Query 032491
Match_columns 139
No_of_seqs 103 out of 462
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 14:46:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032491.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032491hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1664 Vacuolar H+-ATPase V1 100.0 2E-37 4.3E-42 237.4 14.8 128 1-139 92-219 (220)
2 PRK03963 V-type ATP synthase s 99.9 2.4E-26 5.2E-31 176.4 14.0 113 1-135 86-198 (198)
3 PRK02292 V-type ATP synthase s 99.9 1.2E-23 2.7E-28 160.4 11.5 104 1-136 85-188 (188)
4 PF01991 vATP-synt_E: ATP synt 99.9 5.1E-25 1.1E-29 167.5 3.6 122 1-134 77-198 (198)
5 PRK01194 V-type ATP synthase s 99.8 3.4E-20 7.5E-25 142.0 10.6 98 1-136 85-182 (185)
6 COG1390 NtpE Archaeal/vacuolar 99.8 2.3E-19 5E-24 138.5 11.5 109 1-136 86-194 (194)
7 PRK01558 V-type ATP synthase s 99.5 7.3E-13 1.6E-17 102.4 12.6 96 15-133 100-195 (198)
8 PRK01005 V-type ATP synthase s 99.2 3.8E-10 8.2E-15 88.1 11.3 106 2-136 93-207 (207)
9 TIGR03825 FliH_bacil flagellar 98.9 1.1E-08 2.3E-13 81.8 9.9 91 20-130 158-249 (255)
10 PRK06937 type III secretion sy 98.9 1.3E-08 2.9E-13 78.7 9.4 89 20-128 113-202 (204)
11 PRK06328 type III secretion sy 98.9 2.5E-08 5.4E-13 78.6 10.0 92 20-131 114-206 (223)
12 PRK06669 fliH flagellar assemb 98.8 6.9E-08 1.5E-12 78.0 10.6 90 18-127 186-276 (281)
13 PRK13386 fliH flagellar assemb 98.8 5.8E-08 1.3E-12 77.1 9.1 86 20-135 144-231 (236)
14 PF02108 FliH: Flagellar assem 98.6 2.5E-07 5.4E-12 65.4 8.4 77 20-120 49-127 (128)
15 PRK05687 fliH flagellar assemb 98.6 4.6E-07 9.9E-12 71.8 9.8 85 19-127 156-242 (246)
16 PRK09098 type III secretion sy 98.5 1.2E-06 2.5E-11 69.6 10.1 88 21-129 133-223 (233)
17 COG1317 FliH Flagellar biosynt 98.5 1.2E-06 2.7E-11 69.5 9.7 90 19-130 138-229 (234)
18 PRK06032 fliH flagellar assemb 98.2 1.9E-05 4.1E-10 61.0 9.6 84 22-125 112-196 (199)
19 TIGR02499 HrpE_YscL_not type I 97.9 6E-05 1.3E-09 55.7 7.8 71 18-110 94-165 (166)
20 PF06635 NolV: Nodulation prot 96.8 0.019 4.1E-07 45.0 9.7 87 20-127 113-200 (207)
21 PRK13436 F0F1 ATP synthase sub 96.8 0.011 2.5E-07 44.8 8.3 31 94-126 148-178 (179)
22 PRK13430 F0F1 ATP synthase sub 96.7 0.021 4.5E-07 46.3 9.7 30 94-125 240-269 (271)
23 PRK13434 F0F1 ATP synthase sub 96.6 0.017 3.7E-07 43.9 8.5 31 94-126 144-174 (184)
24 PF06188 HrpE: HrpE/YscL/FliH 96.6 0.022 4.8E-07 43.9 9.0 85 2-112 99-183 (191)
25 TIGR03321 alt_F1F0_F0_B altern 96.4 0.076 1.6E-06 42.2 11.3 29 94-124 216-244 (246)
26 PRK13428 F0F1 ATP synthase sub 96.1 0.054 1.2E-06 46.7 9.3 61 43-125 382-443 (445)
27 PRK13441 F0F1 ATP synthase sub 95.0 0.26 5.7E-06 37.2 8.9 31 94-126 147-177 (180)
28 COG0712 AtpH F0F1-type ATP syn 95.0 0.097 2.1E-06 39.9 6.5 30 94-125 148-177 (178)
29 TIGR01145 ATP_synt_delta ATP s 92.9 1.2 2.5E-05 33.3 8.7 29 94-124 143-171 (172)
30 PRK13429 F0F1 ATP synthase sub 92.8 1.2 2.7E-05 33.3 8.8 30 94-125 148-177 (181)
31 PRK05758 F0F1 ATP synthase sub 92.4 1.4 3E-05 32.9 8.6 30 94-125 146-175 (177)
32 CHL00119 atpD ATP synthase CF1 90.6 3.1 6.8E-05 31.4 8.9 31 94-126 150-180 (184)
33 PF00213 OSCP: ATP synthase de 86.1 0.059 1.3E-06 40.1 -3.2 78 43-124 77-171 (172)
34 PRK08474 F0F1 ATP synthase sub 83.3 13 0.00029 27.8 8.6 30 96-129 143-172 (176)
35 KOG1662 Mitochondrial F1F0-ATP 78.4 6.7 0.00014 30.8 5.5 28 94-123 177-204 (210)
36 PF03927 NapD: NapD protein; 63.3 25 0.00055 23.1 5.0 19 38-56 7-25 (79)
37 KOG0066 eIF2-interacting prote 56.8 19 0.00041 32.2 4.4 15 96-110 751-765 (807)
38 PRK10553 assembly protein for 56.7 24 0.00052 23.8 4.1 19 38-56 9-27 (87)
39 PF04716 ETC_C1_NDUFA5: ETC co 56.5 43 0.00094 20.8 4.9 45 1-54 10-54 (57)
40 PHA03081 putative metalloprote 53.0 74 0.0016 28.5 7.4 82 21-122 149-234 (595)
41 PRK06418 transcription elongat 52.6 18 0.0004 27.4 3.3 57 18-75 101-165 (166)
42 COG0217 Uncharacterized conser 49.6 22 0.00048 28.6 3.4 39 20-58 150-190 (241)
43 PF03410 Peptidase_M44: Protei 49.3 2E+02 0.0043 25.9 9.4 80 21-122 149-234 (590)
44 PF02697 DUF217: Uncharacteriz 43.0 92 0.002 20.2 6.2 55 3-62 8-67 (71)
45 TIGR03299 LGT_TIGR03299 phage/ 42.6 17 0.00038 30.1 1.9 20 99-118 135-165 (309)
46 PRK01379 cyaY frataxin-like pr 41.6 81 0.0017 22.0 4.9 12 18-29 5-16 (103)
47 PF08740 BCS1_N: BCS1 N termin 40.5 94 0.002 22.9 5.5 30 36-65 127-156 (187)
48 PF14164 YqzH: YqzH-like prote 36.0 72 0.0016 20.5 3.6 38 20-57 3-40 (64)
49 PRK12530 RNA polymerase sigma 35.8 36 0.00078 25.2 2.6 26 111-136 164-189 (189)
50 PTZ00389 40S ribosomal protein 34.4 51 0.0011 25.5 3.2 59 17-76 115-181 (184)
51 PF07960 CBP4: CBP4; InterPro 34.1 35 0.00076 24.9 2.2 47 18-64 4-50 (128)
52 COG3882 FkbH Predicted enzyme 33.3 1.2E+02 0.0026 27.3 5.6 39 94-132 232-270 (574)
53 PF09413 DUF2007: Domain of un 30.4 55 0.0012 20.1 2.4 20 39-58 46-65 (67)
54 PF01709 Transcrip_reg: Transc 29.4 57 0.0012 25.8 2.9 41 17-57 143-185 (234)
55 COG3426 Butyrate kinase [Energ 29.2 70 0.0015 26.9 3.4 22 94-115 183-206 (358)
56 PF09561 RE_HpaII: HpaII restr 28.0 51 0.0011 28.0 2.4 20 94-113 290-309 (355)
57 COG0112 GlyA Glycine/serine hy 26.6 91 0.002 27.1 3.7 69 41-138 176-259 (413)
58 PF06903 VirK: VirK protein; 26.2 99 0.0021 21.6 3.2 34 66-103 15-48 (100)
59 KOG4115 Dynein-associated prot 26.1 1E+02 0.0022 21.4 3.3 33 96-129 18-50 (97)
60 KOG3320 40S ribosomal protein 26.0 1.1E+02 0.0023 23.8 3.6 59 17-76 122-188 (192)
61 cd01274 AIDA-1b AIDA-1b Phosph 26.0 2.1E+02 0.0046 20.4 5.1 50 43-111 15-65 (127)
62 PF10944 DUF2630: Protein of u 25.7 1.1E+02 0.0025 20.5 3.3 26 113-138 40-65 (81)
63 PF12860 PAS_7: PAS fold 25.2 65 0.0014 21.4 2.2 20 94-113 3-22 (115)
64 PF14417 MEDS: MEDS: MEthanoge 25.1 2.9E+02 0.0063 20.5 6.0 44 12-57 25-69 (191)
65 PF14695 LINES_C: Lines C-term 24.9 56 0.0012 18.9 1.5 13 127-139 15-27 (39)
66 PF05164 ZapA: Cell division p 23.8 1.7E+02 0.0037 18.7 4.0 33 34-66 6-38 (89)
67 PRK00110 hypothetical protein; 23.7 73 0.0016 25.5 2.5 39 19-57 147-187 (245)
68 PRK12520 RNA polymerase sigma 23.6 93 0.002 22.8 3.0 29 111-139 161-189 (191)
69 PRK15354 type III secretion sy 23.2 3.9E+02 0.0084 21.3 7.0 47 19-77 135-181 (224)
70 PF09439 SRPRB: Signal recogni 21.6 1.7E+02 0.0037 22.3 4.1 31 19-49 95-125 (181)
71 PHA03065 Hypothetical protein; 21.5 5.6E+02 0.012 22.5 7.7 54 21-77 144-197 (438)
72 TIGR01033 DNA-binding regulato 21.2 94 0.002 24.7 2.7 39 19-57 149-189 (238)
73 PF06067 DUF932: Domain of unk 20.7 58 0.0013 25.4 1.4 13 106-118 85-97 (239)
74 PF15513 DUF4651: Domain of un 20.5 2.3E+02 0.005 18.0 3.8 10 94-103 35-44 (62)
No 1
>KOG1664 consensus Vacuolar H+-ATPase V1 sector, subunit E [Energy production and conversion]
Probab=100.00 E-value=2e-37 Score=237.41 Aligned_cols=128 Identities=49% Similarity=0.783 Sum_probs=124.1
Q ss_pred CHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccC
Q 032491 1 MMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIY 80 (139)
Q Consensus 1 l~~~a~~~L~~~~~~~~~Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~ 80 (139)
||++|+++|...+.|++.|+.+|.+||.||+.+|.+|+++||||++|.++|+.++++|..+|....|. .+++.+|++.|
T Consensus 92 i~~ea~k~Ls~i~~~~~~Y~~lL~~LivQ~Ll~L~Ep~~Ivrcre~D~~lVe~~~~~a~~~y~~ka~~-~~e~~id~~~f 170 (220)
T KOG1664|consen 92 ILDEAKKRLSKVSKDTDRYKKLLKDLIVQGLLQLLEPEVIVRCREKDLKLVEAALPKAIEEYKEKAGV-GVEVQIDKKDF 170 (220)
T ss_pred HHHHHHHHHhcccCChHHHHHHHHHHHHHHHHHhCCCeeEEeehhhhhHHHHHHHHHHHHHHHHHhcC-Cceeeechhcc
Confidence 58999999999999999999999999999999999999999999999999999999999999999998 49999999999
Q ss_pred CCCCCCCCCCCCCCccceEEEEecCCcEEEcccHHHHHHHHHHhhhHHHHHHhcCCCCC
Q 032491 81 LPPGPGHHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLVSQVAA 139 (139)
Q Consensus 81 L~~~~~~~~~~~~~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~~LFg~~~~ 139 (139)
||+ +|+|||+++|.||+|+|+|||++||+.++++++|+||+.|||.++.
T Consensus 171 L~~----------~~~GGVvl~s~dgkI~v~NTLesRLeli~~q~lPeIR~aLFG~n~n 219 (220)
T KOG1664|consen 171 LPP----------DVAGGVVLYSRDGKIKVSNTLESRLELIAEQKLPEIRKALFGANPN 219 (220)
T ss_pred CCc----------cccCCeEEEcCCCceEecCcHHHHHHHHHHHhhHHHHHHhcCCCCC
Confidence 987 9999999999999999999999999999999999999999999873
No 2
>PRK03963 V-type ATP synthase subunit E; Provisional
Probab=99.94 E-value=2.4e-26 Score=176.37 Aligned_cols=113 Identities=30% Similarity=0.481 Sum_probs=100.2
Q ss_pred CHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccC
Q 032491 1 MMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIY 80 (139)
Q Consensus 1 l~~~a~~~L~~~~~~~~~Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~ 80 (139)
+|++|+++|.+++.+ .|+++|.+||.+|+..+++++++|+|+|.|..++++.++++.+. +| ++++.+++
T Consensus 86 v~~~a~~~l~~~~~~--~Y~~~l~~li~~a~~~l~~~~i~i~~~~~D~~~~~~~~~~~~~~----~~--~~~i~~~~--- 154 (198)
T PRK03963 86 VLEAVRERLAELPED--EYFETLKALTKEAVEELGEDKVVVRSNERTLKLIDSRLEEIRDE----LG--DVEIELGE--- 154 (198)
T ss_pred HHHHHHHHHHhhhhh--hHHHHHHHHHHHHHHHhCCCcEEEEEccccHHHHHHHHHHHHHH----hC--CeEEEECC---
Confidence 588999999999765 89999999999999999999999999999999999988876543 33 35666652
Q ss_pred CCCCCCCCCCCCCCccceEEEEecCCcEEEcccHHHHHHHHHHhhhHHHHHHhcC
Q 032491 81 LPPGPGHHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLVS 135 (139)
Q Consensus 81 L~~~~~~~~~~~~~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~~LFg 135 (139)
| .+|.|||||+|++|+|+|||||++||+.+++.++|+|++.|||
T Consensus 155 ----~-------~~~~GGvil~s~~g~i~~dnT~e~~l~~~~~~~~~~i~~~LF~ 198 (198)
T PRK03963 155 ----P-------IETIGGVIVETKDGTIRVDNTFEARMERLESELRAKIAKALFG 198 (198)
T ss_pred ----C-------CCccceEEEEeCCCCEEEeCcHHHHHHHHHHHhHHHHHHHhcC
Confidence 1 3889999999999999999999999999999999999999997
No 3
>PRK02292 V-type ATP synthase subunit E; Provisional
Probab=99.90 E-value=1.2e-23 Score=160.44 Aligned_cols=104 Identities=32% Similarity=0.484 Sum_probs=89.7
Q ss_pred CHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccC
Q 032491 1 MMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIY 80 (139)
Q Consensus 1 l~~~a~~~L~~~~~~~~~Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~ 80 (139)
+|++|+++|.+++++ .|+.+|.+||.++ .+++++|+|+|.|..+++.++.++ . + +++ .
T Consensus 85 v~~~a~~kL~~~~~~--~y~~~l~~li~~~----~~~~~~i~~~~~D~~~~~~~~~~~----~---~---~~~--~---- 142 (188)
T PRK02292 85 VRNQVEDEIASLDGD--KREELTKSLLDAA----DADGVRVYSRKDDEDLVKSLLSDY----D---G---LEY--A---- 142 (188)
T ss_pred HHHHHHHHHHhcchh--hHHHHHHHHHHhc----CCCCeEEEEccccHHHHHHHHHhc----c---c---Cee--C----
Confidence 589999999999754 8999999999999 578899999999999999887653 1 1 111 1
Q ss_pred CCCCCCCCCCCCCCccceEEEEecCCcEEEcccHHHHHHHHHHhhhHHHHHHhcCC
Q 032491 81 LPPGPGHHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLVSQ 136 (139)
Q Consensus 81 L~~~~~~~~~~~~~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~~LFg~ 136 (139)
++ .+|.|||||++++|+|+|||||++||+.++++++|+|+++|||.
T Consensus 143 --~~--------~~~~GGvil~~~~g~I~~dnT~~~rl~~~~~~~~~~i~~~LF~~ 188 (188)
T PRK02292 143 --GN--------IDCLGGVVVESEDGRVRVNNTFDSILEDVWEDNLKEISDRLFGE 188 (188)
T ss_pred --CC--------CCCCceEEEEecCCceEEeccHHHHHHHHHHHhhHHHHHHhcCC
Confidence 11 27899999999999999999999999999999999999999984
No 4
>PF01991 vATP-synt_E: ATP synthase (E/31 kDa) subunit; InterPro: IPR002842 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 (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit E from the V1 and A1 complexes of V- and A-ATPases, respectively. Subunit E appears to form a tight interaction with subunit G in the F0 complex, which together may act as stators to prevent certain subunits from rotating with the central rotary element, much in the same way as the F0 complex subunit B does in F-ATPases []. In addition to its key role in stator structure, subunit E appears to have a role in mediating interactions with putative regulatory subunits []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 3LG8_A 2KK7_A 4DT0_A 2DM9_A 2DMA_A 3V6I_A 3K5B_A 3J0J_L 2KZ9_A.
Probab=99.90 E-value=5.1e-25 Score=167.50 Aligned_cols=122 Identities=34% Similarity=0.506 Sum_probs=103.7
Q ss_pred CHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccC
Q 032491 1 MMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIY 80 (139)
Q Consensus 1 l~~~a~~~L~~~~~~~~~Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~ 80 (139)
+|++++++|.+++++++.|+++|.+||.+++..+++++++|+|++.|.++++++++.+...|+...|...+....+. .+
T Consensus 77 v~~~~~~~L~~~~~~~~~Y~~~L~~li~~~~~~~~~~~~~v~~~~~D~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~-~~ 155 (198)
T PF01991_consen 77 VFEEVKEKLKSFSKDPDDYKKFLKKLIEEAAEKLGEGEVIVYVNKKDLELVKEILKRIKKELKSKAGKDSVEVSVDS-DY 155 (198)
T ss_dssp HHHHHHHHHHCTTCCC-THHHHHHHHHHHHHHCCTTSCEEEEECCHHHHCCHCCHCCCCCCHCCCSSTTTEEEEE-T---
T ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHhcCCceEEecccchHHHHHHHHHHHHHHHHHHhCCCcceeecCc-cc
Confidence 47899999999998866899999999999999999999999999999999999887776677655554334444443 23
Q ss_pred CCCCCCCCCCCCCCccceEEEEecCCcEEEcccHHHHHHHHHHhhhHHHHHHhc
Q 032491 81 LPPGPGHHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLV 134 (139)
Q Consensus 81 L~~~~~~~~~~~~~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~~LF 134 (139)
+ .+|.|||+++++||+|+|||||++||+.+++.+.|+|+++||
T Consensus 156 ~-----------~~~~GG~il~~~dg~i~vd~T~e~~l~~~~~~~~~~i~~~LF 198 (198)
T PF01991_consen 156 L-----------IDIIGGFILESEDGKIRVDNTFESRLERLKEEIRPEIAKILF 198 (198)
T ss_dssp ------------BSSSSEEEEECSSSSCEEEEEHHHHHHHCHHHHHHHHHHHHC
T ss_pred c-----------CCccceEEEEECCCCEEEECCHHHHHHHHHHHhHHHHHHHcC
Confidence 2 288999999999999999999999999999999999999999
No 5
>PRK01194 V-type ATP synthase subunit E; Provisional
Probab=99.83 E-value=3.4e-20 Score=142.01 Aligned_cols=98 Identities=16% Similarity=0.352 Sum_probs=83.7
Q ss_pred CHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccC
Q 032491 1 MMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIY 80 (139)
Q Consensus 1 l~~~a~~~L~~~~~~~~~Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~ 80 (139)
+|+.|.++|.++++++ +|+++|++||.+|+.. .+++++|+|+++|.++++.. +++ +
T Consensus 85 v~~~a~e~L~~l~~~~-~Y~~~L~~LI~~a~~~-l~~~~~v~~~~~D~~~i~~~-----------------~l~-----~ 140 (185)
T PRK01194 85 YLDIAYEHLMNITKSK-EYDSILNKMIEVAIKT-LGEDCIIKVSESDKKKINNA-----------------KIK-----F 140 (185)
T ss_pred HHHHHHHHHHcccCCc-hHHHHHHHHHHHHHHh-cCCCeEEEEcHHhHHHHHhC-----------------cee-----e
Confidence 5889999999998765 8999999999999999 56889999999999988752 222 1
Q ss_pred CCCCCCCCCCCCCCccceEEEEecCCcEEEcccHHHHHHHHHHhhhHHHHHHhcCC
Q 032491 81 LPPGPGHHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLVSQ 136 (139)
Q Consensus 81 L~~~~~~~~~~~~~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~~LFg~ 136 (139)
++ .+|.|||||+|.+|+|++||||++.+ ++++|+||..||..
T Consensus 141 ~~----------~~~~GGvil~s~dG~I~ld~~l~~~~----~~~~~~iR~~lf~~ 182 (185)
T PRK01194 141 AD----------IDPYGGILAYSRDGKRELDLRLSSIF----ENILEDLKVYFYEN 182 (185)
T ss_pred CC----------ccccccEEEEeCCCcEEehhhHHHHH----HHhHHHHHHHHHhh
Confidence 21 28999999999999999888888865 89999999999964
No 6
>COG1390 NtpE Archaeal/vacuolar-type H+-ATPase subunit E [Energy production and conversion]
Probab=99.81 E-value=2.3e-19 Score=138.49 Aligned_cols=109 Identities=33% Similarity=0.534 Sum_probs=92.4
Q ss_pred CHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccC
Q 032491 1 MMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIY 80 (139)
Q Consensus 1 l~~~a~~~L~~~~~~~~~Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~ 80 (139)
+|+.+.++|.++.+++ +|.. |..|+.+++..+.+++++|++++.|..++..++.+.. +...+.
T Consensus 86 ~~~~~~e~L~~i~~~~-~~~~-l~~ll~~~~~~~~~~~~iV~~~e~d~~~v~~~~~~~~-----------~~~~~~---- 148 (194)
T COG1390 86 VFEAVEEKLRNIASDP-EYES-LQELLIEALEKLLGGELVVYLNEKDKALVEQILRELK-----------IGVELG---- 148 (194)
T ss_pred HHHHHHHHHHcCcCCc-chHH-HHHHHHHHHHhcCCCCeEEEeCcccHHHHHHHHhhcc-----------cchhcc----
Confidence 3788999999999886 5555 9999999999999999999999999999887766411 111121
Q ss_pred CCCCCCCCCCCCCCccceEEEEecCCcEEEcccHHHHHHHHHHhhhHHHHHHhcCC
Q 032491 81 LPPGPGHHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLVSQ 136 (139)
Q Consensus 81 L~~~~~~~~~~~~~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~~LFg~ 136 (139)
+ .++|.|||+++++||++++||||++||+++++.+.|.|++.|||.
T Consensus 149 --~--------~~d~~GGvvv~~~dG~i~~dnt~~sil~~~~e~~~~~i~~~lf~~ 194 (194)
T COG1390 149 --E--------GIDIIGGVVVESRDGKIRLDNTFESILERVLEELLPEISEKLFGV 194 (194)
T ss_pred --c--------cCCCcceEEEEeCCCceeecCcHHHHHHHHHHHHHHHHHHHHcCC
Confidence 1 138999999999999999999999999999999999999999984
No 7
>PRK01558 V-type ATP synthase subunit E; Provisional
Probab=99.48 E-value=7.3e-13 Score=102.43 Aligned_cols=96 Identities=20% Similarity=0.289 Sum_probs=77.8
Q ss_pred ChhhHHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCC
Q 032491 15 DHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPS 94 (139)
Q Consensus 15 ~~~~Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~ 94 (139)
+++.|..++..|+.... .++++.|+.++.|...+.+.+.. .+++.++. . +++.. + .+
T Consensus 100 ~~e~~~~li~~ll~~~~---~~~~~~I~~~~~D~~~l~~~~~~---~~~~~l~~-g--i~i~~------~--------~~ 156 (198)
T PRK01558 100 DSNFLRELIIRVVDSWV---KGDKLEIILNESDLSELESILRA---ALGNKLKK-G--IELKP------F--------KG 156 (198)
T ss_pred CHHHHHHHHHHHHHHhc---CCCCeeEEECHHHHHHhHHHHHH---HHHHHhcC-C--eEEcc------c--------CC
Confidence 66789999999999864 56788999999999998877543 33444432 2 33431 1 38
Q ss_pred ccceEEEEecCCcEEEcccHHHHHHHHHHhhhHHHHHHh
Q 032491 95 CSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQL 133 (139)
Q Consensus 95 ~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~~L 133 (139)
|.|||+|.+.||.+.+||||+++++.+.+.+-|.++++|
T Consensus 157 ~~gG~iv~~~dg~i~id~T~ea~~~~l~~~L~~~~~~~l 195 (198)
T PRK01558 157 ISKGFKIQQKDGSLYYDFSAEAIADILFSYLNPRFKEVI 195 (198)
T ss_pred cccceEEEEcCCCeEEeCcHHHHHHHHHHHhcHHHHHHH
Confidence 999999999999999999999999999999999999987
No 8
>PRK01005 V-type ATP synthase subunit E; Provisional
Probab=99.17 E-value=3.8e-10 Score=88.08 Aligned_cols=106 Identities=12% Similarity=0.126 Sum_probs=69.3
Q ss_pred HHHHHHHHHhh-ccChhhHHHHHHHHHHHHHHHhCCC--------cEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCe
Q 032491 2 MEAASKEVLNV-SRDHNSYKKLLKGLIVQSLLRLKEP--------AVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPE 72 (139)
Q Consensus 2 ~~~a~~~L~~~-~~~~~~Y~~~L~~LI~qa~~~l~e~--------~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~ 72 (139)
|..+.++|-+- ..| +++|..||..-+...... -+...++|++.+.. +...+.+... .. .
T Consensus 93 f~~a~~~lv~~~~~d----~~~l~~lI~~~v~~~~~~~~~~~~~~~i~~~~~~~~~~~~--~~~~~~~~l~---~~-g-- 160 (207)
T PRK01005 93 FRESLGEWLEHVLTD----PEVSAKLIQALVQAIEAQGISGNLTAYIGKHVSARAVNEL--LGKEVTKKLK---EK-G-- 160 (207)
T ss_pred HHHHHHHHHHHHhcC----HHHHHHHHHHHHHHHhhcccccccchhhhhcCCHHHHHHH--HHHHHHHHHH---Hc-C--
Confidence 45555555443 333 467777777666655322 23345666665543 2222222222 11 2
Q ss_pred EEeccccCCCCCCCCCCCCCCCccceEEEEecCCcEEEcccHHHHHHHHHHhhhHHHHHHhcCC
Q 032491 73 IIVDHHIYLPPGPGHHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLVSQ 136 (139)
Q Consensus 73 i~vd~~~~L~~~~~~~~~~~~~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~~LFg~ 136 (139)
+++.. ..|||+|.+.||++++|||++++++.+++.++|.+|.+|||+
T Consensus 161 v~~~~-----------------~~gG~~v~~~dg~~~vd~t~d~i~~~~~~~l~~~~~~~LF~~ 207 (207)
T PRK01005 161 VSVGS-----------------FVGGAQLKVEEKNWVLDLSSQTLLDLLTRYLQKDFREMIFQG 207 (207)
T ss_pred eEEec-----------------cCCceEEEecCCeeEEeCcHHHHHHHHHHHhhHHHHHHhcCC
Confidence 34431 159999999999999999999999999999999999999984
No 9
>TIGR03825 FliH_bacil flagellar assembly protein FliH. This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes.
Probab=98.91 E-value=1.1e-08 Score=81.77 Aligned_cols=91 Identities=18% Similarity=0.208 Sum_probs=72.0
Q ss_pred HHHHHHHHHHHHHHhCCC-cEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCccce
Q 032491 20 KKLLKGLIVQSLLRLKEP-AVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCSGG 98 (139)
Q Consensus 20 ~~~L~~LI~qa~~~l~e~-~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~GG 98 (139)
+..+..||.+++..+.+. .++|+|+|.|++.+....+.+...+... ..+.|..|+ . -..||
T Consensus 158 ~e~i~~lv~~al~~l~~~~~i~I~v~p~d~~~v~~~~~~l~~~~~~~---~~i~i~~D~--~-------------l~~Gg 219 (255)
T TIGR03825 158 KNAFQALVRQVLSEVREFDEVSIYVHPHWYERVAAQKDELQSILPAC---EHLAVYPDE--K-------------LPDGG 219 (255)
T ss_pred HHHHHHHHHHHHHhccCCCcEEEEECHHHHHHHHHhHHHHHhhcCCC---CceEEEeCC--C-------------CCCCC
Confidence 346789999999999774 8999999999999998877665544322 235666664 2 34599
Q ss_pred EEEEecCCcEEEcccHHHHHHHHHHhhhHHHH
Q 032491 99 VVVASRDGKIVCENTLDARLDVVFRKKLPEIR 130 (139)
Q Consensus 99 Vvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir 130 (139)
++|.+.+|. +|+|+++||+.+++.++-.+.
T Consensus 220 cvIEt~~G~--iDasldtqLe~l~~~l~~~l~ 249 (255)
T TIGR03825 220 CYVETNFGR--IDASVDTQLEQLKEKLLEALK 249 (255)
T ss_pred eEEEcCCce--EEeeHHHHHHHHHHHHHHHHh
Confidence 999999998 699999999999998887764
No 10
>PRK06937 type III secretion system protein; Reviewed
Probab=98.89 E-value=1.3e-08 Score=78.74 Aligned_cols=89 Identities=17% Similarity=0.285 Sum_probs=69.8
Q ss_pred HHHHHHHHHHHHHHhCCC-cEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCccce
Q 032491 20 KKLLKGLIVQSLLRLKEP-AVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCSGG 98 (139)
Q Consensus 20 ~~~L~~LI~qa~~~l~e~-~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~GG 98 (139)
++++..++.+++..+.+. .++|+++|.|.+.+++.+.+....+.+ ...+.|..|+ .| ..||
T Consensus 113 ~e~i~~lv~~al~~l~~~~~v~I~V~P~D~~~v~~~~~~~~~~~~~---~~~l~i~~D~--~L-------------~~Gg 174 (204)
T PRK06937 113 VERTLQVVREALALVSNQKQVVVRVNPDQAAAVREQIAKVLKDFPE---VGYLEVVADA--RL-------------DQGG 174 (204)
T ss_pred HHHHHHHHHHHHHhcccCCeEEEEECHHHHHHHHHHHHHHHHhCCC---CccEEEEeCC--CC-------------CCCC
Confidence 578889999999999764 899999999999999887765554432 1135666664 33 3599
Q ss_pred EEEEecCCcEEEcccHHHHHHHHHHhhhHH
Q 032491 99 VVVASRDGKIVCENTLDARLDVVFRKKLPE 128 (139)
Q Consensus 99 Vvv~s~dG~I~vdNTle~RL~~~~~~~lp~ 128 (139)
++|.+..|. +|+|+++||+.+.+.+...
T Consensus 175 c~iET~~G~--vDasl~tql~~l~~al~~~ 202 (204)
T PRK06937 175 CILETEVGI--IDASLDGQLEALEQAFHST 202 (204)
T ss_pred eEEecCCce--EEccHHHHHHHHHHHHHHH
Confidence 999999998 6999999999888776543
No 11
>PRK06328 type III secretion system protein; Validated
Probab=98.86 E-value=2.5e-08 Score=78.58 Aligned_cols=92 Identities=17% Similarity=0.256 Sum_probs=71.3
Q ss_pred HHHHHHHHHHHHHHhCCC-cEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCccce
Q 032491 20 KKLLKGLIVQSLLRLKEP-AVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCSGG 98 (139)
Q Consensus 20 ~~~L~~LI~qa~~~l~e~-~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~GG 98 (139)
++.+..++.+|+..+.+. .++|+|+|.|.+.|+...+++...+... ..+.|..|+ .|+ .||
T Consensus 114 ~e~il~lV~~aL~~l~~~~~v~I~VnP~D~~~v~~~~~~l~~~~~~~---~~~~I~~D~--~L~-------------~Gg 175 (223)
T PRK06328 114 PETIVSIIANSLKELTQHKRIIIHVNPKDLAIVEKSRPELKKIVEYA---DSLIISPKA--DVT-------------PGG 175 (223)
T ss_pred HHHHHHHHHHHHHhcccCCceEEEECHHHHHHHHHHHHHHHHhccCC---CceEEEeCC--CCC-------------CCC
Confidence 467779999999988654 8999999999999998777665544432 246777774 343 499
Q ss_pred EEEEecCCcEEEcccHHHHHHHHHHhhhHHHHH
Q 032491 99 VVVASRDGKIVCENTLDARLDVVFRKKLPEIRK 131 (139)
Q Consensus 99 Vvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~ 131 (139)
++|.+..|.| |.|+++||+.+.+.+.-.++.
T Consensus 176 CiIET~~G~V--Dasle~ql~~l~~al~~~l~~ 206 (223)
T PRK06328 176 CIIETEAGII--NAQLDVQLAALEKAFSTILKH 206 (223)
T ss_pred eEEEeCCceE--EecHHHHHHHHHHHHHHHHcc
Confidence 9999999985 999999998888776555543
No 12
>PRK06669 fliH flagellar assembly protein H; Validated
Probab=98.78 E-value=6.9e-08 Score=77.98 Aligned_cols=90 Identities=19% Similarity=0.278 Sum_probs=71.9
Q ss_pred hHHHHHHHHHHHHHHHhCC-CcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCcc
Q 032491 18 SYKKLLKGLIVQSLLRLKE-PAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCS 96 (139)
Q Consensus 18 ~Y~~~L~~LI~qa~~~l~e-~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~ 96 (139)
..+.++..+|.+++..+.+ +.++|+++|.|+++++....++...+... ..+.|..|+ . -..
T Consensus 186 ~~~~~i~~li~~al~~l~~~~~i~I~V~p~d~~~l~~~~~~l~~~l~~~---~~i~I~~D~--~-------------l~~ 247 (281)
T PRK06669 186 NSKEIALALVKELLKEVKDATDITIRVNPEDYEYVKEQKDELISLLDNE---EHLKIYEDD--A-------------ISK 247 (281)
T ss_pred cCHHHHHHHHHHHHHHcCcCCcEEEEECHHHHHHHHHhHHHHHHhcCCC---CCeEEEECC--C-------------CCC
Confidence 3678889999999999876 48999999999999999888776554432 246666664 2 334
Q ss_pred ceEEEEecCCcEEEcccHHHHHHHHHHhhhH
Q 032491 97 GGVVVASRDGKIVCENTLDARLDVVFRKKLP 127 (139)
Q Consensus 97 GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp 127 (139)
|||+|.+.+|. +|+|+++||+++++.++.
T Consensus 248 GgcvIet~~G~--IDasi~tqLe~l~~~L~e 276 (281)
T PRK06669 248 GGCVIETDFGN--IDARIDTQLKQLKEKLLE 276 (281)
T ss_pred CCeEEEcCCCe--eeccHHHHHHHHHHHHHh
Confidence 99999999998 699999999998887654
No 13
>PRK13386 fliH flagellar assembly protein H; Provisional
Probab=98.75 E-value=5.8e-08 Score=77.06 Aligned_cols=86 Identities=13% Similarity=0.293 Sum_probs=64.9
Q ss_pred HHHHHHHHHHHHHHhCC--CcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCccc
Q 032491 20 KKLLKGLIVQSLLRLKE--PAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCSG 97 (139)
Q Consensus 20 ~~~L~~LI~qa~~~l~e--~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~G 97 (139)
++.+-.+|.+|+..+-. ..|+|+|||.|.+.+++..++. ...+++..|+ .|. .|
T Consensus 144 p~~il~~v~eaL~~lp~~~~~v~I~vnP~D~~~l~~~~~e~---------~~~~~l~~D~--~l~-------------~G 199 (236)
T PRK13386 144 PQQILALVEETLAALPDDPEQLKVHLNPEEFGRLKDLAPEK---------VQAWGLVADP--SLS-------------AG 199 (236)
T ss_pred HHHHHHHHHHHHHhccccCCCeEEEECHHHHHHHHHhhhcc---------ccCeEEEeCC--CcC-------------CC
Confidence 34577999999999843 5899999999999999776541 1146777774 332 49
Q ss_pred eEEEEecCCcEEEcccHHHHHHHHHHhhhHHHHHHhcC
Q 032491 98 GVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQLVS 135 (139)
Q Consensus 98 GVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~~LFg 135 (139)
|++|.+.+|.| |.|+++||+.+.+ .++..|.+
T Consensus 200 gC~Iet~~g~i--Da~ietRl~~~~~----~l~~~l~~ 231 (236)
T PRK13386 200 ECRIVTDTSEA--DAGCEHRLDACMD----AVKEHLLT 231 (236)
T ss_pred CEEEEeCCceE--eeCHHHHHHHHHH----HHHHhccc
Confidence 99999999985 9999999976655 44555544
No 14
>PF02108 FliH: Flagellar assembly protein FliH; InterPro: IPR018035 This entry represents a region found in the flagellar assembly protein FliH, as well as in type III secretion system protein HrpE. Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export []. The sequence of fliH has been deduced and shown to encode a protein of molecular mass of 25,782 Da. Bacterial HrpE proteins are belived to function on the type III secretion system, specifically the secretion of HrpZ (harpinPss) [].
Probab=98.63 E-value=2.5e-07 Score=65.43 Aligned_cols=77 Identities=25% Similarity=0.406 Sum_probs=58.6
Q ss_pred HHHHHHHHHHHH-HHhCCC-cEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCccc
Q 032491 20 KKLLKGLIVQSL-LRLKEP-AVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCSG 97 (139)
Q Consensus 20 ~~~L~~LI~qa~-~~l~e~-~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~G 97 (139)
+..+..+|.+++ ..+... .++|+++|.|.+.++..+.+....+ .+++..|+ .|+ .|
T Consensus 49 ~~~i~~~i~~al~~~~~~~~~v~I~v~p~d~~~l~~~~~~~~~~~-------~~~l~~D~--~l~-------------~G 106 (128)
T PF02108_consen 49 PEAILNLIREALQELPRDEEKVTIRVHPDDYEALEELLEDELPEL-------GWELVADP--SLA-------------PG 106 (128)
T ss_pred HHHHHHHHHHHHHHhhccCCCeEEEECHHHHHHHHHHHHHHHhhc-------CCEEEecC--CCC-------------CC
Confidence 467778899999 555444 8999999999999998877432211 34677774 333 49
Q ss_pred eEEEEecCCcEEEcccHHHHHHH
Q 032491 98 GVVVASRDGKIVCENTLDARLDV 120 (139)
Q Consensus 98 GVvv~s~dG~I~vdNTle~RL~~ 120 (139)
|+++.+++|.| |.|+++||+.
T Consensus 107 ~c~iet~~g~i--D~~i~~ql~~ 127 (128)
T PF02108_consen 107 DCRIETEDGII--DASIETQLEA 127 (128)
T ss_pred CEEEEECCeeE--EeCHHHHHhc
Confidence 99999999975 9999999974
No 15
>PRK05687 fliH flagellar assembly protein H; Validated
Probab=98.59 E-value=4.6e-07 Score=71.85 Aligned_cols=85 Identities=25% Similarity=0.323 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHHHHHhC--CCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCcc
Q 032491 19 YKKLLKGLIVQSLLRLK--EPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCS 96 (139)
Q Consensus 19 Y~~~L~~LI~qa~~~l~--e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~ 96 (139)
-++.+..+|.+++..+. .+.++|+|+|.|.++|+..+... .. .. .+.|..|+ .|+ .
T Consensus 156 ~~~~il~~v~~al~~lp~~~~~v~i~v~P~D~~~v~~~~~~~---~~-~~---~~~l~~D~--~l~-------------~ 213 (246)
T PRK05687 156 DPSAILAAIRELLQALPMFSGKPQLRVNPDDLELVEQLLGAE---LS-LH---GWRLLADP--SLH-------------R 213 (246)
T ss_pred CHHHHHHHHHHHHHhccccCCCceEEECHHHHHHHHHHHhhH---HH-hC---CeEEEeCC--CcC-------------C
Confidence 34577789999999873 46899999999999999887632 11 11 46777774 332 4
Q ss_pred ceEEEEecCCcEEEcccHHHHHHHHHHhhhH
Q 032491 97 GGVVVASRDGKIVCENTLDARLDVVFRKKLP 127 (139)
Q Consensus 97 GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp 127 (139)
||++|.+.+|. ||.|+++||+++++.+.+
T Consensus 214 Ggc~iet~~g~--vDa~l~~r~~~l~~~l~~ 242 (246)
T PRK05687 214 GGCRISAEEGD--VDASLETRWQEVCRLLAP 242 (246)
T ss_pred CCeEEEeCCCc--eeccHHHHHHHHHHHHhc
Confidence 99999999998 589999999999887754
No 16
>PRK09098 type III secretion system protein HrpB; Validated
Probab=98.51 E-value=1.2e-06 Score=69.57 Aligned_cols=88 Identities=20% Similarity=0.222 Sum_probs=63.8
Q ss_pred HHHHHHHHHHHHHh--CCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCC-CCCeEEeccccCCCCCCCCCCCCCCCccc
Q 032491 21 KLLKGLIVQSLLRL--KEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQV-HPPEIIVDHHIYLPPGPGHHNAHGPSCSG 97 (139)
Q Consensus 21 ~~L~~LI~qa~~~l--~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~-~~~~i~vd~~~~L~~~~~~~~~~~~~~~G 97 (139)
..|-..+.+++..+ +.+.++|+++|.|.+.+...+...... .|+ ..+.|..|+ .|+ .|
T Consensus 133 ~~ll~~v~~al~~~~~~~~~v~IrV~P~D~~~v~~~~~~~~~~----~g~~~~l~Iv~Dp--~L~-------------~G 193 (233)
T PRK09098 133 AALFARAAQTLERVVDGASYLTVRVHPADLDAARAAFGAAAAA----GGRNVPVEVVGDP--RLA-------------PG 193 (233)
T ss_pred HHHHHHHHHHHHHHhccCCcEEEEECHHHHHHHHHHHHHHHHh----cCCCcceEEEeCC--CCC-------------CC
Confidence 34556677888665 345899999999999999877765433 222 135566664 443 49
Q ss_pred eEEEEecCCcEEEcccHHHHHHHHHHhhhHHH
Q 032491 98 GVVVASRDGKIVCENTLDARLDVVFRKKLPEI 129 (139)
Q Consensus 98 GVvv~s~dG~I~vdNTle~RL~~~~~~~lp~I 129 (139)
|+++.+..|.| |.||++||+.+.+.+...+
T Consensus 194 gCviET~~G~I--Dasl~~ql~~L~~al~~~l 223 (233)
T PRK09098 194 ACVCEWDFGVF--DASLDTQLRALRRALARAL 223 (233)
T ss_pred CeEEEeCCCeE--ecCHHHHHHHHHHHHHHHh
Confidence 99999999985 9999999988877665443
No 17
>COG1317 FliH Flagellar biosynthesis/type III secretory pathway protein [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=98.49 E-value=1.2e-06 Score=69.46 Aligned_cols=90 Identities=23% Similarity=0.348 Sum_probs=68.9
Q ss_pred HHHHHHHHHHHHHHHhCCC--cEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCcc
Q 032491 19 YKKLLKGLIVQSLLRLKEP--AVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCS 96 (139)
Q Consensus 19 Y~~~L~~LI~qa~~~l~e~--~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~ 96 (139)
-++.|-.+|.|++..+... .++++|||.|++++....++..+. .++. +.|..|+ .+ ..
T Consensus 138 ~~~~ll~~v~e~L~~~~~~~~~i~l~VnP~d~e~i~~~~~~~~~~----~~~~-l~l~~D~--~l-------------~~ 197 (234)
T COG1317 138 DPEALLAAVREALEEVPLFAAAITLRVNPDDLEIIRQQLDEELSL----LGWR-LELVADP--AL-------------SP 197 (234)
T ss_pred CHHHHHHHHHHHHHhccccccCeEEEECHHHHHHHHHHHHHHHhh----cchh-eeeccCC--CC-------------CC
Confidence 3578888999999887544 799999999999999988755433 3331 2344442 32 35
Q ss_pred ceEEEEecCCcEEEcccHHHHHHHHHHhhhHHHH
Q 032491 97 GGVVVASRDGKIVCENTLDARLDVVFRKKLPEIR 130 (139)
Q Consensus 97 GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir 130 (139)
|||++++..|.| |-|+++||+.+.+.+.+..+
T Consensus 198 GgC~IeTe~G~i--Dasld~ql~~L~~~~~~~~~ 229 (234)
T COG1317 198 GGCIIETEFGII--DASLDTQLAALKRALLESLK 229 (234)
T ss_pred CCeEEEecCccc--cccHHHHHHHHHHHHHhhhc
Confidence 999999999986 99999999999998887653
No 18
>PRK06032 fliH flagellar assembly protein H; Validated
Probab=98.17 E-value=1.9e-05 Score=61.03 Aligned_cols=84 Identities=13% Similarity=0.079 Sum_probs=62.3
Q ss_pred HHHHHHHHHHHHhCCC-cEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCccceEE
Q 032491 22 LLKGLIVQSLLRLKEP-AVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCSGGVV 100 (139)
Q Consensus 22 ~L~~LI~qa~~~l~e~-~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~GGVv 100 (139)
.+..++.+++..+.+. +++|+++|.|.+.++..+++......- .+ .+.|..|+ .|+ .||++
T Consensus 112 ~v~~~v~eal~~l~~~~~v~I~v~P~d~~~l~~~l~~~~~~~~~-~~--~~~l~~D~--~L~-------------~G~c~ 173 (199)
T PRK06032 112 EITAAVRDCLRHLVATPHLVVRVNDALVEAARERLERLARESGF-EG--RLVVLADP--DMA-------------PGDCR 173 (199)
T ss_pred HHHHHHHHHHHHhcCCCcEEEEECHHHHHHHHHHHHHHHHhcCc-Cc--cEEEeeCC--CCC-------------CCCeE
Confidence 4778888888887664 699999999999999988776543221 11 35555553 443 49999
Q ss_pred EEecCCcEEEcccHHHHHHHHHHhh
Q 032491 101 VASRDGKIVCENTLDARLDVVFRKK 125 (139)
Q Consensus 101 v~s~dG~I~vdNTle~RL~~~~~~~ 125 (139)
|.+.+|.| |+|+++|+.++.+.+
T Consensus 174 vet~~G~v--d~d~~~~~~~I~~al 196 (199)
T PRK06032 174 LEWADGGV--VRDRAAIEARIEEAV 196 (199)
T ss_pred EEeCCCeE--ecCHHHHHHHHHHHh
Confidence 99999986 888999888776543
No 19
>TIGR02499 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family. This model is related to Pfam model pfam06188, but is broader. pfam06188 describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This model includes also the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This model excludes the related protein FliH of the bacterial flagellar apparatus (see pfam02108)
Probab=97.92 E-value=6e-05 Score=55.74 Aligned_cols=71 Identities=20% Similarity=0.172 Sum_probs=53.4
Q ss_pred hHHHHHHHHHHHHHHHhCC-CcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCcc
Q 032491 18 SYKKLLKGLIVQSLLRLKE-PAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCS 96 (139)
Q Consensus 18 ~Y~~~L~~LI~qa~~~l~e-~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~ 96 (139)
..++++..++.+++..+.+ +.++|+|+|.|.+.++..+.+.... . .+++..|+ . -..
T Consensus 94 ~~~e~l~~lv~~al~~~~~~~~v~I~v~P~d~~~l~~~l~~~~~~----~---~~~i~~D~--~-------------l~~ 151 (166)
T TIGR02499 94 DEPERLVRLLRQLLRAVANQGRLTLRVHPEQLDEVREALAERLAL----E---PWELEPDA--S-------------LAP 151 (166)
T ss_pred CCHHHHHHHHHHHHHhCCCCCceEEEECHHHHHHHHHHHHHHhcc----C---CeEEeeCC--C-------------CCC
Confidence 4568889999999998876 4999999999999999887754221 1 14555553 2 346
Q ss_pred ceEEEEecCCcEEE
Q 032491 97 GGVVVASRDGKIVC 110 (139)
Q Consensus 97 GGVvv~s~dG~I~v 110 (139)
||++|.+.+|.|-+
T Consensus 152 G~c~vet~~G~vda 165 (166)
T TIGR02499 152 GACVLETESGVVDL 165 (166)
T ss_pred CCEEEEeCCceeeC
Confidence 99999999998743
No 20
>PF06635 NolV: Nodulation protein NolV; InterPro: IPR010586 This family consists of several nodulation protein NolV sequences from different Rhizobium species []. The function of this family is unclear.; GO: 0009877 nodulation
Probab=96.77 E-value=0.019 Score=44.96 Aligned_cols=87 Identities=24% Similarity=0.279 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHHHHhCCC-cEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCccce
Q 032491 20 KKLLKGLIVQSLLRLKEP-AVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCSGG 98 (139)
Q Consensus 20 ~~~L~~LI~qa~~~l~e~-~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~GG 98 (139)
.++|.+.+.+++..+.+. .|+|++.|.|.+.+...+..+.. + .|...+.|..|+ .|++ |.
T Consensus 113 ~ell~r~vr~Al~~~~~~~~v~l~V~P~~vd~l~~~la~~~~-~---~g~~~i~I~aDp--~La~-------------~~ 173 (207)
T PF06635_consen 113 DELLVRAVRQALSQIRQGAEVTLRVAPADVDMLRRELAALEG-R---PGRPKIRIVADP--RLAA-------------GQ 173 (207)
T ss_pred HHHHHHHHHHHHHHHhcCCeEEEEECHHHHHHHHHHHHhhhc-c---CCCCceeeecCC--CCCC-------------CC
Confidence 467888888999988777 89999999999999988766522 2 233345666663 5543 88
Q ss_pred EEEEecCCcEEEcccHHHHHHHHHHhhhH
Q 032491 99 VVVASRDGKIVCENTLDARLDVVFRKKLP 127 (139)
Q Consensus 99 Vvv~s~dG~I~vdNTle~RL~~~~~~~lp 127 (139)
+|+.|+-|.| |=+|++-|.-+...+.|
T Consensus 174 Cvlese~G~V--dagL~aQL~ALr~a~~~ 200 (207)
T PF06635_consen 174 CVLESEFGVV--DAGLDAQLRALRLAFGP 200 (207)
T ss_pred eeeecccchh--hccHHHHHHHHHHHhcc
Confidence 9999999985 88999988877776654
No 21
>PRK13436 F0F1 ATP synthase subunit delta; Provisional
Probab=96.75 E-value=0.011 Score=44.76 Aligned_cols=31 Identities=19% Similarity=0.345 Sum_probs=27.0
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHhhh
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRKKL 126 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~l 126 (139)
+.+||+++.. |.-++|.|+.+||+++...+.
T Consensus 148 slIGGi~i~~--gd~viD~Sik~~L~~l~~~l~ 178 (179)
T PRK13436 148 KLIAGIKIKV--DNKVFENSIKSKLKELKKQVL 178 (179)
T ss_pred HHcCceEEEE--CCEEeehhHHHHHHHHHHHHh
Confidence 8899999998 667789999999999887654
No 22
>PRK13430 F0F1 ATP synthase subunit delta; Provisional
Probab=96.68 E-value=0.021 Score=46.27 Aligned_cols=30 Identities=30% Similarity=0.464 Sum_probs=26.7
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHhh
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRKK 125 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~ 125 (139)
+.+||++|.. |.-++|+|+.+||+++...+
T Consensus 240 sLIGGivI~v--Gd~viD~Sv~~rL~~L~~~L 269 (271)
T PRK13430 240 SVLGGMRVQV--GDEVIDGSVAGRLERLRRRL 269 (271)
T ss_pred cccCcEEEEE--CCEEEehhHHHHHHHHHHHh
Confidence 8899999999 66789999999999887765
No 23
>PRK13434 F0F1 ATP synthase subunit delta; Provisional
Probab=96.62 E-value=0.017 Score=43.90 Aligned_cols=31 Identities=23% Similarity=0.358 Sum_probs=27.7
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHhhh
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRKKL 126 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~l 126 (139)
+.+||+++.. |.-++|.|+.+||+++.+.+.
T Consensus 144 sLIGG~ii~i--gd~viD~Svk~~L~~l~~~l~ 174 (184)
T PRK13434 144 NLLGGFVVQF--NDLKIEKSIASQLGEIKKAML 174 (184)
T ss_pred HHcCceEEEE--CCEEEeHhHHHHHHHHHHHHH
Confidence 8899999999 667889999999999888774
No 24
>PF06188 HrpE: HrpE/YscL/FliH and V-type ATPase subunit E; InterPro: IPR009335 This family consists of several bacterial HrpE proteins, which are believed to function on the type III secretion system, specifically the secretion of HrpZ (harpinPss) []. This family also includes V-type proton ATPase subunit E proteins. This subunit appears to form a tight interaction with subunit G in the F0 complex. Subunits E and G may act together as stators to prevent certain subunits from rotating with the central rotary element []. PF01991 from PFAM also contains V-type ATPase subunit E proteins. There is an evolutionary link between type III secretion systems and membrane-associated proton translocating ATPases [].
Probab=96.59 E-value=0.022 Score=43.89 Aligned_cols=85 Identities=20% Similarity=0.314 Sum_probs=60.4
Q ss_pred HHHHHHHHHhhccChhhHHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCC
Q 032491 2 MEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYL 81 (139)
Q Consensus 2 ~~~a~~~L~~~~~~~~~Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L 81 (139)
+..|.++|-.-..++..+..+++.|+.+- ..+.+++++|+|.+.+.|...+.+-. ...+++..|+ .|
T Consensus 99 l~~al~~lL~e~~~~qrv~aLlr~l~~~~---~~~~~~tL~~hP~~~~~V~~~L~~~~--------~~~w~l~~D~--sl 165 (191)
T PF06188_consen 99 LSQALERLLDETPDQQRVAALLRQLLASQ---RQESEATLRCHPDQLEEVAAWLAEHP--------ALHWQLQADE--SL 165 (191)
T ss_pred HHHHHHHHHHcCCchHHHHHHHHHHHHhc---ccccceEEEECHHHHHHHHHHHHhCC--------CcceeeccCC--CC
Confidence 44555565554456667888888887553 45678999999999999998887521 1135666664 55
Q ss_pred CCCCCCCCCCCCCccceEEEEecCCcEEEcc
Q 032491 82 PPGPGHHNAHGPSCSGGVVVASRDGKIVCEN 112 (139)
Q Consensus 82 ~~~~~~~~~~~~~~~GGVvv~s~dG~I~vdN 112 (139)
++ |..++.+..|...+|.
T Consensus 166 ~~-------------~~l~L~t~~G~~~l~w 183 (191)
T PF06188_consen 166 AP-------------DQLKLETANGEFRLDW 183 (191)
T ss_pred CC-------------CceEEEcCCCcEEECH
Confidence 44 7899999999988773
No 25
>TIGR03321 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase.
Probab=96.41 E-value=0.076 Score=42.20 Aligned_cols=29 Identities=17% Similarity=0.255 Sum_probs=25.6
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHh
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRK 124 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~ 124 (139)
+.+||+++.. |..++|+|+.++|+.+...
T Consensus 216 ~ligGi~l~~--g~~~id~Si~~~L~~l~~~ 244 (246)
T TIGR03321 216 DLIGGIELTA--GGHKLAWSVDDYLESLEED 244 (246)
T ss_pred hhcCceEEEE--CCEEEechHHHHHHHHHhh
Confidence 8899999998 6778999999999887764
No 26
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=96.05 E-value=0.054 Score=46.75 Aligned_cols=61 Identities=21% Similarity=0.272 Sum_probs=41.0
Q ss_pred eccccHHHHHHHHHHHHHHHHHhhCCC-CCeEEeccccCCCCCCCCCCCCCCCccceEEEEecCCcEEEcccHHHHHHHH
Q 032491 43 CRKDDHHLVESVLESAKEEYAQKLQVH-PPEIIVDHHIYLPPGPGHHNAHGPSCSGGVVVASRDGKIVCENTLDARLDVV 121 (139)
Q Consensus 43 ~~~~D~~lv~~~l~~~~~~~~~~~~~~-~~~i~vd~~~~L~~~~~~~~~~~~~~~GGVvv~s~dG~I~vdNTle~RL~~~ 121 (139)
..|=+.+-.+.+...+.+.| |.+ .+++.|| ++.+||++|.- |..++|+|+.+||+.+
T Consensus 382 A~pLs~~q~~~L~~~L~k~~----g~~V~l~~~VD----------------psLiGGivI~v--Gd~viD~Sv~~rL~~l 439 (445)
T PRK13428 382 AAELSDAQRTRLTEVLSRIY----GRPVSVQLHID----------------PELLGGLSIAV--GDEVIDGTLSSRLAAA 439 (445)
T ss_pred ecCCCHHHHHHHHHHHHHHH----CCceEEEeeeC----------------chhhCceEEEE--CCEEeehhHHHHHHHH
Confidence 45555555555555444444 431 2334445 28899999998 7788999999999988
Q ss_pred HHhh
Q 032491 122 FRKK 125 (139)
Q Consensus 122 ~~~~ 125 (139)
...+
T Consensus 440 ~~~l 443 (445)
T PRK13428 440 EAQL 443 (445)
T ss_pred HhhC
Confidence 7653
No 27
>PRK13441 F0F1 ATP synthase subunit delta; Provisional
Probab=95.04 E-value=0.26 Score=37.17 Aligned_cols=31 Identities=29% Similarity=0.274 Sum_probs=27.2
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHhhh
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRKKL 126 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~l 126 (139)
+.+||+++.. |.-++|+|+.+||+.+...++
T Consensus 147 sliGG~~i~i--g~~~~D~Sik~~L~~l~~~l~ 177 (180)
T PRK13441 147 SLIAGAVVEF--EGKRLDVTVQGRLKKIAREVL 177 (180)
T ss_pred HHhCcEEEEE--CCEEEeHhHHHHHHHHHHHHh
Confidence 8899999998 557789999999999888775
No 28
>COG0712 AtpH F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]
Probab=95.01 E-value=0.097 Score=39.94 Aligned_cols=30 Identities=20% Similarity=0.411 Sum_probs=25.9
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHhh
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRKK 125 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~ 125 (139)
+.+||+++.. |.-++|+|+.++|+++...+
T Consensus 148 sliGG~iI~v--gd~viD~Svr~~L~~l~~~l 177 (178)
T COG0712 148 SLIGGLIIKV--GDEVIDGSVRGKLKRLAKAL 177 (178)
T ss_pred HHhCceEEEE--CCEEEechHHHHHHHHHHhc
Confidence 8899999999 66778999999999876653
No 29
>TIGR01145 ATP_synt_delta ATP synthase, F1 delta subunit. This model describes the ATP synthase delta subunit in bacteria, mitochondria, and chloroplasts. It is sometimes called OSCP for Oligomycin Sensitivity Conferring Protein. F1/F0-ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and organelles of higher eukaryotes, namely, mitochondria and chloroplast. This enzyme is principally involved in the synthesis of ATP from ADP and inorganic phosphate by coupling the energy derived from the proton electrochemical gradient across the biological membrane. A brief description of this multisubunit enzyme complex: F1 and F0 represent two major clusters of subunits. Delta subunit belongs to the F1 cluster or sector and functionally implicated in the overall stability of the complex. Expression of truncated forms of this subunit results in low ATPase activity.
Probab=92.91 E-value=1.2 Score=33.27 Aligned_cols=29 Identities=24% Similarity=0.465 Sum_probs=24.7
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHh
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRK 124 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~ 124 (139)
+.+||+++.. |..++|+|+.++|+.+...
T Consensus 143 ~ligGi~i~~--~~~~iD~Si~~~L~~l~~~ 171 (172)
T TIGR01145 143 DLIGGVIIRI--GDRVIDGSVRGQLKRLSRQ 171 (172)
T ss_pred HHhCceEEEE--CCEEEehhHHHHHHHHHhh
Confidence 7899999998 5577999999999887654
No 30
>PRK13429 F0F1 ATP synthase subunit delta; Provisional
Probab=92.84 E-value=1.2 Score=33.31 Aligned_cols=30 Identities=30% Similarity=0.369 Sum_probs=25.4
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHhh
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRKK 125 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~ 125 (139)
+.+||+++.. |.-++|+|+.++|+.+.+.+
T Consensus 148 sligG~~i~~--~~~~iD~Si~~~L~~l~~~l 177 (181)
T PRK13429 148 SLIGGVVVKI--GDKVLDASVRTQLRRLKETL 177 (181)
T ss_pred hhhCceEEEE--CCEEEehhHHHHHHHHHHHH
Confidence 7799999998 44678999999998887665
No 31
>PRK05758 F0F1 ATP synthase subunit delta; Validated
Probab=92.45 E-value=1.4 Score=32.92 Aligned_cols=30 Identities=23% Similarity=0.412 Sum_probs=25.7
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHhh
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRKK 125 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~ 125 (139)
+.+||+++.. |..++|+|+.++|+...+.+
T Consensus 146 ~ligG~~i~~--~~~~~d~Si~~~L~~l~~~l 175 (177)
T PRK05758 146 SLIGGVIIKV--GDRVIDGSVRGKLERLKDAL 175 (177)
T ss_pred HHhCceEEEE--CCEEeehhHHHHHHHHHHHh
Confidence 7799999998 44778999999998887765
No 32
>CHL00119 atpD ATP synthase CF1 delta subunit; Validated
Probab=90.56 E-value=3.1 Score=31.41 Aligned_cols=31 Identities=19% Similarity=0.309 Sum_probs=25.8
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHhhh
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRKKL 126 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~l 126 (139)
+.+||+++.. |..++|+|+.++|+...+.+.
T Consensus 150 ~ligGi~i~~--g~~~~D~Si~~~L~~l~~~l~ 180 (184)
T CHL00119 150 SLIGGFLIKI--GSKVIDTSIKGQLKQLASHLD 180 (184)
T ss_pred HHhCcEEEEE--CCEEEeHhHHHHHHHHHHHHH
Confidence 7799999998 557789999999988776553
No 33
>PF00213 OSCP: ATP synthase delta (OSCP) subunit; InterPro: IPR000711 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 (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which 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 family represents subunits called delta in bacterial and chloroplast ATPase, or OSCP (oligomycin sensitivity conferral protein) in mitochondrial ATPase (note that in mitochondria there is a different delta subunit, IPR001469 from INTERPRO). The OSCP/delta subunit appears to be part of the peripheral stalk that holds the F1 complex alpha3beta3 catalytic core stationary against the torque of the rotating central stalk, and links subunit A of the F0 complex with the F1 complex. In mitochondria, the peripheral stalk consists of OSCP, as well as F0 components F6, B and D. In bacteria and chloroplasts the peripheral stalks have different subunit compositions: delta and two copies of F0 component B (bacteria), or delta and F0 components B and B' (chloroplasts) [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0015986 ATP synthesis coupled proton transport; PDB: 2A7U_B 1ABV_A 2WSS_S 2BO5_A 2JMX_A.
Probab=86.09 E-value=0.059 Score=40.06 Aligned_cols=78 Identities=19% Similarity=0.291 Sum_probs=28.6
Q ss_pred eccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCC-----------------CCCCCCCccceEEEEecC
Q 032491 43 CRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGH-----------------HNAHGPSCSGGVVVASRD 105 (139)
Q Consensus 43 ~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~-----------------~~~~~~~~~GGVvv~s~d 105 (139)
+...-..++..++.++...|....|. ..++|-....|+++... ...-+++.+||+++..
T Consensus 77 ~~~~r~~~l~~i~~~~~~~~~~~~~~--~~~~V~sA~~l~~~q~~~l~~~l~~~~~~~~v~~~~~vD~sLigG~~i~~-- 152 (172)
T PF00213_consen 77 IDNNRLSLLPEILEEFEELVNEHNGI--VEATVTSAFPLSEEQKKKLEKKLKKKYGKKKVELNYKVDPSLIGGFIIEV-- 152 (172)
T ss_dssp CCTT-CCCHHHHHHHHHHHHHHHCCT--S-B-SSS-B----SSSTTTTTTCCCTTTT-----------------------
T ss_pred HhcCCcccHHHHHHHHHHHHHHHcCe--EEEEEEEecCCCHHHHHHHHHHHHHHHCCCeeeEEEEEccccCcEEEEEE--
Confidence 34444445566666666666555554 23333333344433311 0122468899999999
Q ss_pred CcEEEcccHHHHHHHHHHh
Q 032491 106 GKIVCENTLDARLDVVFRK 124 (139)
Q Consensus 106 G~I~vdNTle~RL~~~~~~ 124 (139)
|..++|.|+.+||+++...
T Consensus 153 ~~~~iD~Sv~~~L~~l~~~ 171 (172)
T PF00213_consen 153 GDKVIDASVKSRLEQLKKE 171 (172)
T ss_dssp ----TTTTTTTTTTTT-TT
T ss_pred CCEEEehhHHHHHHHHHhc
Confidence 6677899999999876554
No 34
>PRK08474 F0F1 ATP synthase subunit delta; Validated
Probab=83.27 E-value=13 Score=27.78 Aligned_cols=30 Identities=17% Similarity=0.119 Sum_probs=21.2
Q ss_pred cceEEEEecCCcEEEcccHHHHHHHHHHhhhHHH
Q 032491 96 SGGVVVASRDGKIVCENTLDARLDVVFRKKLPEI 129 (139)
Q Consensus 96 ~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~I 129 (139)
+||+++.. |..++|. ...|+++...+..-|
T Consensus 143 IGG~ii~i--gd~v~D~--s~~l~~~~~~~~~~~ 172 (176)
T PRK08474 143 YDGIKVEV--DDLGVEV--SFSKDRLKNQLIEYI 172 (176)
T ss_pred CCCEEEEE--CCEEEEe--eeeHHHHHHHHHHHH
Confidence 89999998 6677788 456666666555444
No 35
>KOG1662 consensus Mitochondrial F1F0-ATP synthase, subunit OSCP/ATP5 [Energy production and conversion]
Probab=78.45 E-value=6.7 Score=30.78 Aligned_cols=28 Identities=25% Similarity=0.455 Sum_probs=23.9
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHH
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFR 123 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~ 123 (139)
+++||.+|+. |.-.+|-+..+|++..-.
T Consensus 177 SI~GGliVei--GdK~vDmSI~tr~q~l~~ 204 (210)
T KOG1662|consen 177 SIIGGLIVEI--GDKYVDMSIKTRLQKLNK 204 (210)
T ss_pred hhhcceEEEE--cCeeEeeeHHHHHHHHHH
Confidence 8999999977 666789999999977654
No 36
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=63.26 E-value=25 Score=23.06 Aligned_cols=19 Identities=16% Similarity=0.309 Sum_probs=14.3
Q ss_pred cEEEEeccccHHHHHHHHH
Q 032491 38 AVLLRCRKDDHHLVESVLE 56 (139)
Q Consensus 38 ~v~V~~~~~D~~lv~~~l~ 56 (139)
.++|+|+|...+-|.+.+.
T Consensus 7 s~vV~~~p~~~~~v~~~l~ 25 (79)
T PF03927_consen 7 SLVVHARPERLEEVAEALA 25 (79)
T ss_dssp EEEEEE-CCCHHHHHHHHC
T ss_pred EEEEEECchhHHHHHHHHH
Confidence 4689999999888876653
No 37
>KOG0066 consensus eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis]
Probab=56.78 E-value=19 Score=32.22 Aligned_cols=15 Identities=33% Similarity=0.835 Sum_probs=12.7
Q ss_pred cceEEEEecCCcEEE
Q 032491 96 SGGVVVASRDGKIVC 110 (139)
Q Consensus 96 ~GGVvv~s~dG~I~v 110 (139)
-||||+.|+|-|+++
T Consensus 751 ~GgVi~VsHDeRLi~ 765 (807)
T KOG0066|consen 751 NGGVIMVSHDERLIV 765 (807)
T ss_pred cCcEEEEecccceee
Confidence 499999999998865
No 38
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=56.75 E-value=24 Score=23.84 Aligned_cols=19 Identities=5% Similarity=0.274 Sum_probs=15.5
Q ss_pred cEEEEeccccHHHHHHHHH
Q 032491 38 AVLLRCRKDDHHLVESVLE 56 (139)
Q Consensus 38 ~v~V~~~~~D~~lv~~~l~ 56 (139)
.++|+|+|+...-|...+.
T Consensus 9 SlVV~~~Pe~~~~V~~~l~ 27 (87)
T PRK10553 9 SLVVQAKSERISDISTQLN 27 (87)
T ss_pred EEEEEeChHHHHHHHHHHH
Confidence 4789999999888877654
No 39
>PF04716 ETC_C1_NDUFA5: ETC complex I subunit conserved region; InterPro: IPR006806 This is a family of eukaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC) (1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 29.9 kDa protein. The conserved region is found at the N terminus of the member proteins [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022904 respiratory electron transport chain, 0005743 mitochondrial inner membrane
Probab=56.48 E-value=43 Score=20.80 Aligned_cols=45 Identities=16% Similarity=0.331 Sum_probs=36.0
Q ss_pred CHHHHHHHHHhhccChhhHHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHH
Q 032491 1 MMEAASKEVLNVSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESV 54 (139)
Q Consensus 1 l~~~a~~~L~~~~~~~~~Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~ 54 (139)
+|....+.|..++++ ..|+.-.+.++.+=+..+.+ ..|.+.+++.
T Consensus 10 lY~~~L~~L~~~P~~-a~YR~~tE~it~~Rl~iv~~--------~~d~~~iE~~ 54 (57)
T PF04716_consen 10 LYNKTLKALKKIPED-AAYRQYTEAITKHRLKIVEE--------EEDIEKIEKK 54 (57)
T ss_pred HHHHHHHHHHhCCCc-cHHHHHHHHHHHHHHHHHHc--------cccHHHHHHH
Confidence 467788899999988 58999999999999988866 5566666654
No 40
>PHA03081 putative metalloprotease; Provisional
Probab=53.01 E-value=74 Score=28.52 Aligned_cols=82 Identities=15% Similarity=0.240 Sum_probs=51.7
Q ss_pred HHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCccceEE
Q 032491 21 KLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCSGGVV 100 (139)
Q Consensus 21 ~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~GGVv 100 (139)
+-+.+++..-|..|.+|.++|.++.-+...+.=+-. . .| .||.-|..--.+-..++||=+
T Consensus 149 ~~i~~~L~~RM~~I~GpniVIFVk~ln~~~l~lL~~----T----FG------------tLP~~P~~Ip~~~~~~i~gKi 208 (595)
T PHA03081 149 NDVRDMLSNRMHRISGPNIVIFVKELNPNTLSLLNN----T----FG------------TLPSCPETIPPPILVSIGGKI 208 (595)
T ss_pred HHHHHHHHHHHHhhcCCcEEEEEeccCHHHHHHHHH----h----cC------------CCCCCccccCCCCccCcCCeE
Confidence 346678888999999999999999888766643311 1 22 233323100001135567766
Q ss_pred EEecC----CcEEEcccHHHHHHHHH
Q 032491 101 VASRD----GKIVCENTLDARLDVVF 122 (139)
Q Consensus 101 v~s~d----G~I~vdNTle~RL~~~~ 122 (139)
|--+. =.|+|+||++.-|..++
T Consensus 209 VMmPsPFYTvmv~V~~tl~NiLai~c 234 (595)
T PHA03081 209 VMMPSPFYTVMVRVDPTLDNILAILC 234 (595)
T ss_pred EEecCCceEEEEEcCccHHHHHHHHH
Confidence 65553 36789999999886654
No 41
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=52.55 E-value=18 Score=27.38 Aligned_cols=57 Identities=16% Similarity=0.116 Sum_probs=40.7
Q ss_pred hHHHHHHHHHHHHHH-------HhCCCcEE-EEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEe
Q 032491 18 SYKKLLKGLIVQSLL-------RLKEPAVL-LRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIV 75 (139)
Q Consensus 18 ~Y~~~L~~LI~qa~~-------~l~e~~v~-V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~v 75 (139)
.-++++++|+.=|-. .-++..++ |++.++|...+..-++.+...|++++|+ ++.+++
T Consensus 101 d~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV~Vd~~Dk~~l~~k~e~~~~v~~kltgk-~v~~~f 165 (166)
T PRK06418 101 DIKKLAVQLLSPARVLGVNTVWLPDGTVQYVIRVSRRDRRRLPAKPELLESILSKITGT-EVKIRV 165 (166)
T ss_pred CHHHHHHhcCCCcEEEEEEEEEeCCCcEEEEEEECHHHhhcccccHHHHHHHHHHHHCC-cEEEEe
Confidence 345666666654332 11233555 8999999999999999999999999998 566543
No 42
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=49.62 E-value=22 Score=28.57 Aligned_cols=39 Identities=23% Similarity=0.310 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHhCCCc--EEEEeccccHHHHHHHHHHH
Q 032491 20 KKLLKGLIVQSLLRLKEPA--VLLRCRKDDHHLVESVLESA 58 (139)
Q Consensus 20 ~~~L~~LI~qa~~~l~e~~--v~V~~~~~D~~lv~~~l~~~ 58 (139)
.++|..+|..|+.-+...+ ++|+|-|.|...|++++..+
T Consensus 150 d~l~e~~ieagaeDv~~~~~~~~V~t~p~~~~~V~~~L~~~ 190 (241)
T COG0217 150 DELLEAAIEAGAEDVEEDEGSIEVYTEPEDFNKVKEALEAA 190 (241)
T ss_pred HHHHHHHHHCCchhhhcCCCeEEEEEChHHHHHHHHHHHHc
Confidence 7899999999988887665 89999999999999998864
No 43
>PF03410 Peptidase_M44: Protein G1; InterPro: IPR005072 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: 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-, N-, 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. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; 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. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 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 []. This group of metallopeptidases belong to MEROPS peptidase family M44 (clan ME). The active site residues for members of this family and family M16 occur in the motif HXXEHProtein. The type example is the vaccinia virus-type metalloendopeptidase G1 from vaccinia virus, it is a metalloendopeptidase expressed by many Poxviridae which appears to play a role in the maturation of viral proteins.; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0019067 viral assembly, maturation, egress, and release
Probab=49.28 E-value=2e+02 Score=25.93 Aligned_cols=80 Identities=19% Similarity=0.318 Sum_probs=51.7
Q ss_pred HHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCC--CCCCCCCCCccce
Q 032491 21 KLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGP--GHHNAHGPSCSGG 98 (139)
Q Consensus 21 ~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~--~~~~~~~~~~~GG 98 (139)
+-+.+++..-+..|.+|.++|.+++=+...+.=+-. . .| .||.-| ++.+ -..++||
T Consensus 149 ~~i~~mL~~RM~~I~GpniVIFVk~l~~~~l~lL~~----T----FG------------tLP~cP~~Ip~~--~~~~~~g 206 (590)
T PF03410_consen 149 NDIRNMLSNRMHRIIGPNIVIFVKELNPNILSLLSN----T----FG------------TLPSCPLTIPPN--AFSSIGG 206 (590)
T ss_pred HHHHHHHHHHHHhhcCCcEEEEEeccCHHHHHHHHH----h----cC------------CCCCCcccccCc--cccCCCC
Confidence 345677888899999999999999888776653321 1 22 233222 1111 1256677
Q ss_pred EEEEecC----CcEEEcccHHHHHHHHH
Q 032491 99 VVVASRD----GKIVCENTLDARLDVVF 122 (139)
Q Consensus 99 Vvv~s~d----G~I~vdNTle~RL~~~~ 122 (139)
=+|--+. =.|.|+||++.-|..++
T Consensus 207 KivMmPsPFYTvmv~V~~tl~NiLai~c 234 (590)
T PF03410_consen 207 KIVMMPSPFYTVMVRVDNTLDNILAIMC 234 (590)
T ss_pred cEEEecCCceEEEEEcCccHHHHHHHHH
Confidence 6665553 36789999999886553
No 44
>PF02697 DUF217: Uncharacterized ACR, COG1753; InterPro: IPR003847 This entry is represented by Natrialba phage PhiCh1, Orf96. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=43.00 E-value=92 Score=20.20 Aligned_cols=55 Identities=15% Similarity=0.346 Sum_probs=36.4
Q ss_pred HHHHHHHHhhccChhhHHHHHHHHHH-----HHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHH
Q 032491 3 EAASKEVLNVSRDHNSYKKLLKGLIV-----QSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEY 62 (139)
Q Consensus 3 ~~a~~~L~~~~~~~~~Y~~~L~~LI~-----qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~ 62 (139)
++|.++|....++...|.+++..||. ..+..+.+. ....|.+-+.+.+.+...++
T Consensus 8 devY~rL~~~K~~~eSFSdvI~rli~~~~~~~~l~~~~g~-----l~deea~~~~~~i~e~r~~~ 67 (71)
T PF02697_consen 8 DEVYERLKKLKREDESFSDVIERLIEKEKKRRDLMDYFGI-----LSDEEADEMEKDIKEEREEF 67 (71)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhcccchhHHHHHhcc-----CChhhHHHHHHHHHHHHHHH
Confidence 57899999998666789999999998 333333221 34455555665555554443
No 45
>TIGR03299 LGT_TIGR03299 phage/plasmid-related protein TIGR03299. Members of this uncharacterized protein family are found in various Mycobacterium phage genomes, in Streptomyces coelicolor plasmid SCP1, and in bacterial genomes near various markers that suggest lateral gene transfer. The function is unknown.
Probab=42.63 E-value=17 Score=30.13 Aligned_cols=20 Identities=45% Similarity=0.896 Sum_probs=15.7
Q ss_pred EEEEecCC-----------cEEEcccHHHHH
Q 032491 99 VVVASRDG-----------KIVCENTLDARL 118 (139)
Q Consensus 99 Vvv~s~dG-----------~I~vdNTle~RL 118 (139)
+++.|+|| |+||.|||-.=+
T Consensus 135 lL~NSHDGssa~~~~~t~vRvVC~NTL~~a~ 165 (309)
T TIGR03299 135 LLATAHDGTLATTAQFTSVRVVCANTLAAAL 165 (309)
T ss_pred EEEeccCCccceEEecCcEEEEecCHHHHhc
Confidence 56677788 689999997655
No 46
>PRK01379 cyaY frataxin-like protein; Provisional
Probab=41.59 E-value=81 Score=21.98 Aligned_cols=12 Identities=17% Similarity=0.318 Sum_probs=5.0
Q ss_pred hHHHHHHHHHHH
Q 032491 18 SYKKLLKGLIVQ 29 (139)
Q Consensus 18 ~Y~~~L~~LI~q 29 (139)
+|..+-..++.+
T Consensus 5 ef~~lad~~L~~ 16 (103)
T PRK01379 5 EFSKIAETTIAY 16 (103)
T ss_pred HHHHHHHHHHHH
Confidence 344444444333
No 47
>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].
Probab=40.45 E-value=94 Score=22.90 Aligned_cols=30 Identities=27% Similarity=0.480 Sum_probs=26.8
Q ss_pred CCcEEEEeccccHHHHHHHHHHHHHHHHHh
Q 032491 36 EPAVLLRCRKDDHHLVESVLESAKEEYAQK 65 (139)
Q Consensus 36 e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~ 65 (139)
...++|+|--.+.+.+++++.+++..|.+.
T Consensus 127 ~e~l~l~~lg~s~~~l~~ll~ear~~~~~~ 156 (187)
T PF08740_consen 127 DETLTLSCLGRSPKPLKDLLEEAREYYLKK 156 (187)
T ss_pred ceEEEEEEecCCHHHHHHHHHHHHHHHHHh
Confidence 458899999999999999999999988754
No 48
>PF14164 YqzH: YqzH-like protein
Probab=36.04 E-value=72 Score=20.49 Aligned_cols=38 Identities=11% Similarity=0.195 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHH
Q 032491 20 KKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLES 57 (139)
Q Consensus 20 ~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~ 57 (139)
++++.++|.+++.+.+.+.-..-..+.|.+.+...+..
T Consensus 3 ek~I~Kmi~~~l~QYg~d~~~~pls~~E~~~L~~~i~~ 40 (64)
T PF14164_consen 3 EKLIEKMIINCLRQYGYDVECMPLSDEEWEELCKHIQE 40 (64)
T ss_pred HHHHHHHHHHHHHHhCCcccCCCCCHHHHHHHHHHHHH
Confidence 47899999999999977644566677777766655544
No 49
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=35.83 E-value=36 Score=25.24 Aligned_cols=26 Identities=12% Similarity=-0.023 Sum_probs=23.4
Q ss_pred cccHHHHHHHHHHhhhHHHHHHhcCC
Q 032491 111 ENTLDARLDVVFRKKLPEIRKQLVSQ 136 (139)
Q Consensus 111 dNTle~RL~~~~~~~lp~Ir~~LFg~ 136 (139)
-+|..+||.++...+...+.+.+||+
T Consensus 164 ~~tVk~~l~RAr~~Lr~~l~~~~~~~ 189 (189)
T PRK12530 164 TSNLHVLLYRARLQLQACLSKNWFDG 189 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 36999999999999999999999984
No 50
>PTZ00389 40S ribosomal protein S7; Provisional
Probab=34.37 E-value=51 Score=25.48 Aligned_cols=59 Identities=15% Similarity=0.127 Sum_probs=45.6
Q ss_pred hhHHHHHHHHHHHHH-------HHhCCC-cEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEec
Q 032491 17 NSYKKLLKGLIVQSL-------LRLKEP-AVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVD 76 (139)
Q Consensus 17 ~~Y~~~L~~LI~qa~-------~~l~e~-~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd 76 (139)
+-|..+|.+|+-=|- ..+++. -+.|++.++|...++.-++.+...|+.++|+ ++.++..
T Consensus 115 aVhdaiLeDLvyPaeIvGkRir~~~DGsk~~KV~Ld~~d~~~ve~Kletf~~VykkLTgk-dV~fefp 181 (184)
T PTZ00389 115 AVHEAILEDLVYPSEIVGKRTRVRVDGSKLLKVFLDPKDRKNVEEKLDAFSAVYKKLTGR-DVVFEFP 181 (184)
T ss_pred HHHHHHHHHhccchheeeeEEEEecCCcEEEEEEeCHHHhcccchhHHHHHHHHHHHhCC-CeEEEec
Confidence 458888888876553 223333 4678999999999999999999999999998 6776653
No 51
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=34.07 E-value=35 Score=24.87 Aligned_cols=47 Identities=13% Similarity=0.259 Sum_probs=39.9
Q ss_pred hHHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHH
Q 032491 18 SYKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQ 64 (139)
Q Consensus 18 ~Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~ 64 (139)
.+...++-++.-|++..+++-++-+++|.|.+++...-+++...|..
T Consensus 4 ~w~~W~K~~~~G~~ii~~G~~l~~y~tPTeEeL~~r~sPELrkr~~~ 50 (128)
T PF07960_consen 4 NWRRWAKMLVAGAVIIGGGPALVKYTTPTEEELFKRYSPELRKRYLE 50 (128)
T ss_pred hHHHHHHHHHhcceeEeechHHheecCCCHHHHHHhcCHHHHHHHHH
Confidence 46778888888888888888999999999999999988887766644
No 52
>COG3882 FkbH Predicted enzyme involved in methoxymalonyl-ACP biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=33.30 E-value=1.2e+02 Score=27.27 Aligned_cols=39 Identities=21% Similarity=0.245 Sum_probs=32.4
Q ss_pred CccceEEEEecCCcEEEcccHHHHHHHHHHhhhHHHHHH
Q 032491 94 SCSGGVVVASRDGKIVCENTLDARLDVVFRKKLPEIRKQ 132 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~Ir~~ 132 (139)
..+||||-...=.-|...||.++-.-..+|+....+++.
T Consensus 232 TLWGGVIGedGv~GI~Ls~~~~G~~fk~fQ~~Ik~l~kq 270 (574)
T COG3882 232 TLWGGVIGEDGVDGIRLSNSAEGEAFKTFQNFIKGLKKQ 270 (574)
T ss_pred cccccccccccccceeecCCCCchhHHHHHHHHHHHHhc
Confidence 449999988774459999999999988999988888764
No 53
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=30.42 E-value=55 Score=20.08 Aligned_cols=20 Identities=20% Similarity=0.228 Sum_probs=18.2
Q ss_pred EEEEeccccHHHHHHHHHHH
Q 032491 39 VLLRCRKDDHHLVESVLESA 58 (139)
Q Consensus 39 v~V~~~~~D~~lv~~~l~~~ 58 (139)
+.|++.++|.+.+.+++.++
T Consensus 46 ~~v~V~~~d~~~A~~il~~~ 65 (67)
T PF09413_consen 46 VEVYVPEEDYERAREILEEF 65 (67)
T ss_dssp EEEEEEGGGHHHHHHHHHHT
T ss_pred eEEEECHHHHHHHHHHHHHh
Confidence 88999999999999999864
No 54
>PF01709 Transcrip_reg: Transcriptional regulator; InterPro: IPR002876 This entry represents the core region of several hypothetical proteins found in bacteria, plants, and yeast proteins. This core region can be subdivided into three domains: a 3-helical bundle domain, and two alpha+beta domains with different folds, where domain 3 (ferredoxin-like fold) is inserted within domain 2. This core region is found in the following hypothetical proteins: YebC from Escherichia coli, HP0162 from Helicobacter pylori (Campylobacter pylori) and aq1575 from Aquifex aeolicus []. The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined. A structural homology search reveals that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 A x 10 A x 20 A in the centre of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites [].; PDB: 1LFP_A 1MW7_A 1KON_A.
Probab=29.40 E-value=57 Score=25.82 Aligned_cols=41 Identities=17% Similarity=0.225 Sum_probs=33.5
Q ss_pred hhHHHHHHHHHHHHHHHhC--CCcEEEEeccccHHHHHHHHHH
Q 032491 17 NSYKKLLKGLIVQSLLRLK--EPAVLLRCRKDDHHLVESVLES 57 (139)
Q Consensus 17 ~~Y~~~L~~LI~qa~~~l~--e~~v~V~~~~~D~~lv~~~l~~ 57 (139)
..+.+++...|.-|+.=+. ++.+.|+|.|.|...|...+.+
T Consensus 143 ~~~d~~~e~aIe~GaeDve~~d~~~~~~c~p~~~~~v~~~L~~ 185 (234)
T PF01709_consen 143 LDEDELMEDAIEAGAEDVEEDDGEFEFICDPSDLSAVKKALEK 185 (234)
T ss_dssp S-HHHHHHHHHHHTESEEEECTSEEEEEEEGGGHHHHHHHHHH
T ss_pred CChHHHHHHHHhCCCcEeeecCCeEEEEECHHHHHHHHHHHHH
Confidence 3678888888888877665 4589999999999999999886
No 55
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=29.24 E-value=70 Score=26.88 Aligned_cols=22 Identities=32% Similarity=0.676 Sum_probs=16.2
Q ss_pred CccceEEEEec-CCcE-EEcccHH
Q 032491 94 SCSGGVVVASR-DGKI-VCENTLD 115 (139)
Q Consensus 94 ~~~GGVvv~s~-dG~I-~vdNTle 115 (139)
..-||+-|..+ +||+ -|+||++
T Consensus 183 HmGggiSV~ah~~GrvIDvnnald 206 (358)
T COG3426 183 HMGGGISVGAHKQGRVIDVNNALD 206 (358)
T ss_pred eccCceEEEEecCCcEEeccCCCC
Confidence 44688888776 5664 4889998
No 56
>PF09561 RE_HpaII: HpaII restriction endonuclease; InterPro: IPR019062 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This family includes HpaII, which recognises the double-stranded sequence CCGG and cleaves after C-1.
Probab=27.96 E-value=51 Score=28.04 Aligned_cols=20 Identities=30% Similarity=0.808 Sum_probs=17.7
Q ss_pred CccceEEEEecCCcEEEccc
Q 032491 94 SCSGGVVVASRDGKIVCENT 113 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNT 113 (139)
+..||.+|...||.|+|.--
T Consensus 290 ~a~gGyivV~~dGevlcYHi 309 (355)
T PF09561_consen 290 DATGGYIVVKEDGEVLCYHI 309 (355)
T ss_pred cccceEEEEeCCCCEEEEEe
Confidence 67899999999999999743
No 57
>COG0112 GlyA Glycine/serine hydroxymethyltransferase [Amino acid transport and metabolism]
Probab=26.60 E-value=91 Score=27.05 Aligned_cols=69 Identities=14% Similarity=0.179 Sum_probs=42.8
Q ss_pred EEeccccHHHHHHHHHHHHHH-------HHHh--hCC--CCCe----EEeccccCCCCCCCCCCCCCCCccceEEEEecC
Q 032491 41 LRCRKDDHHLVESVLESAKEE-------YAQK--LQV--HPPE----IIVDHHIYLPPGPGHHNAHGPSCSGGVVVASRD 105 (139)
Q Consensus 41 V~~~~~D~~lv~~~l~~~~~~-------~~~~--~~~--~~~~----i~vd~~~~L~~~~~~~~~~~~~~~GGVvv~s~d 105 (139)
.|+|+-|.+..+++.+++..- +.++ .|. .++. ++-.++.+|..+ -||+|++..
T Consensus 176 aY~r~id~~~~reIad~VGA~L~~DmAHiaGLVA~G~~p~P~~~AdvVTtTTHKTlrGP-----------rGG~Il~~~- 243 (413)
T COG0112 176 AYSRPIDFKRFREIADEVGAYLMVDMAHVAGLIAGGVHPNPLPHADVVTTTTHKTLRGP-----------RGGIILTND- 243 (413)
T ss_pred ccccccCHHHHHHHHHHhCceEEehHHHHHHHHhcccCCCCCCccceEeCCcccCCCCC-----------CceEEEecc-
Confidence 689999999999988764210 0111 111 0111 444455566543 488888775
Q ss_pred CcEEEcccHHHHHHHHHHhhhHHHHHHhcCCCC
Q 032491 106 GKIVCENTLDARLDVVFRKKLPEIRKQLVSQVA 138 (139)
Q Consensus 106 G~I~vdNTle~RL~~~~~~~lp~Ir~~LFg~~~ 138 (139)
+++-..|.+.+||..+
T Consensus 244 -----------------eel~kkin~aVFPg~q 259 (413)
T COG0112 244 -----------------EELAKKINSAVFPGLQ 259 (413)
T ss_pred -----------------HHHHHHhhhhcCCccC
Confidence 6777888888998654
No 58
>PF06903 VirK: VirK protein; InterPro: IPR010694 This family consists of several bacterial VirK proteins of around 145 residues in length. The function of this family is unknown [].
Probab=26.17 E-value=99 Score=21.55 Aligned_cols=34 Identities=15% Similarity=0.302 Sum_probs=21.1
Q ss_pred hCCCCCeEEeccccCCCCCCCCCCCCCCCccceEEEEe
Q 032491 66 LQVHPPEIIVDHHIYLPPGPGHHNAHGPSCSGGVVVAS 103 (139)
Q Consensus 66 ~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~GGVvv~s 103 (139)
.|+ +|++.+|-..+-|+. ...+.....||+.+.+
T Consensus 15 ~Gk-~V~v~iDls~Ct~~~---~~~~~s~t~Gg~~i~a 48 (100)
T PF06903_consen 15 AGK-NVTVVIDLSQCTPEG---EGTPPSKTRGGLRIDA 48 (100)
T ss_pred cCC-eEEEEEEHHHCccCC---CCCCCcccCcccceee
Confidence 454 788888876666551 1112247789987765
No 59
>KOG4115 consensus Dynein-associated protein Roadblock [Cell cycle control, cell division, chromosome partitioning; Cell motility]
Probab=26.15 E-value=1e+02 Score=21.40 Aligned_cols=33 Identities=21% Similarity=0.373 Sum_probs=26.6
Q ss_pred cceEEEEecCCcEEEcccHHHHHHHHHHhhhHHH
Q 032491 96 SGGVVVASRDGKIVCENTLDARLDVVFRKKLPEI 129 (139)
Q Consensus 96 ~GGVvv~s~dG~I~vdNTle~RL~~~~~~~lp~I 129 (139)
.-|++|.+..| +.+--||+.+.-+.+..++-..
T Consensus 18 V~giiv~d~~G-vpikTt~d~~~t~~ya~~l~~L 50 (97)
T KOG4115|consen 18 VTGIIVVDNAG-VPIKTTLDNTTTQQYAALLHPL 50 (97)
T ss_pred ceeEEEECCCC-cEeEeccCchHHHHHHHHHHHH
Confidence 34999999999 8888899998888887766543
No 60
>KOG3320 consensus 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis]
Probab=26.04 E-value=1.1e+02 Score=23.79 Aligned_cols=59 Identities=15% Similarity=0.162 Sum_probs=44.6
Q ss_pred hhHHHHHHHHHHHHHH-------HhCCC-cEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEec
Q 032491 17 NSYKKLLKGLIVQSLL-------RLKEP-AVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVD 76 (139)
Q Consensus 17 ~~Y~~~L~~LI~qa~~-------~l~e~-~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd 76 (139)
+-+..+|.+|.-=+.. .+.+. -+.|...++|...++.-++.+...|.++||+ ++..++.
T Consensus 122 aVhdaiLed~vfP~eIvGkR~rv~ldg~ki~kV~LD~~~~n~~e~K~e~f~~vy~kLtGK-dv~fEfp 188 (192)
T KOG3320|consen 122 AVHDAILEDLVFPAEIVGKRTRVKLDGSKLVKVHLDKKQQNNVEHKVETFSAVYKKLTGK-DVVFEFP 188 (192)
T ss_pred HHHHHHHHhccchhhhcceeEEEEecCcEEEEEEechhhccchHHhHHHHHHHHHHhcCC-ceEEecC
Confidence 3577788887765543 23444 3458899999999999999999999999998 6766654
No 61
>cd01274 AIDA-1b AIDA-1b Phosphotyrosine-binding (PTB) domain. AIDA-1b Phosphotyrosine-binding (PTB) domain. AIDA-1b is an amyloid-beta precursor protein interacting protein. It consists of ankyrin repeats, a SAM domain and a C-terminal PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=26.02 E-value=2.1e+02 Score=20.35 Aligned_cols=50 Identities=10% Similarity=0.067 Sum_probs=26.8
Q ss_pred eccccHHHHHHHHHHHHHHHHHhhCCCCCeEEeccccCCCCCCCCCCCCCCCccceEEEEecCCc-EEEc
Q 032491 43 CRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDHHIYLPPGPGHHNAHGPSCSGGVVVASRDGK-IVCE 111 (139)
Q Consensus 43 ~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~~~~L~~~~~~~~~~~~~~~GGVvv~s~dG~-I~vd 111 (139)
..|+-.+.+++++..++.......+...+.+.|. .+||.+.+.+.+ +.++
T Consensus 15 ~~~~G~~~~~~Am~kik~~~~~~~k~~~V~L~IS-------------------~~Gv~v~d~~tk~~i~~ 65 (127)
T cd01274 15 GELEGTDSTHAAMTKIKESIIDWETIPRVTLDLT-------------------CNGVKFIDETFKTLIDG 65 (127)
T ss_pred cCCCCcHHHHHHHHHHHHhhhccCCCCEEEEEEe-------------------CCeEEEEECCCCeEEEE
Confidence 3444555667777766544432111224555544 488888887643 3444
No 62
>PF10944 DUF2630: Protein of unknown function (DUF2630); InterPro: IPR020311 This entry contains proteins with no known function.
Probab=25.71 E-value=1.1e+02 Score=20.48 Aligned_cols=26 Identities=12% Similarity=0.124 Sum_probs=22.0
Q ss_pred cHHHHHHHHHHhhhHHHHHHhcCCCC
Q 032491 113 TLDARLDVVFRKKLPEIRKQLVSQVA 138 (139)
Q Consensus 113 Tle~RL~~~~~~~lp~Ir~~LFg~~~ 138 (139)
.++..|++||.-+...=.+.=||.+|
T Consensus 40 ~lE~~LDQCWDLLRqRRA~r~~G~dP 65 (81)
T PF10944_consen 40 QLEVELDQCWDLLRQRRARREAGEDP 65 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence 68999999999888877777788776
No 63
>PF12860 PAS_7: PAS fold
Probab=25.21 E-value=65 Score=21.42 Aligned_cols=20 Identities=40% Similarity=0.509 Sum_probs=17.0
Q ss_pred CccceEEEEecCCcEEEccc
Q 032491 94 SCSGGVVVASRDGKIVCENT 113 (139)
Q Consensus 94 ~~~GGVvv~s~dG~I~vdNT 113 (139)
+..-||.+.+.+|++++-|.
T Consensus 3 ~l~~Gv~v~D~~~rl~~~N~ 22 (115)
T PF12860_consen 3 SLPQGVAVFDSDGRLVFWNQ 22 (115)
T ss_pred CcCceEEEEcCCCeEEeEcH
Confidence 44689999999999998874
No 64
>PF14417 MEDS: MEDS: MEthanogen/methylotroph, DcmR Sensory domain
Probab=25.07 E-value=2.9e+02 Score=20.54 Aligned_cols=44 Identities=16% Similarity=0.144 Sum_probs=32.9
Q ss_pred hccChhhHHHHHHHHHHHHHHHhCCCcEEEEec-cccHHHHHHHHHH
Q 032491 12 VSRDHNSYKKLLKGLIVQSLLRLKEPAVLLRCR-KDDHHLVESVLES 57 (139)
Q Consensus 12 ~~~~~~~Y~~~L~~LI~qa~~~l~e~~v~V~~~-~~D~~lv~~~l~~ 57 (139)
+-+++++|-+.+...|.+|+.. ...+.+.+. +.+.+.+.+.+.+
T Consensus 25 ~Y~~~~e~~~~~~~Fi~~GL~~--ge~~l~v~~~~~~~~~l~~~L~~ 69 (191)
T PF14417_consen 25 FYDDEEELLEVLVPFIREGLAR--GERCLYVAPDPRRVEELRDELRK 69 (191)
T ss_pred EECCHHHHHHHHHHHHHHHHHC--CCeEEEEECCCCCHHHHHHHHHh
Confidence 3456779999999999999986 334555555 7888888877754
No 65
>PF14695 LINES_C: Lines C-terminus
Probab=24.92 E-value=56 Score=18.95 Aligned_cols=13 Identities=23% Similarity=0.258 Sum_probs=9.7
Q ss_pred HHHHHHhcCCCCC
Q 032491 127 PEIRKQLVSQVAA 139 (139)
Q Consensus 127 p~Ir~~LFg~~~~ 139 (139)
--.++.|||.|++
T Consensus 15 rL~~k~LFPYN~~ 27 (39)
T PF14695_consen 15 RLVRKNLFPYNPS 27 (39)
T ss_pred HHHHCCCCCCChH
Confidence 3467889998874
No 66
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=23.85 E-value=1.7e+02 Score=18.67 Aligned_cols=33 Identities=12% Similarity=0.249 Sum_probs=26.5
Q ss_pred hCCCcEEEEeccccHHHHHHHHHHHHHHHHHhh
Q 032491 34 LKEPAVLLRCRKDDHHLVESVLESAKEEYAQKL 66 (139)
Q Consensus 34 l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~ 66 (139)
|.+....|.|.+.|.+.++++...+...+.+..
T Consensus 6 I~G~~y~i~~~~~~ee~l~~~a~~i~~~i~~~~ 38 (89)
T PF05164_consen 6 ILGREYRIKCPDEDEEYLRKAAELINEKINEIK 38 (89)
T ss_dssp ETTEEEEECETGCGHHHHHHHHHHHHHHHHHHC
T ss_pred ECCEEEEeecCCCCHHHHHHHHHHHHHHHHHHH
Confidence 445677899999999999999888877777653
No 67
>PRK00110 hypothetical protein; Validated
Probab=23.70 E-value=73 Score=25.55 Aligned_cols=39 Identities=13% Similarity=0.201 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHh--CCCcEEEEeccccHHHHHHHHHH
Q 032491 19 YKKLLKGLIVQSLLRL--KEPAVLLRCRKDDHHLVESVLES 57 (139)
Q Consensus 19 Y~~~L~~LI~qa~~~l--~e~~v~V~~~~~D~~lv~~~l~~ 57 (139)
-.+++..+|.-|+.-+ .++.+.|+|.|.|...|.+.|.+
T Consensus 147 ~d~~~e~aieaGaeDv~~e~~~~~i~~~p~~~~~v~~~L~~ 187 (245)
T PRK00110 147 EDELMEAALEAGAEDVETDDESFEVITAPEDFEAVRDALEA 187 (245)
T ss_pred HHHHHHHHHhCCCCEeeccCCeEEEEECHHHHHHHHHHHHH
Confidence 4567777777676444 44468999999999999998864
No 68
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=23.64 E-value=93 Score=22.85 Aligned_cols=29 Identities=7% Similarity=-0.171 Sum_probs=25.0
Q ss_pred cccHHHHHHHHHHhhhHHHHHHhcCCCCC
Q 032491 111 ENTLDARLDVVFRKKLPEIRKQLVSQVAA 139 (139)
Q Consensus 111 dNTle~RL~~~~~~~lp~Ir~~LFg~~~~ 139 (139)
-||..+||.++...+...+.+.-|++.|+
T Consensus 161 ~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~ 189 (191)
T PRK12520 161 ATNAWVLLYRARMRLRECLDLHWFGNPPA 189 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHccCCcc
Confidence 46999999999999999999999887653
No 69
>PRK15354 type III secretion system protein SsaK; Provisional
Probab=23.25 E-value=3.9e+02 Score=21.29 Aligned_cols=47 Identities=17% Similarity=0.201 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEecc
Q 032491 19 YKKLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDH 77 (139)
Q Consensus 19 Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~ 77 (139)
=.-+..+|-.|....-.++.+++++.|+....+...+.+ .+.+.+++
T Consensus 135 sq~Li~RLa~Qv~~mA~eg~LtL~VHP~~~~am~~afG~------------R~~~v~d~ 181 (224)
T PRK15354 135 DSVMCHRLARQATAMAEEGALYLRIHPEKEALMRETFGK------------RFTLIIEP 181 (224)
T ss_pred HHHHHHHHHHHHHHHHhcCceEEEECHHHHHHHHHHHhc------------ceeeeecC
Confidence 345667788888888899999999999999888766542 46777764
No 70
>PF09439 SRPRB: Signal recognition particle receptor beta subunit; InterPro: IPR019009 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. The SR receptor is a monomer consisting of the loosely membrane-associated SR-alpha homologue FtsY, while the eukaryotic SR receptor is a heterodimer of SR-alpha (70 kDa) and SR-beta (25 kDa), both of which contain a GTP-binding domain []. SR-alpha regulates the targeting of SRP-ribosome-nascent polypeptide complexes to the translocon []. SR-alpha binds to the SRP54 subunit of the SRP complex. The SR-beta subunit is a transmembrane GTPase that anchors the SR-alpha subunit (a peripheral membrane GTPase) to the ER membrane []. SR-beta interacts with the N-terminal SRX-domain of SR-alpha, which is not present in the bacterial FtsY homologue. SR-beta also functions in recruiting the SRP-nascent polypeptide to the protein-conducting channel. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase, which anchors the alpha subunit to the endoplasmic reticulum membrane []. ; PDB: 2GED_B 1NRJ_B 2GO5_2 2FH5_B.
Probab=21.56 E-value=1.7e+02 Score=22.28 Aligned_cols=31 Identities=19% Similarity=0.484 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHhCCCcEEEEeccccHH
Q 032491 19 YKKLLKGLIVQSLLRLKEPAVLLRCRKDDHH 49 (139)
Q Consensus 19 Y~~~L~~LI~qa~~~l~e~~v~V~~~~~D~~ 49 (139)
=.++|-+++...-..-..+.+.|.||+.|.-
T Consensus 95 ~Ae~Ly~iL~~~~~~~~~~piLIacNK~Dl~ 125 (181)
T PF09439_consen 95 VAEYLYDILSDTEVQKNKPPILIACNKQDLF 125 (181)
T ss_dssp HHHHHHHHHHHHHCCTT--EEEEEEE-TTST
T ss_pred HHHHHHHHHHhhhhccCCCCEEEEEeCcccc
Confidence 3456777776665444566899999999943
No 71
>PHA03065 Hypothetical protein; Provisional
Probab=21.51 E-value=5.6e+02 Score=22.50 Aligned_cols=54 Identities=31% Similarity=0.343 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHhCCCcEEEEeccccHHHHHHHHHHHHHHHHHhhCCCCCeEEecc
Q 032491 21 KLLKGLIVQSLLRLKEPAVLLRCRKDDHHLVESVLESAKEEYAQKLQVHPPEIIVDH 77 (139)
Q Consensus 21 ~~L~~LI~qa~~~l~e~~v~V~~~~~D~~lv~~~l~~~~~~~~~~~~~~~~~i~vd~ 77 (139)
+-|+.++.+++..+++.-=+++|.--|.+.+ +...+++. ...+|.=+.=|+.|.
T Consensus 144 ~nlk~~l~~~L~~~~~~v~I~yCdgvDAEfv--MC~~ak~~-a~~~g~WPl~iStDQ 197 (438)
T PHA03065 144 NNLKRLLESALARLGENVEIVYCDGVDAEFV--MCARAKEL-AATTGEWPLLISTDQ 197 (438)
T ss_pred hhHHHHHHHHHHhccCCceEEEECCcchhHH--HHHHHHHH-HhhcCCCceEEeccC
Confidence 4588999999999987766799999999987 33344333 334553144455553
No 72
>TIGR01033 DNA-binding regulatory protein, YebC/PmpR family. This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein.
Probab=21.16 E-value=94 Score=24.74 Aligned_cols=39 Identities=13% Similarity=0.178 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHh--CCCcEEEEeccccHHHHHHHHHH
Q 032491 19 YKKLLKGLIVQSLLRL--KEPAVLLRCRKDDHHLVESVLES 57 (139)
Q Consensus 19 Y~~~L~~LI~qa~~~l--~e~~v~V~~~~~D~~lv~~~l~~ 57 (139)
-.+++..+|.-|+.-+ .++.+.|+|.|.|...|++.|.+
T Consensus 149 ~d~~~e~aieaGAedv~~~~~~~~v~~~~~~~~~v~~~L~~ 189 (238)
T TIGR01033 149 EEDLMEAAIEAGAEDIDVDDDEFEVYTAPEELEKVKEALEA 189 (238)
T ss_pred HHHHHHHHHhCCCceeeccCCcEEEEECHHHHHHHHHHHHH
Confidence 4567777777666444 33468999999999999988864
No 73
>PF06067 DUF932: Domain of unknown function (DUF932); InterPro: IPR017686 Members of this uncharacterised protein are found in various Mycobacterium phage genomes, in Streptomyces coelicolor Plasmid SCP1 and in bacterial genomes near various markers that suggest lateral gene transfer. The function of this protein is unknown.
Probab=20.66 E-value=58 Score=25.39 Aligned_cols=13 Identities=54% Similarity=0.741 Sum_probs=10.0
Q ss_pred CcEEEcccHHHHH
Q 032491 106 GKIVCENTLDARL 118 (139)
Q Consensus 106 G~I~vdNTle~RL 118 (139)
=|+||+|||-.-|
T Consensus 85 ~R~VC~Ntl~~A~ 97 (239)
T PF06067_consen 85 FRVVCSNTLVAAL 97 (239)
T ss_pred EEEEccCCceecc
Confidence 3789999987744
No 74
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=20.46 E-value=2.3e+02 Score=18.03 Aligned_cols=10 Identities=40% Similarity=0.730 Sum_probs=8.5
Q ss_pred CccceEEEEe
Q 032491 94 SCSGGVVVAS 103 (139)
Q Consensus 94 ~~~GGVvv~s 103 (139)
...||||+++
T Consensus 35 ~~~GGvV~eD 44 (62)
T PF15513_consen 35 RLTGGVVMED 44 (62)
T ss_pred eEeccEEEeC
Confidence 7789999975
Done!