----------CCCCCCCCHHHHHHHCCC--CCEE-EEE-ECCCCCCCCCCCCC
Q ss_conf 663334898-40443-2338236611-----------158887310333331068--7313-667-50689877670242
Q gi|254780225|r 82 PNLENYLVI-HDDLD-LDFGTLRLKT-----------GGGDAGHNGLKSISEKCG--KNYK-RLR-IGIGRPPDTAHIIR 144 (189)
Q Consensus 82 ~~~~~ilVi-hDdld-L~~G~irlk~-----------~Gg~gGHNGlksI~~~lg--~~f~-RlR-IGIG~P~~~~~v~~ 144 (189)
+..+||| -=|.+ +++|++|+=. ..-+.-..++..++..+- .+++ |+- |||- | ......+
T Consensus 61 --~~~~iivDA~~~~~~~pG~v~~i~~~d~~p~~~~~~~~s~H~~~~~~~l~~~~~~~~~P~~~~l~G~~-p-~~~~~~~ 136 (170)
T TIGR00072 61 --PKKVIIVDAIDFGSLEPGTVRIIEVEDEIPNFLKAKKMSTHQLPLSEVLRLLKEKGELPAEVILIGVQ-P-KEISLED 136 (170)
T ss_pred --CCEEEEEEEEECCCCCCCEEEEEECCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEEEEE-E-EEEEEEC
T ss_conf --85789997775689898758997321034675221356536679899999999984385005888754-6-7887506
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 4378988899999999999999999999
Q gi|254780225|r 145 HVLGNFSSPERYFLLPIIDNIARSLPLL 172 (189)
Q Consensus 145 yVL~~f~~~E~~~i~~~i~~~~~~i~~~ 172 (189)
| =..+|++.+..++.+++.+.+.+..+
T Consensus 137 ~-~~~Ls~~v~~av~~a~~~i~~~l~~~ 163 (170)
T TIGR00072 137 F-GGGLSPEVKKAVDKAVEQILAELRAS 163 (170)
T ss_pred C-CCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 6-77669899987999999999998615
No 38
>pfam00472 RF-1 RF-1 domain. This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis.
Probab=22.59 E-value=36 Score=15.80 Aligned_cols=23 Identities=22% Similarity=0.455 Sum_probs=17.2
Q ss_pred ECCCCCCCCEEEE--CCCCCCCCCH
Q ss_conf 0443233823661--1158887310
Q gi|254780225|r 92 DDLDLDFGTLRLK--TGGGDAGHNG 114 (189)
Q Consensus 92 DdldL~~G~irlk--~~Gg~gGHNG 114 (189)
.++++|.-.+++. .++|+||+|=
T Consensus 6 ~~i~i~~~dl~~~~~RssGpGGQ~V 30 (114)
T pfam00472 6 VEIEIPPSDLRIDTFRSSGPGGQNV 30 (114)
T ss_pred CCEECCHHHEEEEEEECCCCCCCCC
T ss_conf 1114187994899888789865654
No 39
>COG1663 LpxK Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]
Probab=22.13 E-value=29 Score=16.36 Aligned_cols=37 Identities=24% Similarity=0.273 Sum_probs=17.7
Q ss_pred CEEEEE----ECCCCCCCCC--------CC-CCCCC---CCCCHHHHHHHHHH
Q ss_conf 313667----5068987767--------02-42437---89888999999999
Q gi|254780225|r 125 NYKRLR----IGIGRPPDTA--------HI-IRHVL---GNFSSPERYFLLPI 161 (189)
Q Consensus 125 ~f~RlR----IGIG~P~~~~--------~v-~~yVL---~~f~~~E~~~i~~~ 161 (189)
++.+.| =|||+|..-. .+ .-+-+ ..|+.+|.+.+...
T Consensus 230 ~~~~~~v~afaGIg~P~rFf~tL~~~g~~~~~~~~FpDH~~f~~~~l~~l~~~ 282 (336)
T COG1663 230 DLKGKRVVAFAGIGNPQRFFATLRNLGIQVVETLAFPDHYDFSAADLEDLAKK 282 (336)
T ss_pred HCCCCEEEEEEECCCHHHHHHHHHHCCCCEEEEECCCCHHHCCHHHHHHHHHH
T ss_conf 25774599998537839999999971765454364886233359889999863
No 40
>TIGR00417 speE spermidine synthase; InterPro: IPR001045 Synonym(s): Spermidine aminopropyltransferase A group of polyamine biosynthetic enzymes involved in the fifth (last) step in the biosynthesis of spermidine from arginine and methionine which includes; spermidine synthase (), spermine synthase () and putrescine N-methyltransferase () . The Thermotoga maritima spermidine synthase monomer consists of two domains: an N-terminal domain composed of six beta-strands, and a Rossmann-like C- terminal domain . The larger C-terminal catalytic core domain consists of a seven-stranded beta-sheet flanked by nine alpha helices. This domain resembles a topology observed in a number of nucleotide and dinucleotide-binding enzymes, and in S-adenosyl-L-methionine (AdoMet)- dependent methyltransferase (MTases) . ; GO: 0003824 catalytic activity.
Probab=22.11 E-value=52 Score=14.80 Aligned_cols=22 Identities=50% Similarity=0.946 Sum_probs=16.4
Q ss_pred CCCCCEEEEEECCCCCCCCEEEECCCCCCC-------CCHHHHH
Q ss_conf 663334898404432338236611158887-------3103333
Q gi|254780225|r 82 PNLENYLVIHDDLDLDFGTLRLKTGGGDAG-------HNGLKSI 118 (189)
Q Consensus 82 ~~~~~ilVihDdldL~~G~irlk~~Gg~gG-------HNGlksI 118 (189)
++|.++||| |||+|| |+-+++|
T Consensus 74 ~NPk~VLvI---------------GGGDGG~lREV~KH~sVE~~ 102 (284)
T TIGR00417 74 PNPKKVLVI---------------GGGDGGVLREVVKHKSVEKA 102 (284)
T ss_pred CCCCEEEEE---------------ECCCCCEEEEEEECCCCCEE
T ss_conf 988547899---------------63888468788755981679
No 41
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=21.81 E-value=53 Score=14.77 Aligned_cols=29 Identities=21% Similarity=0.441 Sum_probs=22.2
Q ss_pred HHCCCCCCCCCEEEEEECCCCCCCCEEEEC
Q ss_conf 940575663334898404432338236611
Q gi|254780225|r 76 MNFYKLPNLENYLVIHDDLDLDFGTLRLKT 105 (189)
Q Consensus 76 ~~~~~i~~~~~ilVihDdldL~~G~irlk~ 105 (189)
+...+. .++..+|..|||..+-|....|.
T Consensus 131 ~~~Lr~-~~~kFIlFcDDLSFe~gd~~yK~ 159 (287)
T COG2607 131 VELLRA-RPEKFILFCDDLSFEEGDDAYKA 159 (287)
T ss_pred HHHHHC-CCCEEEEEECCCCCCCCCHHHHH
T ss_conf 999961-88608999567777778138999
No 42
>cd02168 NMNAT_Nudix This domain represents the N-terminal NMNAT (Nicotinamide/nicotinate mononucleotide adenylyltransferase) domain of a novel bifunctional enzyme endowed with NMN adenylyltransferase and #Nudix' hydrolase activities. This domain is highly homologous to the archeal NMN adenyltransferase that catalyzes NAD synthesis from NMN and ATP. NMNAT is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. The C-terminal domain of this enzyme shares homology with the archaeal ADP-ribose pyrophosphatase, a member of the 'Nudix' hydrolase family.
Probab=21.53 E-value=67 Score=14.15 Aligned_cols=21 Identities=5% Similarity=-0.134 Sum_probs=8.5
Q ss_pred ECCCHHHHCC--HHHHHHHHCCC
Q ss_conf 2334020033--79999994057
Q gi|254780225|r 60 KPQTFMNLSG--QSLLEVMNFYK 80 (189)
Q Consensus 60 kP~tyMN~SG--~sv~~~~~~~~ 80 (189)
.|...+|.+= ..|++.+..+-
T Consensus 71 v~D~~yn~~~Wv~~V~~~V~~~~ 93 (179)
T cd02168 71 LRDHLYNDNLWVADVQQKVLAIA 93 (179)
T ss_pred CCCCCCCHHHHHHHHHHHCCCCC
T ss_conf 88888887999999999576113
No 43
>cd06063 H2MP_Cyano-H2up This group of endopeptidases include HupW enzymes that are specific to the cyanobacterial hydrogenase and are involved in the C-terminal cleavage of the hydrogenase large subunit precursor protein. Cyanobacterial nickel-iron (NiFe)-hydrogenases are found exclusively in the N2-fixing strains and are encoded by hup (hydrogen uptake) genes. These uptake hydrogenases are heterodimers with a large (hupL) and small subunit (hupS) and catalyze the consumption of the H2 produced during N2 fixation. Sequence similarity shows that the putative metal-binding resides are well conserved in this group of hydrogen maturation proteases. This group also includes such proteins as the hydrogenase III from Aquifex aeolicus.
Probab=21.50 E-value=39 Score=15.52 Aligned_cols=126 Identities=17% Similarity=0.244 Sum_probs=59.3
Q ss_pred EEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCEEEEEEECCCHHHHCCHHHHHHHHCCCC
Q ss_conf 89998587873660674104899999999982798544432127885147974899982334020033799999940575
Q gi|254780225|r 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQSLLEVMNFYKL 81 (189)
Q Consensus 2 ~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~l~kP~tyMN~SG~sv~~~~~~~~i 81 (189)
.+|+|+|||= ..=--+|-.+++.|++. ..+ ..|.++---| .| ..++.+.
T Consensus 1 ilVlGiGN~l----~gDDGvG~~vv~~L~~~-~~p-----------------~~v~~id~gt----~g---~~ll~~~-- 49 (146)
T cd06063 1 LTIIGCGNLN----RGDDGVGPILIRRLQAY-LLP-----------------PHVRLVDCGT----AG---MEVMFRA-- 49 (146)
T ss_pred CEEEEECCCC----CCCCCHHHHHHHHHHCC-CCC-----------------CCEEEEECCC----CH---HHHHHHH--
T ss_conf 9999978600----16381899999998613-799-----------------9859998888----36---8888643--
Q ss_pred CCCCCEEEEEE--CCCCCCCCEEEEC--------CCCCCCCC-HHHHHHH----CCCCCEE-EEEE-CCCCCCCCCCCCC
Q ss_conf 66333489840--4432338236611--------15888731-0333331----0687313-6675-0689877670242
Q gi|254780225|r 82 PNLENYLVIHD--DLDLDFGTLRLKT--------GGGDAGHN-GLKSISE----KCGKNYK-RLRI-GIGRPPDTAHIIR 144 (189)
Q Consensus 82 ~~~~~ilVihD--dldL~~G~irlk~--------~Gg~gGHN-GlksI~~----~lg~~f~-RlRI-GIG~P~~~~~v~~ 144 (189)
...+.+ ++-| +.+.++|+++.-. ..+..-|. |+.+... .++..++ ++.+ ||- | ... +
T Consensus 50 ~~~~~v-IiVDAv~~g~~PGti~~~~~~~l~~~~~~~~s~H~~~l~~~L~~~~~~l~~~~P~~i~i~gIe-~-~~~---~ 123 (146)
T cd06063 50 RGAKQL-IIIDASSTGSEPGAVFEVPGEELEALPEPSYNLHDFRWDHALAAGRKIFGDDFPKDVTVYLIE-A-KSL---D 123 (146)
T ss_pred CCCCEE-EEEEEECCCCCCCEEEEECHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEE-E-CCC---C
T ss_conf 378837-999985379999769996667741035677785527889999999998356899869999963-5-567---6
Q ss_pred CCCCCCCHHHHHHHHHHHHHH
Q ss_conf 437898889999999999999
Q gi|254780225|r 145 HVLGNFSSPERYFLLPIIDNI 165 (189)
Q Consensus 145 yVL~~f~~~E~~~i~~~i~~~ 165 (189)
|- ...|++=+..++++.+.+
T Consensus 124 ~g-~~LSp~V~~av~~~v~~I 143 (146)
T cd06063 124 FG-LELSPPVKQAAERVAEMI 143 (146)
T ss_pred CC-CCCCHHHHHHHHHHHHHH
T ss_conf 89-998999999899999999
No 44
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=21.25 E-value=55 Score=14.68 Aligned_cols=34 Identities=24% Similarity=0.415 Sum_probs=24.7
Q ss_pred EEECCCCCCCCEEEEC--CCCCCCCCHHHHHHHCCC-CC-EEEEEE
Q ss_conf 8404432338236611--158887310333331068-73-136675
Q gi|254780225|r 90 IHDDLDLDFGTLRLKT--GGGDAGHNGLKSISEKCG-KN-YKRLRI 131 (189)
Q Consensus 90 ihDdldL~~G~irlk~--~Gg~gGHNGlksI~~~lg-~~-f~RlRI 131 (189)
++.++++|.+.+++.. .+|+||+| .+ ++ =.||+.
T Consensus 101 ~~i~i~I~~~dl~idt~RASGaGGQh--------VNKt~SAVrlth 138 (239)
T COG1186 101 ISIEIEIPDDDLRIDTYRASGAGGQH--------VNKTDSAVRLTH 138 (239)
T ss_pred CCCCEECCCCCEEEEEEECCCCCCCC--------CCCCCCCEEEEE
T ss_conf 65310048521699988757999886--------555244289998
No 45
>pfam03418 Peptidase_A25 Germination protease.
Probab=21.00 E-value=50 Score=14.93 Aligned_cols=78 Identities=18% Similarity=0.289 Sum_probs=43.6
Q ss_pred EEEEECCCCCHHHHCCCCCHHHHHHHHHHHHHCC-CCCCCCCCEEEEEECCCC-EEEEEEEC----CCHHHHCCHHHHHH
Q ss_conf 8999858787366067410489999999998279-854443212788514797-48999823----34020033799999
Q gi|254780225|r 2 FIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFF-PAWKKKFHAEISEGQLDG-LRTILIKP----QTFMNLSGQSLLEV 75 (189)
Q Consensus 2 ~livGLGNPG~~y~~TRHNvG~~~ld~l~~~~~~-~~~~~k~~~~~~~~~~~~-~~v~l~kP----~tyMN~SG~sv~~~ 75 (189)
.|+|||||- .-|--..|=.+++.+.-...+ ........ ++ .+|--+-| +|-|- ++.-|+.+
T Consensus 99 vLVVGLGNw----nvTPDALGP~vv~~l~VTRHL~~~~pe~~~--------~g~r~VsaiaPGVmg~TGiE-T~eIi~gi 165 (355)
T pfam03418 99 CLIVGLGNL----NVTPDALGPKAVDNLLITRHLFELQPENVQ--------DGFRPVSAFAPGVMGITGIE-TSDIIFGV 165 (355)
T ss_pred EEEEECCCC----CCCCCCCCHHHHHCCHHHHHHHHHCCHHHC--------CCCCEEEEECCCCCCCCCCC-HHHHHHHH
T ss_conf 799966777----778755260200103010546664731222--------57504557757633154302-99999999
Q ss_pred HHCCCCCCCCCEEEEEECCCC
Q ss_conf 940575663334898404432
Q gi|254780225|r 76 MNFYKLPNLENYLVIHDDLDL 96 (189)
Q Consensus 76 ~~~~~i~~~~~ilVihDdldL 96 (189)
+...| | +++|+-|-|.-
T Consensus 166 v~~~k---P-d~vIaIDALAa 182 (355)
T pfam03418 166 IEKSK---P-DFIIAIDALAA 182 (355)
T ss_pred HHHCC---C-CEEEEEHHHHC
T ss_conf 85208---9-88999644230
Done!