Query psy9708
Match_columns 99
No_of_seqs 107 out of 135
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 17:36:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9708.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9708hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02580 trehalose-phosphatase 99.6 2.2E-14 4.8E-19 114.1 9.9 95 2-96 167-287 (384)
2 PLN02151 trehalose-phosphatase 99.6 2.2E-14 4.8E-19 113.1 9.7 95 2-96 146-255 (354)
3 PF02358 Trehalose_PPase: Treh 99.5 1E-13 2.3E-18 101.8 9.4 95 2-96 47-152 (235)
4 PLN03017 trehalose-phosphatase 99.5 1.9E-13 4.1E-18 108.3 9.8 95 2-96 159-269 (366)
5 COG1877 OtsB Trehalose-6-phosp 99.4 1E-12 2.2E-17 100.3 8.4 94 2-95 68-168 (266)
6 TIGR00685 T6PP trehalose-phosp 99.3 8.2E-12 1.8E-16 92.4 7.6 93 3-95 54-153 (244)
7 PLN03063 alpha,alpha-trehalose 98.6 4.1E-07 9E-12 78.0 9.4 84 2-88 560-653 (797)
8 PLN03064 alpha,alpha-trehalose 98.5 4.2E-07 9.2E-12 79.3 8.4 71 2-75 650-729 (934)
9 PRK10187 trehalose-6-phosphate 98.2 1.3E-05 2.9E-10 60.4 9.6 85 3-91 65-155 (266)
10 PLN02205 alpha,alpha-trehalose 98.0 3.1E-05 6.8E-10 67.2 8.1 93 2-94 644-747 (854)
11 PLN03017 trehalose-phosphatase 97.3 0.00059 1.3E-08 54.5 6.0 58 5-62 217-279 (366)
12 PLN02580 trehalose-phosphatase 97.2 0.00095 2.1E-08 53.6 5.6 40 10-49 241-280 (384)
13 PLN02151 trehalose-phosphatase 97.1 0.0015 3.2E-08 52.0 6.2 53 10-62 209-265 (354)
14 PRK14501 putative bifunctional 97.1 0.0031 6.7E-08 53.6 8.3 90 3-95 543-643 (726)
15 PF02358 Trehalose_PPase: Treh 96.9 0.0023 5E-08 46.9 5.2 40 10-49 102-145 (235)
16 COG1877 OtsB Trehalose-6-phosp 96.4 0.0041 8.9E-08 47.7 3.8 56 10-65 123-182 (266)
17 TIGR00685 T6PP trehalose-phosp 96.1 0.01 2.2E-07 43.8 4.4 37 11-47 108-146 (244)
18 KOG1050|consensus 95.4 0.062 1.4E-06 46.5 6.9 72 9-83 553-629 (732)
19 PLN03063 alpha,alpha-trehalose 95.0 0.055 1.2E-06 47.0 5.6 53 10-62 615-675 (797)
20 PLN03064 alpha,alpha-trehalose 93.6 0.15 3.3E-06 45.2 5.5 38 10-47 705-743 (934)
21 TIGR01484 HAD-SF-IIB HAD-super 90.0 1 2.2E-05 31.6 5.5 59 12-71 55-121 (204)
22 PRK10187 trehalose-6-phosphate 87.9 2.4 5.1E-05 31.9 6.4 40 10-50 116-155 (266)
23 KOG1050|consensus 86.7 1.4 3E-05 38.5 5.0 42 11-55 598-640 (732)
24 TIGR02471 sucr_syn_bact_C sucr 80.5 19 0.00041 25.9 8.7 83 9-93 51-140 (236)
25 PLN02205 alpha,alpha-trehalose 79.9 1.8 4E-05 38.2 3.1 25 10-34 700-724 (854)
26 cd00995 PBP2_NikA_DppA_OppA_li 67.7 21 0.00046 27.6 6.1 50 40-95 306-355 (466)
27 PF07364 DUF1485: Protein of u 66.6 21 0.00045 27.8 5.8 91 1-91 87-225 (292)
28 COG3889 Predicted solute bindi 61.5 23 0.00049 31.6 5.5 87 10-97 140-234 (872)
29 cd08495 PBP2_NikA_DppA_OppA_li 57.4 37 0.0008 26.9 5.9 49 40-95 316-366 (482)
30 PRK14501 putative bifunctional 56.4 27 0.00059 29.9 5.2 26 11-36 596-621 (726)
31 COG5476 Uncharacterized conser 55.3 10 0.00022 31.6 2.4 37 2-38 88-124 (488)
32 cd08500 PBP2_NikA_DppA_OppA_li 53.8 48 0.001 26.7 6.0 55 40-95 316-376 (499)
33 TIGR03006 pepcterm_polyde poly 53.0 40 0.00086 25.6 5.2 73 9-94 63-135 (265)
34 cd08490 PBP2_NikA_DppA_OppA_li 47.7 67 0.0015 25.1 5.9 55 40-95 295-353 (470)
35 PF00356 LacI: Bacterial regul 46.7 35 0.00076 19.2 3.1 23 73-95 24-46 (46)
36 PF02834 LigT_PEase: LigT like 46.4 48 0.001 20.0 4.0 57 30-87 3-61 (87)
37 PF05116 S6PP: Sucrose-6F-phos 46.2 63 0.0014 23.9 5.2 81 11-94 60-147 (247)
38 COG0726 CDA1 Predicted xylanas 45.3 78 0.0017 22.2 5.4 44 7-50 111-154 (267)
39 cd08517 PBP2_NikA_DppA_OppA_li 44.0 70 0.0015 25.1 5.5 53 40-95 314-366 (480)
40 PF01522 Polysacc_deac_1: Poly 43.4 45 0.00098 21.0 3.6 46 4-50 49-94 (123)
41 PF03585 Herpes_ICP4_C: Herpes 43.2 9.1 0.0002 31.4 0.3 19 1-19 136-156 (425)
42 cd08509 PBP2_TmCBP_oligosaccha 43.1 75 0.0016 25.5 5.6 55 40-95 325-384 (509)
43 COG1514 LigT 2'-5' RNA ligase 43.0 43 0.00093 24.1 3.8 61 30-93 9-70 (180)
44 cd08504 PBP2_OppA The substrat 40.9 80 0.0017 25.0 5.4 50 40-95 326-376 (498)
45 TIGR02764 spore_ybaN_pdaB poly 40.8 51 0.0011 23.0 3.9 40 11-50 56-95 (191)
46 PF15475 UPF0444: Transmembran 39.7 19 0.00041 23.6 1.4 14 12-25 32-46 (92)
47 PRK11702 hypothetical protein; 38.6 37 0.00079 23.0 2.7 33 61-93 22-56 (108)
48 TIGR02631 xylA_Arthro xylose i 38.2 88 0.0019 25.0 5.2 22 74-95 64-85 (382)
49 cd08510 PBP2_Lactococcal_OppA_ 37.8 1.1E+02 0.0023 24.7 5.7 55 40-95 344-404 (516)
50 cd08514 PBP2_AppA_like The sub 37.6 1E+02 0.0022 24.4 5.5 55 40-95 312-371 (483)
51 PF14226 DIOX_N: non-haem diox 36.7 49 0.0011 20.9 3.0 35 3-46 18-53 (116)
52 TIGR01893 aa-his-dipept aminoa 36.2 1.8E+02 0.0038 23.5 6.7 40 56-95 346-385 (477)
53 cd08496 PBP2_NikA_DppA_OppA_li 33.3 1.4E+02 0.003 23.5 5.6 46 40-95 301-346 (454)
54 PF04914 DltD_C: DltD C-termin 33.1 23 0.0005 24.3 1.1 28 67-94 65-92 (130)
55 PF14606 Lipase_GDSL_3: GDSL-l 32.9 1.3E+02 0.0029 21.7 5.0 63 27-90 69-131 (178)
56 cd08512 PBP2_NikA_DppA_OppA_li 32.2 1.8E+02 0.0039 22.9 6.1 48 40-95 319-366 (476)
57 cd08492 PBP2_NikA_DppA_OppA_li 32.1 2.1E+02 0.0045 22.5 6.5 55 40-95 317-376 (484)
58 cd08515 PBP2_NikA_DppA_OppA_li 32.1 1.8E+02 0.0039 22.8 6.1 49 40-95 309-357 (460)
59 cd08518 PBP2_NikA_DppA_OppA_li 31.2 1.7E+02 0.0038 23.0 5.9 55 40-95 300-358 (464)
60 cd04893 ACT_GcvR_1 ACT domains 30.9 1.2E+02 0.0027 18.1 5.5 39 56-95 35-73 (77)
61 PF03778 DUF321: Protein of un 30.4 35 0.00076 16.4 1.1 12 14-25 3-14 (20)
62 PF07862 Nif11: Nitrogen fixat 29.2 38 0.00082 18.8 1.3 18 82-99 31-48 (49)
63 PRK12677 xylose isomerase; Pro 28.8 1.8E+02 0.0039 23.3 5.6 21 75-95 64-84 (384)
64 TIGR03212 uraD_N-term-dom puta 28.7 94 0.002 24.0 3.9 44 7-50 110-153 (297)
65 PF02971 FTCD: Formiminotransf 28.2 1.5E+02 0.0032 21.1 4.4 44 56-99 45-89 (145)
66 cd08519 PBP2_NikA_DppA_OppA_li 27.4 2.3E+02 0.0049 22.4 5.9 49 40-94 310-359 (469)
67 cd08498 PBP2_NikA_DppA_OppA_li 27.0 2.4E+02 0.0052 22.3 6.0 49 40-95 315-363 (481)
68 COG3317 NlpB Uncharacterized l 25.8 1E+02 0.0023 24.8 3.7 44 49-95 84-127 (342)
69 cd08513 PBP2_thermophilic_Hb8_ 25.7 2.7E+02 0.0058 21.9 6.1 55 40-95 310-369 (482)
70 PHA03307 transcriptional regul 25.6 25 0.00054 32.9 0.2 19 1-19 1060-1080(1352)
71 cd08499 PBP2_Ylib_like The sub 25.3 2.4E+02 0.0053 22.2 5.8 47 40-95 304-350 (474)
72 cd08520 PBP2_NikA_DppA_OppA_li 25.2 2.5E+02 0.0053 22.1 5.8 54 40-95 305-361 (468)
73 PRK15104 oligopeptide ABC tran 25.1 2.6E+02 0.0055 22.8 6.0 49 40-95 368-417 (543)
74 cd08511 PBP2_NikA_DppA_OppA_li 24.7 2E+02 0.0044 22.5 5.2 46 40-95 305-350 (467)
75 PRK11041 DNA-binding transcrip 24.6 2.7E+02 0.0059 20.0 6.4 60 36-95 6-69 (309)
76 PF08608 Wyosine_form: Wyosine 24.0 65 0.0014 19.4 1.8 41 56-96 6-50 (62)
77 TIGR02884 spore_pdaA delta-lac 23.5 1.2E+02 0.0026 22.1 3.5 42 9-50 85-126 (224)
78 cd08506 PBP2_clavulanate_OppA2 23.5 2.6E+02 0.0056 22.0 5.6 46 40-95 305-350 (466)
79 COG3171 Uncharacterized protei 23.5 87 0.0019 21.5 2.5 35 61-95 30-66 (119)
80 cd08503 PBP2_NikA_DppA_OppA_li 23.5 3E+02 0.0064 21.6 5.9 47 40-95 308-354 (460)
81 PF04320 DUF469: Protein with 23.2 1.1E+02 0.0024 20.4 2.9 34 61-94 16-50 (101)
82 PF00816 Histone_HNS: H-NS his 23.2 67 0.0014 20.2 1.8 23 74-96 20-42 (93)
83 PRK11303 DNA-binding transcrip 22.8 3.1E+02 0.0068 20.0 6.3 62 30-95 30-95 (328)
84 PF10250 O-FucT: GDP-fucose pr 22.7 1.3E+02 0.0029 22.7 3.7 32 33-71 174-205 (351)
85 PF13740 ACT_6: ACT domain; PD 22.4 1.3E+02 0.0027 18.0 2.9 39 56-95 36-74 (76)
86 PF12077 DUF3556: Transmembran 22.3 95 0.0021 26.6 3.0 34 40-73 503-541 (574)
87 cd08489 PBP2_NikA The substrat 22.2 3.8E+02 0.0082 21.2 6.3 55 40-95 307-366 (488)
88 TIGR02609 doc_partner putative 21.9 2E+02 0.0043 17.5 4.3 47 43-91 16-66 (74)
89 PRK08652 acetylornithine deace 21.6 1.6E+02 0.0035 22.0 3.9 36 59-94 219-254 (347)
90 PRK14648 UDP-N-acetylenolpyruv 21.6 2.4E+02 0.0052 22.7 5.0 54 41-94 276-334 (354)
91 PF12936 Kri1_C: KRI1-like fam 21.5 43 0.00093 21.9 0.7 14 62-75 25-38 (93)
92 PF02288 Dehydratase_MU: Dehyd 21.5 2.3E+02 0.005 18.9 4.3 24 50-74 56-79 (112)
93 TIGR03384 betaine_BetI transcr 21.5 78 0.0017 21.3 2.0 23 73-95 7-29 (189)
94 TIGR00259 thylakoid_BtpA membr 21.3 1.8E+02 0.0038 22.3 4.1 45 9-55 40-84 (257)
95 PRK10727 DNA-binding transcrip 21.1 3.5E+02 0.0077 20.0 6.3 62 30-95 28-93 (343)
96 PF02873 MurB_C: UDP-N-acetyle 21.0 2.6E+02 0.0055 18.4 4.9 54 41-94 39-97 (105)
97 cd07051 BMC_like_1_repeat1 Bac 21.0 2.8E+02 0.0061 18.8 5.7 47 45-97 53-100 (111)
98 PF03437 BtpA: BtpA family; I 20.8 3.6E+02 0.0079 20.6 5.7 43 50-94 41-83 (254)
99 PLN02750 oxidoreductase, 2OG-F 20.8 1.2E+02 0.0025 23.7 3.1 20 3-22 45-65 (345)
100 TIGR02417 fruct_sucro_rep D-fr 20.5 3.5E+02 0.0077 19.8 6.4 62 30-95 29-94 (327)
101 PRK14996 TetR family transcrip 20.2 79 0.0017 21.7 1.9 24 72-95 6-29 (192)
102 cd02641 R3H_Smubp-2_like R3H d 20.1 1.3E+02 0.0029 17.6 2.6 23 72-94 23-45 (60)
103 PF00120 Gln-synt_C: Glutamine 20.1 84 0.0018 23.4 2.1 61 33-95 66-132 (259)
No 1
>PLN02580 trehalose-phosphatase
Probab=99.56 E-value=2.2e-14 Score=114.08 Aligned_cols=95 Identities=16% Similarity=0.120 Sum_probs=77.1
Q ss_pred hhHHHhhhCCCC-eEEecccceeeeec------------------------cCCccchhHHHHHHHHHHHHHhCCCCceE
Q psy9708 2 LKWIERHYCKQG-AWVENKGPLLTFHY------------------------TNTPVELRPEMVSLATQLIESAGFKAGAW 56 (99)
Q Consensus 2 l~dl~~~v~~~g-~~vgnhG~el~~h~------------------------~~~p~e~~~~l~~~a~~L~e~~~~~~G~~ 56 (99)
+++|++.++.++ +|+|+||+++.... .+.+.++.+.+.+..+.|.+.....+|++
T Consensus 167 ~~~L~~~l~~~~l~laGsHG~e~~~p~~~~~~~~~~~~~~~~~~~g~~~~~~~~a~~~~~~i~~v~~~l~e~~~~~pGs~ 246 (384)
T PLN02580 167 RDKVYELVGLTELYYAGSHGMDIMGPVRESVSNDHPNCIKSTDQQGKEVNLFQPASEFLPMIDEVFRSLVESTKDIKGAK 246 (384)
T ss_pred HHHHHHHhCCCCccEEEeCCceeecCCCCcccccccccccccccccccccccccchhhhhhHHHHHHHHHHHhccCCCCE
Confidence 578999999999 99999999975410 01124567777888888888888899999
Q ss_pred EeecCCeeeEeecCCCCCchHHHHHHHHHHHHHh-Cccccc
Q psy9708 57 VENKGPLLTFHYTNTPVELRPEMVSLATQLIESA-GFKAGE 96 (99)
Q Consensus 57 VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~-G~~~~~ 96 (99)
||+|++++++|||++|++..+.+.+.++++.+.+ +|++++
T Consensus 247 VE~K~~svavHYR~a~~~~~~~~~~~l~~~l~~~~~l~v~~ 287 (384)
T PLN02580 247 VENHKFCVSVHYRNVDEKNWPLVAQCVHDVLKKYPRLRLTH 287 (384)
T ss_pred EEecCcEEEEEeCCCCchHHHHHHHHHHHHHHhCCceEEEe
Confidence 9999999999999999988888888888888776 477654
No 2
>PLN02151 trehalose-phosphatase
Probab=99.56 E-value=2.2e-14 Score=113.10 Aligned_cols=95 Identities=12% Similarity=0.107 Sum_probs=76.2
Q ss_pred hhHHHhhhCCCC-eEEecccceeeee----c---------cCCccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEe
Q psy9708 2 LKWIERHYCKQG-AWVENKGPLLTFH----Y---------TNTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFH 67 (99)
Q Consensus 2 l~dl~~~v~~~g-~~vgnhG~el~~h----~---------~~~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~H 67 (99)
+.+|++.++.++ +|+||||+++..- . .+.+.++.+.+.+..+.|.+.....+|++||+|++++++|
T Consensus 146 ~~~l~~~~~~~~l~laGsHG~e~~~p~~g~~~~~~~~~~~~~~~~~~~~~i~~v~~~l~~~~~~~pG~~VE~K~~slavH 225 (354)
T PLN02151 146 REKVSSFVKLTELYYAGSHGMDIKGPEQGSKYKKENQSLLCQPATEFLPVINEVYKKLVEKTKSIPGAKVENNKFCASVH 225 (354)
T ss_pred HHHHHHHcCCccceEEEeCCceeecCCCCccccccccccccccchhhHHHHHHHHHHHHHHHhcCCCCEEEecCcEEEEE
Confidence 468899999999 9999999997531 1 1223466788888888888777788999999999999999
Q ss_pred ecCCCCCchHHHHHHHHHHHHHh-Cccccc
Q psy9708 68 YTNTPVELRPEMVSLATQLIESA-GFKAGE 96 (99)
Q Consensus 68 yR~v~~~~~~~v~~~~~~~~~~~-G~~~~~ 96 (99)
||++|++...++...+++++..+ ||++++
T Consensus 226 YR~a~~~~~~~l~~~l~~v~~~~~~l~v~~ 255 (354)
T PLN02151 226 FRCVEENKWSDLANQVRSVLKNYPKLMLTQ 255 (354)
T ss_pred eCCCChHHHHHHHHHHHHHHhhCCCcEEec
Confidence 99999887677778888888775 477754
No 3
>PF02358 Trehalose_PPase: Trehalose-phosphatase; InterPro: IPR003337 Trehalose-phosphatases 3.1.3.12 from EC catalyse the de-phosphorylation of trehalose-6-phosphate to trehalose and orthophosphate. Trehalose is a common disaccharide of bacteria, fungi and invertebrates that appears to play a major role in desiccation tolerance. A pathway for trehalose biosynthesis may also exist in plants []. The trehalose-phosphatase signature is found in the C terminus of trehalose-6-phosphate synthase 2.4.1.15 from EC adjacent to the trehalose-6-phosphate synthase domain (see IPR001830 from INTERPRO). It would appear that the two equivalent genes in the Escherichia coli otsBA operon: otsA, the trehalose-6-phosphate synthase and otsB, trehalose-phosphatase (this family) have undergone gene fusion in most eukaryotes [].; GO: 0003824 catalytic activity, 0005992 trehalose biosynthetic process; PDB: 1U02_A.
Probab=99.51 E-value=1e-13 Score=101.80 Aligned_cols=95 Identities=20% Similarity=0.163 Sum_probs=66.1
Q ss_pred hhHHHhhhCCCC-eEEecccceeeeecc-----CCccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCC-
Q psy9708 2 LKWIERHYCKQG-AWVENKGPLLTFHYT-----NTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVE- 74 (99)
Q Consensus 2 l~dl~~~v~~~g-~~vgnhG~el~~h~~-----~~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~- 74 (99)
+++++.+.++++ +|+|+||+++..... ..+....+.+..+...|.......+|.+||+|+++++||||+++++
T Consensus 47 ~~~~~~~~~~~~i~l~gehG~e~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~pG~~iE~K~~sv~~Hyr~~~~~~ 126 (235)
T PF02358_consen 47 LDDLERFGGIPNIGLAGEHGAEIRRPGGSEWTNLPADEDLEWKDEVREILEYFAERTPGSFIEDKEFSVAFHYRNAPPEF 126 (235)
T ss_dssp HHHHHHH-S-SS-EEEEGGGTEEEETTE-EEE-TTGGGGHHHHHHHHHHHTTHHHHSTT-EEEEETTEEEEE-TTS-ST-
T ss_pred HHHhHHhcCCCCceEEEEeeEEeccCccccccccccccchHHHHHHHHHHHHHHhhccCcEEEECCeEEEEEecCCCcch
Confidence 356788889999 999999999887322 2233444444444444444444568999999999999999999998
Q ss_pred ---chHHHHHHHHHHHHHh-Cccccc
Q psy9708 75 ---LRPEMVSLATQLIESA-GFKAGE 96 (99)
Q Consensus 75 ---~~~~v~~~~~~~~~~~-G~~~~~ 96 (99)
...++...+.+++..+ |+++..
T Consensus 127 ~~~~~~~l~~~l~~~~~~~~~~~v~~ 152 (235)
T PF02358_consen 127 GEAQARELAEQLREILASHPGLEVVP 152 (235)
T ss_dssp ---THHHHHHHHHHHHHHH-T-EEEE
T ss_pred hhhHHHHHHHHHHHHHHhCCCEEEEE
Confidence 6788888899988887 998754
No 4
>PLN03017 trehalose-phosphatase
Probab=99.49 E-value=1.9e-13 Score=108.26 Aligned_cols=95 Identities=15% Similarity=0.117 Sum_probs=76.1
Q ss_pred hhHHHhhhCCCC-eEEecccceeeeec--------------cCCccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeE
Q psy9708 2 LKWIERHYCKQG-AWVENKGPLLTFHY--------------TNTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTF 66 (99)
Q Consensus 2 l~dl~~~v~~~g-~~vgnhG~el~~h~--------------~~~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~ 66 (99)
+.++++.+++.+ +|+|+||+++..-. .+.+.++.+.+.+..+.|.+.....+|++||+|++++++
T Consensus 159 ~~~l~~~~~l~~l~l~g~hGa~i~~p~~~~~~~~~~~~~~~~~~~~~~~~~i~~v~~~L~~~~~~~pGa~VE~K~~~vav 238 (366)
T PLN03017 159 IDKVYNFVKLAELYYAGSHGMDIKGPAKGFSRHKRVKQSLLYQPANDYLPMIDEVYRQLLEKTKSTPGAKVENHKFCASV 238 (366)
T ss_pred HHHHHHhhcccCceEEEcCCcEEecCCCcceeccccccccccccchhhHHHHHHHHHHHHHHHhcCCCCEEEecCcEEEE
Confidence 456777777877 99999999976411 112345778888888889888888999999999999999
Q ss_pred eecCCCCCchHHHHHHHHHHHHHh-Cccccc
Q psy9708 67 HYTNTPVELRPEMVSLATQLIESA-GFKAGE 96 (99)
Q Consensus 67 HyR~v~~~~~~~v~~~~~~~~~~~-G~~~~~ 96 (99)
|||++|++...++...++++++.+ ||++++
T Consensus 239 HyR~ad~~~~~~l~~~~~~vl~~~~~l~v~~ 269 (366)
T PLN03017 239 HFRCVDEKKWSELVLQVRSVLKNFPTLKLTQ 269 (366)
T ss_pred EcCcCCHHHHHHHHHHHHHHHHhCCCcEEeC
Confidence 999998887788888888888876 477754
No 5
>COG1877 OtsB Trehalose-6-phosphatase [Carbohydrate transport and metabolism]
Probab=99.41 E-value=1e-12 Score=100.28 Aligned_cols=94 Identities=15% Similarity=0.154 Sum_probs=78.7
Q ss_pred hhHHHhhhCCCC-eEEecccceeee-----eccCCccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCc
Q psy9708 2 LKWIERHYCKQG-AWVENKGPLLTF-----HYTNTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVEL 75 (99)
Q Consensus 2 l~dl~~~v~~~g-~~vgnhG~el~~-----h~~~~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~ 75 (99)
++++...+++|| +++|+||++..- |++-.+.+..+-+.+.++.|+..+...||..||.|++.++||||+++++.
T Consensus 68 ~~~l~~~~~v~~i~l~aehGa~~r~~~g~~~~~~~~~~~~~~~~~v~~~l~~~v~r~pGs~iE~K~~a~~~Hyr~a~~~~ 147 (266)
T COG1877 68 LAELERLFGVPGIGLIAEHGAEVRDPNGKWWINLAEEADLRWLKEVAAILEYYVERTPGSYIERKGFAVALHYRNAEDDE 147 (266)
T ss_pred HHHHHHhcCCCCccEEEecceEEecCCCCeeEecCHHHHhhHHHHHHHHHHHHhhcCCCeEEEEcCcEEEEeeccCCchh
Confidence 468899999999 899999999832 66777788888888999999999999999999999999999999999988
Q ss_pred hHHHHHHHHHHHHHhC-cccc
Q psy9708 76 RPEMVSLATQLIESAG-FKAG 95 (99)
Q Consensus 76 ~~~v~~~~~~~~~~~G-~~~~ 95 (99)
.......-+......+ ++++
T Consensus 148 ~~~~a~~~~~~~~~~~~~~v~ 168 (266)
T COG1877 148 GAALALAEAATLINELKLRVT 168 (266)
T ss_pred hHHHHHHHHHhccccccEEEE
Confidence 8887665555555555 5543
No 6
>TIGR00685 T6PP trehalose-phosphatase. At least 18 distinct sequences from Arabidopsis have been identified, roughly half of these are of the fungal type, with a fused synthase and half are like the bacterial members having only the phosphatase domain. It has been suggested that trehalose is being used in Arabidopsis as a regulatory molecule in development and possibly other processes.
Probab=99.30 E-value=8.2e-12 Score=92.45 Aligned_cols=93 Identities=19% Similarity=0.174 Sum_probs=66.3
Q ss_pred hHHHhhhCCCC-eEEecccceeee--ec--cCCccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCc--
Q psy9708 3 KWIERHYCKQG-AWVENKGPLLTF--HY--TNTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVEL-- 75 (99)
Q Consensus 3 ~dl~~~v~~~g-~~vgnhG~el~~--h~--~~~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~-- 75 (99)
.++...+..++ +++|+||.++.. .. ...+.+..+.+.+.+.+|.+.+..++|.+||+|+.++++|||++|+..
T Consensus 54 ~~~~~~~~~~~~~l~g~hG~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~~~~~~pG~~iE~K~~s~~~hyr~a~d~~~~ 133 (244)
T TIGR00685 54 LEKWLGVKLPGLGLAGEHGCEMKDNGSCQDWVNLTEKIPSWKVRANELREEITTRPGVFIERKGVALAWHYRQAPVPELA 133 (244)
T ss_pred hhccccCCCCceeEEeecCEEEecCCCcceeeechhhhhhHHHHHHHHHHHHhcCCCcEEEecceEEEEEeccCCCcHHH
Confidence 45666777888 899999999753 11 112233335667777888888866799999999999999999997643
Q ss_pred hHHHHHHHHHHHHHhCcccc
Q psy9708 76 RPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 76 ~~~v~~~~~~~~~~~G~~~~ 95 (99)
..++.+.+..+.+..||.+.
T Consensus 134 ~~~~~~~~~~~~~~~~~~v~ 153 (244)
T TIGR00685 134 RFRAKELKEKILSFTDLEVM 153 (244)
T ss_pred HHHHHHHHHHHhcCCCEEEE
Confidence 23344556666666677664
No 7
>PLN03063 alpha,alpha-trehalose-phosphate synthase (UDP-forming); Provisional
Probab=98.56 E-value=4.1e-07 Score=78.03 Aligned_cols=84 Identities=12% Similarity=0.252 Sum_probs=55.3
Q ss_pred hhHHHhhhCCCC-eEEecccceeee---ecc-CCc----cchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCCC
Q psy9708 2 LKWIERHYCKQG-AWVENKGPLLTF---HYT-NTP----VELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTP 72 (99)
Q Consensus 2 l~dl~~~v~~~g-~~vgnhG~el~~---h~~-~~p----~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~ 72 (99)
+++|++.++.++ ..+|+||+++-. ... ..+ .++.+.+...++... ...||.+||+|+.++++|||+++
T Consensus 560 ~~~L~~~~~~~~l~l~aeHG~~~r~~~~~w~~~~~~~~~~~w~~~v~~~l~~~~---~rtpGs~iE~K~~sla~HyR~ad 636 (797)
T PLN03063 560 KDILDKNFGEYNIWLAAENGMFLRHTSGEWVTTMPEHMNLDWVDGVKNVFKYFT---DRTPRSYVEKSETSLVWNYEYAD 636 (797)
T ss_pred HHHHHHHhCCCCCcEEEeCCEEEecCCCceeeccccccChhHHHHHHHHHHHHH---HhCCCcEEEEcCeEEEEEcCCCC
Confidence 468889998888 899999999642 111 111 234444444433333 45679999999999999999997
Q ss_pred CCch-HHHHHHHHHHHH
Q psy9708 73 VELR-PEMVSLATQLIE 88 (99)
Q Consensus 73 ~~~~-~~v~~~~~~~~~ 88 (99)
++.. ....+.+..+.+
T Consensus 637 p~~g~~~a~el~~~l~~ 653 (797)
T PLN03063 637 VEFGRAQARDMLQHLWA 653 (797)
T ss_pred hHHHHHHHHHHHHHHHH
Confidence 6653 444454555433
No 8
>PLN03064 alpha,alpha-trehalose-phosphate synthase (UDP-forming); Provisional
Probab=98.52 E-value=4.2e-07 Score=79.30 Aligned_cols=71 Identities=11% Similarity=0.211 Sum_probs=48.8
Q ss_pred hhHHHhhhCCCC-eEEecccceeee---ecc-CCcc----chhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCCC
Q psy9708 2 LKWIERHYCKQG-AWVENKGPLLTF---HYT-NTPV----ELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTP 72 (99)
Q Consensus 2 l~dl~~~v~~~g-~~vgnhG~el~~---h~~-~~p~----e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~ 72 (99)
+++|++.++..+ ..+|+||+++-. ... ..+. ++.+.+....+.. ....||.+||.|+.++++|||+++
T Consensus 650 ~~~Le~~fg~~~L~LaAEHG~~~R~~~~~w~~~~~~~~~~~W~~~v~~ile~~---~eRtPGS~IE~K~~SLawHYR~AD 726 (934)
T PLN03064 650 RSVLDENFGEFDMWLAAENGMFLRHTKGEWMTTMPEHLNMDWVDSVKHVFEYF---TERTPRSHFETRETSLVWNYKYAD 726 (934)
T ss_pred HHHHHHHhCCCCceEEeeCCeEEecCCCcceeccccccchHHHHHHHHHHHHH---HhcCCCcEEEEcCcEEEEEecCCC
Confidence 467888898888 899999999642 111 1222 2333333333333 345679999999999999999996
Q ss_pred CCc
Q psy9708 73 VEL 75 (99)
Q Consensus 73 ~~~ 75 (99)
++.
T Consensus 727 pe~ 729 (934)
T PLN03064 727 VEF 729 (934)
T ss_pred hhh
Confidence 665
No 9
>PRK10187 trehalose-6-phosphate phosphatase; Provisional
Probab=98.23 E-value=1.3e-05 Score=60.38 Aligned_cols=85 Identities=16% Similarity=0.173 Sum_probs=55.2
Q ss_pred hHHHhhhCCCC-eEEecccceeee-----eccCCccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCch
Q psy9708 3 KWIERHYCKQG-AWVENKGPLLTF-----HYTNTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELR 76 (99)
Q Consensus 3 ~dl~~~v~~~g-~~vgnhG~el~~-----h~~~~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~ 76 (99)
.++.+.+...+ .++++||.++.. +...++.+....+.+. +.+.+...+|.+||+|+.++++|||++|+ ..
T Consensus 65 ~~~~~~~~~~~~~~i~~nGa~i~~~~~~~~~~~l~~~~~~~i~~~---l~~~~~~~pg~~ve~k~~~~~~h~r~~~~-~~ 140 (266)
T PRK10187 65 VELDALAKPYRFPLAGVHGAERRDINGKTHIVHLPDAIARDISVQ---LHTALAQLPGAELEAKGMAFALHYRQAPQ-HE 140 (266)
T ss_pred HHHHHhcCcccceEEEeCCCeeecCCCCeeeccCChhHHHHHHHH---HHHHhccCCCcEEEeCCcEEEEECCCCCc-cH
Confidence 45556665556 799999998753 2233455554444443 43334456799999999999999999854 33
Q ss_pred HHHHHHHHHHHHHhC
Q psy9708 77 PEMVSLATQLIESAG 91 (99)
Q Consensus 77 ~~v~~~~~~~~~~~G 91 (99)
+.+......+.+.++
T Consensus 141 ~~~~~l~~~i~~~~~ 155 (266)
T PRK10187 141 DALLALAQRITQIWP 155 (266)
T ss_pred HHHHHHHHHHHhhCC
Confidence 444444556666665
No 10
>PLN02205 alpha,alpha-trehalose-phosphate synthase [UDP-forming]
Probab=97.98 E-value=3.1e-05 Score=67.23 Aligned_cols=93 Identities=11% Similarity=0.172 Sum_probs=58.1
Q ss_pred hhHHHhhhCC-CC-eEEecccceeeeecc----CCccchhHHHHHHHHHHHHHh-CCCCceEEeecCCeeeEeecCCCCC
Q psy9708 2 LKWIERHYCK-QG-AWVENKGPLLTFHYT----NTPVELRPEMVSLATQLIESA-GFKAGAWVENKGPLLTFHYTNTPVE 74 (99)
Q Consensus 2 l~dl~~~v~~-~g-~~vgnhG~el~~h~~----~~p~e~~~~l~~~a~~L~e~~-~~~~G~~VE~K~~~~a~HyR~v~~~ 74 (99)
..+|++..+. ++ .++++||+++-.... .........+.+.+..+.+.+ ...+|.+||.|+.++++|||+++++
T Consensus 644 ~~~L~~~f~~~~~l~laaEHG~~ir~~~~~~w~~~~~~~~~~w~~~v~~i~~~y~ertpGs~IE~K~~slv~HyR~adpd 723 (854)
T PLN02205 644 RKTLADWFSPCEKLGIAAEHGYFLRLKRDVEWETCVPVADCSWKQIAEPVMQLYTETTDGSTIEDKETALVWCYEDADPD 723 (854)
T ss_pred HHHHHHHhCCCCCeEEEEeCCEEEEeCCCceeeecchhhhHHHHHHHHHHHHHHhcCCCchhheecceEEEEehhhCChH
Confidence 3567777765 56 899999998753211 111111122223333333433 4568999999999999999999765
Q ss_pred ch----HHHHHHHHHHHHHhCccc
Q psy9708 75 LR----PEMVSLATQLIESAGFKA 94 (99)
Q Consensus 75 ~~----~~v~~~~~~~~~~~G~~~ 94 (99)
.. .++.+.....+...++.+
T Consensus 724 ~~~~qa~el~~~l~~~l~~~~~~v 747 (854)
T PLN02205 724 FGSCQAKELLDHLESVLANEPVTV 747 (854)
T ss_pred HhhhhhHHHHHHHHHHHhcCceEE
Confidence 43 356666666666655543
No 11
>PLN03017 trehalose-phosphatase
Probab=97.31 E-value=0.00059 Score=54.53 Aligned_cols=58 Identities=17% Similarity=0.165 Sum_probs=41.5
Q ss_pred HHhhh-CCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhC---CCCce-EEeecCC
Q psy9708 5 IERHY-CKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG---FKAGA-WVENKGP 62 (99)
Q Consensus 5 l~~~v-~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~---~~~G~-~VE~K~~ 62 (99)
|++.. ..||+|||+|++.++.|||.+|.+....+...+....+..+ ...|- .+|-||+
T Consensus 217 L~~~~~~~pGa~VE~K~~~vavHyR~ad~~~~~~l~~~~~~vl~~~~~l~v~~GkkVlEvRP~ 279 (366)
T PLN03017 217 LLEKTKSTPGAKVENHKFCASVHFRCVDEKKWSELVLQVRSVLKNFPTLKLTQGRKVFEIRPM 279 (366)
T ss_pred HHHHHhcCCCCEEEecCcEEEEEcCcCCHHHHHHHHHHHHHHHHhCCCcEEeCCCeEEEecCC
Confidence 44444 67999999999999999999987665555555565555553 23444 8888875
No 12
>PLN02580 trehalose-phosphatase
Probab=97.15 E-value=0.00095 Score=53.63 Aligned_cols=40 Identities=23% Similarity=0.261 Sum_probs=32.9
Q ss_pred CCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHh
Q psy9708 10 CKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESA 49 (99)
Q Consensus 10 ~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~ 49 (99)
+.||+|||+|++.++.|||.+|.+..+.+.+.++++.+++
T Consensus 241 ~~pGs~VE~K~~svavHYR~a~~~~~~~~~~~l~~~l~~~ 280 (384)
T PLN02580 241 DIKGAKVENHKFCVSVHYRNVDEKNWPLVAQCVHDVLKKY 280 (384)
T ss_pred cCCCCEEEecCcEEEEEeCCCCchHHHHHHHHHHHHHHhC
Confidence 5689999999999999999999887777766666665544
No 13
>PLN02151 trehalose-phosphatase
Probab=97.10 E-value=0.0015 Score=52.01 Aligned_cols=53 Identities=15% Similarity=0.175 Sum_probs=38.9
Q ss_pred CCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhC---CCCce-EEeecCC
Q psy9708 10 CKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG---FKAGA-WVENKGP 62 (99)
Q Consensus 10 ~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~---~~~G~-~VE~K~~ 62 (99)
..||+|+|+|++.++.|||.+|.+....+...+.++.+.++ ...|- .+|-||+
T Consensus 209 ~~pG~~VE~K~~slavHYR~a~~~~~~~l~~~l~~v~~~~~~l~v~~GkkVvEvrP~ 265 (354)
T PLN02151 209 SIPGAKVENNKFCASVHFRCVEENKWSDLANQVRSVLKNYPKLMLTQGRKVLEIRPI 265 (354)
T ss_pred cCCCCEEEecCcEEEEEeCCCChHHHHHHHHHHHHHHhhCCCcEEecCCEEEEEeCC
Confidence 57899999999999999999987643444455555555543 24454 8888875
No 14
>PRK14501 putative bifunctional trehalose-6-phosphate synthase/HAD hydrolase subfamily IIB; Provisional
Probab=97.08 E-value=0.0031 Score=53.59 Aligned_cols=90 Identities=18% Similarity=0.301 Sum_probs=56.9
Q ss_pred hHHHhhhCCCC-eEEecccceeeeeccC------CccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCc
Q psy9708 3 KWIERHYCKQG-AWVENKGPLLTFHYTN------TPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVEL 75 (99)
Q Consensus 3 ~dl~~~v~~~g-~~vgnhG~el~~h~~~------~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~ 75 (99)
.+|++.++..+ .++++||..+-..... .+..+.+.+......+.+ ..+|.++|+|+.++++|||+++++.
T Consensus 543 ~~l~~~~~~~~l~liaenG~~i~~~~~~w~~~~~~~~~w~~~v~~il~~~~~---~~~gs~ie~k~~~l~~~~r~~d~~~ 619 (726)
T PRK14501 543 DTLERWFGDLPIHLVAEHGAWSRAPGGEWQLLEPVATEWKDAVRPILEEFVD---RTPGSFIEEKEASLAWHYRNADPEL 619 (726)
T ss_pred HHHHHHhCCCCeEEEEeCCEEEeCCCCceEECCCcchhHHHHHHHHHHHHHh---cCCCcEEEEcceEEEEEccCCCHHH
Confidence 46677777667 8999999987531111 123444444444444333 4679999999999999999987655
Q ss_pred hHH----HHHHHHHHHHHhCcccc
Q psy9708 76 RPE----MVSLATQLIESAGFKAG 95 (99)
Q Consensus 76 ~~~----v~~~~~~~~~~~G~~~~ 95 (99)
... +......++...++.+.
T Consensus 620 ~~~~a~~l~~~l~~~~~~~~~~v~ 643 (726)
T PRK14501 620 GEARANELILALSSLLSNAPLEVL 643 (726)
T ss_pred HHHHHHHHHHHHHHHhcCCCeEEE
Confidence 433 44444555555555543
No 15
>PF02358 Trehalose_PPase: Trehalose-phosphatase; InterPro: IPR003337 Trehalose-phosphatases 3.1.3.12 from EC catalyse the de-phosphorylation of trehalose-6-phosphate to trehalose and orthophosphate. Trehalose is a common disaccharide of bacteria, fungi and invertebrates that appears to play a major role in desiccation tolerance. A pathway for trehalose biosynthesis may also exist in plants []. The trehalose-phosphatase signature is found in the C terminus of trehalose-6-phosphate synthase 2.4.1.15 from EC adjacent to the trehalose-6-phosphate synthase domain (see IPR001830 from INTERPRO). It would appear that the two equivalent genes in the Escherichia coli otsBA operon: otsA, the trehalose-6-phosphate synthase and otsB, trehalose-phosphatase (this family) have undergone gene fusion in most eukaryotes [].; GO: 0003824 catalytic activity, 0005992 trehalose biosynthetic process; PDB: 1U02_A.
Probab=96.88 E-value=0.0023 Score=46.91 Aligned_cols=40 Identities=28% Similarity=0.505 Sum_probs=26.6
Q ss_pred CCCCeEEecccceeeeeccCCccc----hhHHHHHHHHHHHHHh
Q psy9708 10 CKQGAWVENKGPLLTFHYTNTPVE----LRPEMVSLATQLIESA 49 (99)
Q Consensus 10 ~~~g~~vgnhG~el~~h~~~~p~e----~~~~l~~~a~~L~e~~ 49 (99)
..||.|++.|++.+++|||.++.+ ....+...+.++....
T Consensus 102 ~~pG~~iE~K~~sv~~Hyr~~~~~~~~~~~~~l~~~l~~~~~~~ 145 (235)
T PF02358_consen 102 RTPGSFIEDKEFSVAFHYRNAPPEFGEAQARELAEQLREILASH 145 (235)
T ss_dssp HSTT-EEEEETTEEEEE-TTS-ST----THHHHHHHHHHHHHHH
T ss_pred hccCcEEEECCeEEEEEecCCCcchhhhHHHHHHHHHHHHHHhC
Confidence 369999999999999999999987 3444444444444443
No 16
>COG1877 OtsB Trehalose-6-phosphatase [Carbohydrate transport and metabolism]
Probab=96.39 E-value=0.0041 Score=47.75 Aligned_cols=56 Identities=20% Similarity=0.302 Sum_probs=40.6
Q ss_pred CCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhC---CCCce-EEeecCCeee
Q psy9708 10 CKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG---FKAGA-WVENKGPLLT 65 (99)
Q Consensus 10 ~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~---~~~G~-~VE~K~~~~a 65 (99)
..||+|++.||+.+.+|||.++.+.........+.+..... ..+|- .||-||..++
T Consensus 123 r~pGs~iE~K~~a~~~Hyr~a~~~~~~~~a~~~~~~~~~~~~~~v~~gk~vVEvrp~~~~ 182 (266)
T COG1877 123 RTPGSYIERKGFAVALHYRNAEDDEGAALALAEAATLINELKLRVTPGKMVVELRPPGVS 182 (266)
T ss_pred cCCCeEEEEcCcEEEEeeccCCchhhHHHHHHHHHhccccccEEEEeCceEEEEeeCCcc
Confidence 46899999999999999999998877776655444433332 12233 8888887765
No 17
>TIGR00685 T6PP trehalose-phosphatase. At least 18 distinct sequences from Arabidopsis have been identified, roughly half of these are of the fungal type, with a fused synthase and half are like the bacterial members having only the phosphatase domain. It has been suggested that trehalose is being used in Arabidopsis as a regulatory molecule in development and possibly other processes.
Probab=96.09 E-value=0.01 Score=43.84 Aligned_cols=37 Identities=32% Similarity=0.658 Sum_probs=26.5
Q ss_pred CCCeEEecccceeeeeccCCcc-c-hhHHHHHHHHHHHH
Q psy9708 11 KQGAWVENKGPLLTFHYTNTPV-E-LRPEMVSLATQLIE 47 (99)
Q Consensus 11 ~~g~~vgnhG~el~~h~~~~p~-e-~~~~l~~~a~~L~e 47 (99)
.||.|+|+|++.+++|||.+|. + ....+.+++..+.+
T Consensus 108 ~pG~~iE~K~~s~~~hyr~a~d~~~~~~~~~~~~~~~~~ 146 (244)
T TIGR00685 108 RPGVFIERKGVALAWHYRQAPVPELARFRAKELKEKILS 146 (244)
T ss_pred CCCcEEEecceEEEEEeccCCCcHHHHHHHHHHHHHHhc
Confidence 3999999999999999999965 3 33334444444444
No 18
>KOG1050|consensus
Probab=95.35 E-value=0.062 Score=46.52 Aligned_cols=72 Identities=15% Similarity=0.233 Sum_probs=45.6
Q ss_pred hCCCC-eEEecccceeeee---ccCC-ccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHH
Q psy9708 9 YCKQG-AWVENKGPLLTFH---YTNT-PVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLA 83 (99)
Q Consensus 9 v~~~g-~~vgnhG~el~~h---~~~~-p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~ 83 (99)
.++++ +.+..||.-+--. ++.+ -.++.+.+....+...+ -.||.++|.|.+++++|||++.++...-.....
T Consensus 553 ~~~~~lgl~aEhG~f~r~~~~w~~~~~~~~w~~~v~~i~~~~~e---rt~GS~ie~k~~~l~~hy~~ad~~~g~~qA~el 629 (732)
T KOG1050|consen 553 FGCKNLGLAAEHGYFVRIPGKWETCVLDLDWKDLVKDIFQYYTE---RTPGSYIERKETALVWHYRNADPEFGELQAKEL 629 (732)
T ss_pred cccccceeecccCceeccCCceeeecccccHHHHHHHHHHHHHh---cCCCceecccCceEEEeeeccCcchhHHHHHHH
Confidence 45667 7888888774331 2222 23555555444333333 568999999999999999999555555433333
No 19
>PLN03063 alpha,alpha-trehalose-phosphate synthase (UDP-forming); Provisional
Probab=94.98 E-value=0.055 Score=46.96 Aligned_cols=53 Identities=19% Similarity=0.254 Sum_probs=36.8
Q ss_pred CCCCeEEecccceeeeeccCCccchh-HHHHHHHHHHHHHh-C-----CCCce-EEeecCC
Q psy9708 10 CKQGAWVENKGPLLTFHYTNTPVELR-PEMVSLATQLIESA-G-----FKAGA-WVENKGP 62 (99)
Q Consensus 10 ~~~g~~vgnhG~el~~h~~~~p~e~~-~~l~~~a~~L~e~~-~-----~~~G~-~VE~K~~ 62 (99)
..||.|+|+|++.+.+|||.++.++. ....+++..|.+.+ + ..+|. .||-||.
T Consensus 615 rtpGs~iE~K~~sla~HyR~adp~~g~~~a~el~~~l~~~~~~~~~~~v~~Gk~vvEvrp~ 675 (797)
T PLN03063 615 RTPRSYVEKSETSLVWNYEYADVEFGRAQARDMLQHLWAGPISNASVDVVRGQKSVEVHAI 675 (797)
T ss_pred hCCCcEEEEcCeEEEEEcCCCChHHHHHHHHHHHHHHHHhhccCCCcEEEECCeEEEEEcC
Confidence 35899999999999999999976664 66666666664443 1 12233 6676654
No 20
>PLN03064 alpha,alpha-trehalose-phosphate synthase (UDP-forming); Provisional
Probab=93.62 E-value=0.15 Score=45.25 Aligned_cols=38 Identities=16% Similarity=0.206 Sum_probs=27.8
Q ss_pred CCCCeEEecccceeeeeccCCccchhHH-HHHHHHHHHH
Q psy9708 10 CKQGAWVENKGPLLTFHYTNTPVELRPE-MVSLATQLIE 47 (99)
Q Consensus 10 ~~~g~~vgnhG~el~~h~~~~p~e~~~~-l~~~a~~L~e 47 (99)
..||.|+|+|++.+.+|||.++.++... ..+++..|.+
T Consensus 705 RtPGS~IE~K~~SLawHYR~ADpe~g~~qA~el~~~L~~ 743 (934)
T PLN03064 705 RTPRSHFETRETSLVWNYKYADVEFGRLQARDMLQHLWT 743 (934)
T ss_pred cCCCcEEEEcCcEEEEEecCCChhhHHHHHHHHHHHHHh
Confidence 3589999999999999999996665333 4455555533
No 21
>TIGR01484 HAD-SF-IIB HAD-superfamily hydrolase, subfamily IIB. The IIB subfamily consists of Trehalose-6-phosphatase (TIGR00685), plant and cyanobacterial Sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase (pfam03332), a large subfamily ("Cof-like hydrolases", TIGR00099) containing many closely related bacterial sequences, a hypothetical equivalog containing the E. coli YedP protein, as well as two small clusters containing sequences whose relationship to the other groups is unclear.
Probab=90.04 E-value=1 Score=31.62 Aligned_cols=59 Identities=19% Similarity=0.445 Sum_probs=35.2
Q ss_pred CCeEEecccceeeee----ccCCccchhHHHHHHHHHHH---HHh-CCCCceEEeecCCeeeEeecCC
Q psy9708 12 QGAWVENKGPLLTFH----YTNTPVELRPEMVSLATQLI---ESA-GFKAGAWVENKGPLLTFHYTNT 71 (99)
Q Consensus 12 ~g~~vgnhG~el~~h----~~~~p~e~~~~l~~~a~~L~---e~~-~~~~G~~VE~K~~~~a~HyR~v 71 (99)
+.+++++||..+..- +.. +.+....+......+. +.+ ...+|.++|.|...+++||++.
T Consensus 55 ~~~~i~~nGa~i~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~ 121 (204)
T TIGR01484 55 PLPLIAENGALIFYPGEILYIE-PSDVFEEILGIKEEIGAELKSLSEHYVGTFIEDKAIAVAIHYVGA 121 (204)
T ss_pred CCCEEECCCcEEEECCEEEEEc-ccccHHHHHHhhhhcCceeeeeccccccceeecccceeeEEEecc
Confidence 348999999998541 222 2233232222112211 111 3456778999999999999985
No 22
>PRK10187 trehalose-6-phosphate phosphatase; Provisional
Probab=87.92 E-value=2.4 Score=31.90 Aligned_cols=40 Identities=25% Similarity=0.378 Sum_probs=29.3
Q ss_pred CCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhC
Q psy9708 10 CKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG 50 (99)
Q Consensus 10 ~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~ 50 (99)
+.||.|+++|+..++.||+.+|. ..+.+.++.+.+.+..+
T Consensus 116 ~~pg~~ve~k~~~~~~h~r~~~~-~~~~~~~l~~~i~~~~~ 155 (266)
T PRK10187 116 QLPGAELEAKGMAFALHYRQAPQ-HEDALLALAQRITQIWP 155 (266)
T ss_pred cCCCcEEEeCCcEEEEECCCCCc-cHHHHHHHHHHHHhhCC
Confidence 45799999999999999998854 34555566566665553
No 23
>KOG1050|consensus
Probab=86.75 E-value=1.4 Score=38.46 Aligned_cols=42 Identities=24% Similarity=0.398 Sum_probs=29.4
Q ss_pred CCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhCC-CCce
Q psy9708 11 KQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGF-KAGA 55 (99)
Q Consensus 11 ~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~~-~~G~ 55 (99)
.||+|+++|+..+++||+.+..+.-...+ ++|.+.+.- ..++
T Consensus 598 t~GS~ie~k~~~l~~hy~~ad~~~g~~qA---~el~~~l~~~~~~~ 640 (732)
T KOG1050|consen 598 TPGSYIERKETALVWHYRNADPEFGELQA---KELLEHLESKNEPV 640 (732)
T ss_pred CCCceecccCceEEEeeeccCcchhHHHH---HHHHHHhcccCCCe
Confidence 38999999999999999999656655544 444444432 3444
No 24
>TIGR02471 sucr_syn_bact_C sucrose phosphate synthase, sucrose phosphatase-like domain, bacterial. Sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP) are the last two enzymes of sucrose biosynthesis. In cyanobacteria and plants, the C-terminal region of most or all versions of SPS has a domain homologous to the known SPP. This domain may serve a binding or regulatory rather than catalytic function. Sequences in this family are bacterial C-terminal regions found in all but two of the putative bacterial sucrose phosphate synthases described by TIGR02472.
Probab=80.53 E-value=19 Score=25.93 Aligned_cols=83 Identities=8% Similarity=0.060 Sum_probs=43.0
Q ss_pred hCCCC--eEEecccceeeeeccCC-ccchhHHHHH--HHHHHHHHhCCCCceEEeecCC--eeeEeecCCCCCchHHHHH
Q psy9708 9 YCKQG--AWVENKGPLLTFHYTNT-PVELRPEMVS--LATQLIESAGFKAGAWVENKGP--LLTFHYTNTPVELRPEMVS 81 (99)
Q Consensus 9 v~~~g--~~vgnhG~el~~h~~~~-p~e~~~~l~~--~a~~L~e~~~~~~G~~VE~K~~--~~a~HyR~v~~~~~~~v~~ 81 (99)
++++. .++++||.++..-..-. +..+...+.. ...++.+.+...+|..+|+++. ...+||+..|+. .+. ..
T Consensus 51 l~l~~~~~~I~~nGa~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~-~~~-~~ 128 (236)
T TIGR02471 51 LNLPSPDVLIARVGTEIYYGPELQPDRFWQKHIDHDWRRQAVVEALADIPGLTLQDDQEQGPFKISYLLDPEG-EPI-LP 128 (236)
T ss_pred CCCCCCCEEEECCCceEEeCCCCCCChhHHHHHhcCCCHHHHHHHHhcCCCcEeCChhcCCCeeEEEEECccc-chH-HH
Confidence 45543 58999999985411111 1222111100 0112333344466789999884 588999985543 222 23
Q ss_pred HHHHHHHHhCcc
Q psy9708 82 LATQLIESAGFK 93 (99)
Q Consensus 82 ~~~~~~~~~G~~ 93 (99)
...+.+++.+..
T Consensus 129 ~~~~~l~~~~~~ 140 (236)
T TIGR02471 129 QIRQRLRQQSQA 140 (236)
T ss_pred HHHHHHHhccCC
Confidence 344455555543
No 25
>PLN02205 alpha,alpha-trehalose-phosphate synthase [UDP-forming]
Probab=79.90 E-value=1.8 Score=38.16 Aligned_cols=25 Identities=20% Similarity=0.453 Sum_probs=21.4
Q ss_pred CCCCeEEecccceeeeeccCCccch
Q psy9708 10 CKQGAWVENKGPLLTFHYTNTPVEL 34 (99)
Q Consensus 10 ~~~g~~vgnhG~el~~h~~~~p~e~ 34 (99)
..||.|+|.|++.+..||+.++.++
T Consensus 700 rtpGs~IE~K~~slv~HyR~adpd~ 724 (854)
T PLN02205 700 TTDGSTIEDKETALVWCYEDADPDF 724 (854)
T ss_pred CCCchhheecceEEEEehhhCChHH
Confidence 3489999999999999999986554
No 26
>cd00995 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is inv
Probab=67.69 E-value=21 Score=27.63 Aligned_cols=50 Identities=30% Similarity=0.469 Sum_probs=36.2
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|...| |+..+++.|..-. .....+....++-.++.|+++.
T Consensus 306 ~kA~~lL~~ag~~~~-----~~~~l~l~~~~~~-~~~~~~a~~i~~~l~~~Gi~v~ 355 (466)
T cd00995 306 EKAKELLAEAGYKDG-----KGLELTLLYNSDG-PTRKEIAEAIQAQLKEIGIKVE 355 (466)
T ss_pred HHHHHHHHHhCCCCC-----CceEEEEEeCCCC-CcHHHHHHHHHHHHHHcCceEE
Confidence 566888888887665 7889999997743 2345566667777777898874
No 27
>PF07364 DUF1485: Protein of unknown function (DUF1485); InterPro: IPR015995 Proteins in this entry are involved in degradation of the cyanobacterial heptapeptide hepatotoxin microcystin LR, and are encoded in the mlr gene cluster []. MlrC from Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273) is believed to mediate the last step of peptidolytic degradation of the tetrapeptide. It is suspected to be a metallopeptidase based on homology to known peptidases and its inhibition by metal chelators. The proteins encoded by the mlr cluster may be involved in cell wall peptidoglycan cycling and subsequently act fortuitously in hydrolysis of microcystin LR. This entry represents the N-terminal region of these proteins.; PDB: 3IUU_A.
Probab=66.57 E-value=21 Score=27.75 Aligned_cols=91 Identities=16% Similarity=0.156 Sum_probs=49.2
Q ss_pred ChhHHHhhhCCCCeEEecccceeee-----------------------------e----------------ccCCcc-ch
Q psy9708 1 MLKWIERHYCKQGAWVENKGPLLTF-----------------------------H----------------YTNTPV-EL 34 (99)
Q Consensus 1 ~l~dl~~~v~~~g~~vgnhG~el~~-----------------------------h----------------~~~~p~-e~ 34 (99)
+|++|+..-.+||.|...||..++- | |+.-|. +.
T Consensus 87 il~~l~~agp~Dgv~L~LHGAmv~e~~~D~EG~Ll~rvR~~vGp~vpI~~tlDlHaNvs~~mv~~ad~~~~yrtyPH~D~ 166 (292)
T PF07364_consen 87 ILDRLRAAGPLDGVLLDLHGAMVAEGYDDGEGDLLRRVRAIVGPDVPIAATLDLHANVSPRMVEAADIIVGYRTYPHIDM 166 (292)
T ss_dssp HHHHHHHS---SEEEEEE-S---BSS-SSHHHHHHHHHHHHHTTTSEEEEEE-TT----HHHHHH-SEEEE---SS---H
T ss_pred HHHHHHhcCCcCEEEEeccCcEeecCCCCchHHHHHHHHHHhCCCCeEEEEeCCCCCccHHHHHhCCEEEEcCCCCccCH
Confidence 3677888777889999999988655 2 444453 55
Q ss_pred hHHHHHHHHHHHHHh--CCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhC
Q psy9708 35 RPEMVSLATQLIESA--GFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG 91 (99)
Q Consensus 35 ~~~l~~~a~~L~e~~--~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G 91 (99)
.+.=.++++-|.+.+ +.+|-.++..-|..+......+..+=-..+++.++++-++-|
T Consensus 167 ~etg~~aa~ll~~~l~g~~rp~~a~~~~P~l~~~~~~~T~~~P~~~l~~~~~~~e~~~g 225 (292)
T PF07364_consen 167 YETGERAARLLLRALRGEIRPVMALRRLPMLLPGENQTTDDEPMKSLYARARELEARPG 225 (292)
T ss_dssp HHHHHHHHHHHHHTTT-SS--EEEEEEE-B--BS----SSSSHHHHHHHHHHHHHTSTT
T ss_pred HHHHHHHHHHHHHHHcCCCCceEEEecCCeEcccCCCCCCcHHHHHHHHHHHHHhcCCC
Confidence 555556666666655 245666777777777766666677777888888888777655
No 28
>COG3889 Predicted solute binding protein [General function prediction only]
Probab=61.50 E-value=23 Score=31.63 Aligned_cols=87 Identities=11% Similarity=0.037 Sum_probs=63.4
Q ss_pred CCCCeEEecccceeeeecc-------CCccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeec-CCCCCchHHHHH
Q psy9708 10 CKQGAWVENKGPLLTFHYT-------NTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYT-NTPVELRPEMVS 81 (99)
Q Consensus 10 ~~~g~~vgnhG~el~~h~~-------~~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR-~v~~~~~~~v~~ 81 (99)
.+.|+|-+.|+.-..+.+- ....-..+-+.++..++.+++. ..|.|++.|.+...||+= -|.++..++...
T Consensus 140 Pm~~~~~~~~~a~~i~a~i~~~lgvt~~~D~A~q~veq~m~e~~a~~~-~~G~~~~~~~~~~dV~fvIRvederkd~~~~ 218 (872)
T COG3889 140 PMYGLYRKLTPAYVIYADIWEWLGVTYDGDYANQYVEQAMAELNAEYM-AKGLWYKVGKPDDDVHFVIRVEDERKDEGFQ 218 (872)
T ss_pred eeeeeecCCCCceEEeeehhHHhCccccccccHHHHHHHHHHHHHHHh-hcCcEEEecCCCceeEEEEEEeeeeeccccc
Confidence 3456777788877655211 1122233778889999999994 789999999999877763 247788888888
Q ss_pred HHHHHHHHhCcccccc
Q psy9708 82 LATQLIESAGFKAGEC 97 (99)
Q Consensus 82 ~~~~~~~~~G~~~~~~ 97 (99)
-..-+-+..||++++.
T Consensus 219 ~~~~~e~~L~f~V~ri 234 (872)
T COG3889 219 PFKWIEYYLGFTVTRI 234 (872)
T ss_pred HHHHHHHHhCceEEEE
Confidence 8888889999998764
No 29
>cd08495 PBP2_NikA_DppA_OppA_like_8 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=57.40 E-value=37 Score=26.93 Aligned_cols=49 Identities=18% Similarity=0.244 Sum_probs=32.3
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCC--CCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTP--VELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~--~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|...| ++ +++.+..-+ .....++...+++-+++.|+++.
T Consensus 316 ~~Ak~lL~~aG~~~~-----~~--l~l~~~~~~~~~~~~~~~a~~i~~~l~~~Gi~v~ 366 (482)
T cd08495 316 DKARALLKEAGYGPG-----LT--LKLRVSASGSGQMQPLPMNEFIQQNLAEIGIDLD 366 (482)
T ss_pred HHHHHHHHHcCCCCC-----Cc--eEEEEecCCCCCCcHHHHHHHHHHHHHHcCceEE
Confidence 667888898887655 33 445555432 24456677777777788999874
No 30
>PRK14501 putative bifunctional trehalose-6-phosphate synthase/HAD hydrolase subfamily IIB; Provisional
Probab=56.37 E-value=27 Score=29.94 Aligned_cols=26 Identities=35% Similarity=0.631 Sum_probs=21.6
Q ss_pred CCCeEEecccceeeeeccCCccchhH
Q psy9708 11 KQGAWVENKGPLLTFHYTNTPVELRP 36 (99)
Q Consensus 11 ~~g~~vgnhG~el~~h~~~~p~e~~~ 36 (99)
.||+|+++++..+++||+..+.++..
T Consensus 596 ~~gs~ie~k~~~l~~~~r~~d~~~~~ 621 (726)
T PRK14501 596 TPGSFIEEKEASLAWHYRNADPELGE 621 (726)
T ss_pred CCCcEEEEcceEEEEEccCCCHHHHH
Confidence 46899999999999999988665543
No 31
>COG5476 Uncharacterized conserved protein [Function unknown]
Probab=55.32 E-value=10 Score=31.63 Aligned_cols=37 Identities=11% Similarity=0.203 Sum_probs=29.4
Q ss_pred hhHHHhhhCCCCeEEecccceeeeeccCCccchhHHH
Q psy9708 2 LKWIERHYCKQGAWVENKGPLLTFHYTNTPVELRPEM 38 (99)
Q Consensus 2 l~dl~~~v~~~g~~vgnhG~el~~h~~~~p~e~~~~l 38 (99)
|++|+.-+.+|+.|.+-||..+.-+|-+.-.++..++
T Consensus 88 l~~lkaalPvDavyL~LHGAmv~egydD~EGdll~rv 124 (488)
T COG5476 88 LDQLKAALPVDAVYLGLHGAMVAEGYDDGEGDLLTRV 124 (488)
T ss_pred HHHHHhcCCcceeeeecchhhhhccCcCchhHHHHHH
Confidence 7889999999999999999998887766544444443
No 32
>cd08500 PBP2_NikA_DppA_OppA_like_4 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=53.83 E-value=48 Score=26.67 Aligned_cols=55 Identities=22% Similarity=0.316 Sum_probs=36.4
Q ss_pred HHHHHHHHHhCCC----CceEE--eecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFK----AGAWV--ENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~----~G~~V--E~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|.. +|.+. ..|+..+++-|+. +......+...+++-.++.|++++
T Consensus 316 e~Ak~lL~~aG~~~~~~dG~~~~~~G~~l~l~i~~~~-~~~~~~~~a~~i~~~l~~~Gi~v~ 376 (499)
T cd08500 316 DKANKLLDEAGLKKKDADGFRLDPDGKPVEFTLITNA-GNSIREDIAELIKDDWRKIGIKVN 376 (499)
T ss_pred HHHHHHHHHcCCcccCCCCcEECCCCcEEEEEEEECC-CCchHHHHHHHHHHHHHHhCCceE
Confidence 6778888888865 34444 2456688888875 223445566666666677898874
No 33
>TIGR03006 pepcterm_polyde polysaccharide deactylase family protein, PEP-CTERM locus subfamily. Members of this protein family belong to the family of polysaccharide deacetylases (pfam01522). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. The highest scoring homologs below the trusted cutoff for this model are found in several species of Methanosarcina, an archaeal genus.
Probab=52.98 E-value=40 Score=25.62 Aligned_cols=73 Identities=18% Similarity=0.141 Sum_probs=40.4
Q ss_pred hCCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHH
Q psy9708 9 YCKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIE 88 (99)
Q Consensus 9 v~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~ 88 (99)
+.-.|+=+||||..=..-..-.+.+.+..|.+..+.|.+..|. ++ ..||. |--....-...+.+++.
T Consensus 63 i~~~GhEIgsHg~sH~~l~~ls~ee~~~eI~~s~~~Le~itG~---------~~---~gfRa-P~~s~~~~t~~a~~iL~ 129 (265)
T TIGR03006 63 IVAAGHELASHGYGHERVTTQTPEAFRADIRRSKALLEDLSGQ---------PV---RGYRA-PSFSIGKKNLWALDVLA 129 (265)
T ss_pred HHHcCCEeeeccccCcCchhCCHHHHHHHHHHHHHHHHHHhCC---------Cc---eEEEC-CCCCCCCCcHHHHHHHH
Confidence 3345799999998733333334557777776665666555541 11 24554 32111111234457788
Q ss_pred HhCccc
Q psy9708 89 SAGFKA 94 (99)
Q Consensus 89 ~~G~~~ 94 (99)
+.||+.
T Consensus 130 e~Gy~Y 135 (265)
T TIGR03006 130 EAGYRY 135 (265)
T ss_pred HCCCEE
Confidence 888875
No 34
>cd08490 PBP2_NikA_DppA_OppA_like_3 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=47.72 E-value=67 Score=25.15 Aligned_cols=55 Identities=20% Similarity=0.290 Sum_probs=33.8
Q ss_pred HHHHHHHHHhCCCCce--EEeecC--CeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGA--WVENKG--PLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~--~VE~K~--~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|+..+. +++.++ +.+++-+..- ......+....++-.++.|+++.
T Consensus 295 ~~A~~lL~~aG~~~~~~~~~~~~G~~~~l~l~~~~~-~~~~~~~a~~i~~~l~~~Gi~v~ 353 (470)
T cd08490 295 EKAKELLAEAGWTDGDGDGIEKDGEPLELTLLTYTS-RPELPPIAEAIQAQLKKIGIDVE 353 (470)
T ss_pred HHHHHHHHHcCCCCCCCcccccCCceEEEEEEecCC-CCchHHHHHHHHHHHHHcCceEE
Confidence 4668888888876533 555544 4555555442 23344556666677788898864
No 35
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=46.69 E-value=35 Score=19.23 Aligned_cols=23 Identities=13% Similarity=0.205 Sum_probs=17.1
Q ss_pred CCchHHHHHHHHHHHHHhCcccc
Q psy9708 73 VELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 73 ~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+...++..+++.+.+++.||+++
T Consensus 24 ~~vs~~tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 24 PRVSEETRERILEAAEELGYRPN 46 (46)
T ss_dssp SSSTHHHHHHHHHHHHHHTB-SS
T ss_pred CCCCHHHHHHHHHHHHHHCCCCC
Confidence 45566777888889999999864
No 36
>PF02834 LigT_PEase: LigT like Phosphoesterase; InterPro: IPR014051 This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA []. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) []. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [].; PDB: 1VGJ_A 1VDX_A 2FYH_A 2D4G_A.
Probab=46.44 E-value=48 Score=19.99 Aligned_cols=57 Identities=21% Similarity=0.470 Sum_probs=40.0
Q ss_pred CccchhHHHHHHHHHHHHHhCCCCce-EEeecCCeeeEeec-CCCCCchHHHHHHHHHHH
Q psy9708 30 TPVELRPEMVSLATQLIESAGFKAGA-WVENKGPLLTFHYT-NTPVELRPEMVSLATQLI 87 (99)
Q Consensus 30 ~p~e~~~~l~~~a~~L~e~~~~~~G~-~VE~K~~~~a~HyR-~v~~~~~~~v~~~~~~~~ 87 (99)
.|.+..+.|.++.+.|.+... ..|. |+-.=.+-+|+.+= +++++..+++++...++.
T Consensus 3 ~p~~~~~~L~~l~~~l~~~~~-~~~~r~~~~~~~HiTL~flg~~~~~~~~~l~~~l~~~~ 61 (87)
T PF02834_consen 3 LPEEIKEQLNQLQERLRQALP-PLGIRWVRPFNPHITLAFLGEVPPDQLPELIEALANIA 61 (87)
T ss_dssp -THHHHHHHHHHHHHHHHHCC-SCTEEEGSCGGSEEEEEEEEEESHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHhhhcc-ccCCcccCCCCCeEEEEeCCCCCHHHHHHHHHHHHhhh
Confidence 466788888888888887774 4455 77555566777654 556677777877777765
No 37
>PF05116 S6PP: Sucrose-6F-phosphate phosphohydrolase; InterPro: IPR006380 This family of sequences represent sucrose phosphate phosphohydrolase (SPP) from plants and cyanobacteria []. SPP is a member of the Class IIB subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. SPP catalyzes the final step in the biosynthesis of sucrose, a critically important molecule for plants. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a "product-like" orientation prior to ligation by the synthase catalytic domain.; PDB: 1TJ5_A 2B1Q_A 1TJ4_A 1S2O_A 1U2T_A 2D2V_A 1TJ3_A 1U2S_A 2B1R_A 3GYG_B ....
Probab=46.18 E-value=63 Score=23.90 Aligned_cols=81 Identities=6% Similarity=0.123 Sum_probs=48.9
Q ss_pred CCCeEEecccceeeeeccCCcc-chhHHHH-----HHHHHHHHHhC-CCCceEEeecCCeeeEeecCCCCCchHHHHHHH
Q psy9708 11 KQGAWVENKGPLLTFHYTNTPV-ELRPEMV-----SLATQLIESAG-FKAGAWVENKGPLLTFHYTNTPVELRPEMVSLA 83 (99)
Q Consensus 11 ~~g~~vgnhG~el~~h~~~~p~-e~~~~l~-----~~a~~L~e~~~-~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~ 83 (99)
.|-.++.|-|.+|..-.+-.|. ++...+. +...++..++. ..+-...+..++-++|.++.. ..+.+++..
T Consensus 60 ~Pd~~I~svGt~I~~~~~~~~d~~w~~~i~~~w~~~~v~~~l~~~~~l~~q~~~~q~~~k~sy~~~~~---~~~~~~~~i 136 (247)
T PF05116_consen 60 QPDYIITSVGTEIYYGENWQPDEEWQAHIDERWDRERVEEILAELPGLRPQPESEQRPFKISYYVDPD---DSADILEEI 136 (247)
T ss_dssp E-SEEEETTTTEEEESSTTEE-HHHHHHHHTT--HHHHHHHHHCHCCEEEGGCCCGCCTCECEEEETT---SHCHHHHHH
T ss_pred CCCEEEecCCeEEEEcCCCcChHHHHHHHHhcCChHHHHHHHHHhhCcccCCccccCCeeEEEEEecc---cchhHHHHH
Confidence 3448999999998882233343 4444444 23334444442 233335566788889988753 223456777
Q ss_pred HHHHHHhCccc
Q psy9708 84 TQLIESAGFKA 94 (99)
Q Consensus 84 ~~~~~~~G~~~ 94 (99)
++..++.|+++
T Consensus 137 ~~~l~~~~l~~ 147 (247)
T PF05116_consen 137 RARLRQRGLRV 147 (247)
T ss_dssp HHHHHCCTCEE
T ss_pred HHHHHHcCCCe
Confidence 78888899876
No 38
>COG0726 CDA1 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]
Probab=45.32 E-value=78 Score=22.20 Aligned_cols=44 Identities=18% Similarity=0.106 Sum_probs=30.5
Q ss_pred hhhCCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhC
Q psy9708 7 RHYCKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG 50 (99)
Q Consensus 7 ~~v~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~ 50 (99)
+++--.|.-+||||.....-....+.+....+...-..|....|
T Consensus 111 ~~~~~~Gheig~H~~~h~~~~~~~~~~~~~~i~~~~~~l~~~~g 154 (267)
T COG0726 111 KRIAEAGHEIGNHGYDHPDLQDLSLEELGAEIARAHDILKKITG 154 (267)
T ss_pred HHHHhccCeehhCcccCCCcccCCHHHHHHHHHHHHHHHHHHhC
Confidence 33444789999999987776666676766666665556666555
No 39
>cd08517 PBP2_NikA_DppA_OppA_like_13 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=43.96 E-value=70 Score=25.13 Aligned_cols=53 Identities=19% Similarity=0.260 Sum_probs=33.7
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|...+. ..+++.+++-|..-. .....+....++-.++.|++++
T Consensus 314 ~~A~~lL~~aG~~~~~--~G~~~~l~l~~~~~~-~~~~~~a~~i~~~l~~iGi~v~ 366 (480)
T cd08517 314 AKAEALLDEAGYPRGA--DGIRFKLRLDPLPYG-EFWKRTAEYVKQALKEVGIDVE 366 (480)
T ss_pred HHHHHHHHHcCCCcCC--CCceEEEEEEecCCC-chHHHHHHHHHHHHHHcCCEEE
Confidence 6678888888866432 123566777775422 2335566667777788898764
No 40
>PF01522 Polysacc_deac_1: Polysaccharide deacetylase; InterPro: IPR002509 This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase []. It also includes chitin deacetylase from yeast [], and endoxylanases which hydrolyses glucosidic bonds in xylan [].; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0005975 carbohydrate metabolic process; PDB: 2IW0_A 2CC0_B 2VYO_A 2J13_A 2C71_A 2C79_A 1W1A_1 1W1B_1 1W17_A 1NY1_B ....
Probab=43.40 E-value=45 Score=20.96 Aligned_cols=46 Identities=26% Similarity=0.175 Sum_probs=26.9
Q ss_pred HHHhhhCCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhC
Q psy9708 4 WIERHYCKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG 50 (99)
Q Consensus 4 dl~~~v~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~ 50 (99)
.+++... .|+=+||||..-.......+.+....|.+.-+.|.+..|
T Consensus 49 ~l~~l~~-~G~ei~~H~~~H~~~~~~~~~~~~~ei~~~~~~l~~~~g 94 (123)
T PF01522_consen 49 QLRELAA-AGHEIGNHGWSHPNLSTLSPEELRREIERSREILEEITG 94 (123)
T ss_dssp HHHHHHH-TT-EEEEE-SSSSCGGGS-HHHHHHHHHHHHHHHHHHHS
T ss_pred cchhHHH-HHHHHHhcCCcccccccCCHHHHHHHHHHHHHHHHHHhC
Confidence 3444333 458999999775544333455777777777666666665
No 41
>PF03585 Herpes_ICP4_C: Herpesvirus ICP4-like protein C-terminal region; InterPro: IPR005205 The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the C-terminal region that probably acts as an enhancer for the N-terminal region [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0042025 host cell nucleus
Probab=43.20 E-value=9.1 Score=31.36 Aligned_cols=19 Identities=26% Similarity=0.550 Sum_probs=17.3
Q ss_pred ChhHHHhhhCCCC--eEEecc
Q psy9708 1 MLKWIERHYCKQG--AWVENK 19 (99)
Q Consensus 1 ~l~dl~~~v~~~g--~~vgnh 19 (99)
||+.|-+++|.|+ +|+||=
T Consensus 136 LLAAl~NRLc~p~s~AWAGnW 156 (425)
T PF03585_consen 136 LLAALSNRLCLPESHAWAGNW 156 (425)
T ss_pred HHHHHhCcccCCcccccccCc
Confidence 6899999999999 899994
No 42
>cd08509 PBP2_TmCBP_oligosaccharides_like The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of a cellulose-binding protein from the hyperthermophilic bacterium Thermotoga maritima (TmCBP) and its closest related proteins. TmCBP binds a variety of lengths of beta-1,4-linked glucose oligomers, ranging from two sugar rings (cellobiose) to five (cellopentose). TmCBP is structurally homologous to domains I and III of the ATP-binding cassette (ABC)-type oligopeptide-binding proteins and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. L
Probab=43.13 E-value=75 Score=25.52 Aligned_cols=55 Identities=22% Similarity=0.303 Sum_probs=36.8
Q ss_pred HHHHHHHHHhCCC---CceEEe--ecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFK---AGAWVE--NKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~---~G~~VE--~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|.. .|.|.- .+++.+++-|+. .......+....++-+++.|+++.
T Consensus 325 ~~A~~lL~~aG~~~~~~G~~~~~~g~~l~l~l~~~~-~~~~~~~~a~~lq~~l~~iGi~v~ 384 (509)
T cd08509 325 DKAKKLLESAGFKKDKDGKWYTPDGTPLKFTIIVPS-GWTDWMAAAQIIAEQLKEFGIDVT 384 (509)
T ss_pred HHHHHHHHHcCCeECCCCeEECCCCceEEEEEEccC-CchHHHHHHHHHHHHHHhcCeEEE
Confidence 6667888888764 466664 345688888876 223344566677777778898763
No 43
>COG1514 LigT 2'-5' RNA ligase [Translation, ribosomal structure and biogenesis]
Probab=43.00 E-value=43 Score=24.06 Aligned_cols=61 Identities=16% Similarity=0.344 Sum_probs=41.0
Q ss_pred CccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecC-CCCCchHHHHHHHHHHHHHhCcc
Q psy9708 30 TPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTN-TPVELRPEMVSLATQLIESAGFK 93 (99)
Q Consensus 30 ~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~-v~~~~~~~v~~~~~~~~~~~G~~ 93 (99)
.|.+.++.+.+..+.+.... .+-|+|.=++-+|+++=. ++++..++|+...+++...+.|.
T Consensus 9 ~p~~i~~~i~~~~~~~~~~~---~~k~v~~en~HiTL~flGev~e~~~~~l~~~l~~i~~~~~f~ 70 (180)
T COG1514 9 PPAEIAERLARIRARLKGAR---AIKWVEPENLHITLKFLGEVDEDKADELIEALARIAAPEPFP 70 (180)
T ss_pred CCHHHHHHHHHHHHhcCccc---ccccccccCceEEEEccCCcCchHHHHHHHHHHHhhcCCceE
Confidence 35555555555444433221 466999999999998865 57788888888888887743443
No 44
>cd08504 PBP2_OppA The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which
Probab=40.86 E-value=80 Score=24.97 Aligned_cols=50 Identities=24% Similarity=0.377 Sum_probs=36.2
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHH-hCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIES-AGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~-~G~~~~ 95 (99)
+.|++|.++.|...|. |++.+++-+..- .....+...+++-+.+ .|+++.
T Consensus 326 ~kA~~lL~~aG~~~~~----~~~~l~i~~~~~--~~~~~~a~~i~~~l~~~iGI~v~ 376 (498)
T cd08504 326 EKAKKLLAEAGYELGK----NPLKLTLLYNTS--ENHKKIAEAIQQMWKKNLGVKVT 376 (498)
T ss_pred HHHHHHHHHcCcccCC----CCceEEEEecCc--hhHHHHHHHHHHHHHHcCCCeEE
Confidence 5668888888765442 678888877653 3455667778888888 899874
No 45
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown.
Probab=40.79 E-value=51 Score=22.98 Aligned_cols=40 Identities=13% Similarity=0.122 Sum_probs=25.5
Q ss_pred CCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhC
Q psy9708 11 KQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG 50 (99)
Q Consensus 11 ~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~ 50 (99)
-.|.-+|||++.=.....-.+.+....|....+.|.+..|
T Consensus 56 ~~Gheig~Ht~~H~~~~~~~~~~~~~ei~~~~~~l~~~~g 95 (191)
T TIGR02764 56 KDGHEIGSHGYRHKNYTTLEDEKIKKDILRAQEIIEKLTG 95 (191)
T ss_pred hCCCEEEECCcCCCCcccCCHHHHHHHHHHHHHHHHHHhC
Confidence 3689999999873332222345667777766666666555
No 46
>PF15475 UPF0444: Transmembrane protein C12orf23, UPF0444
Probab=39.70 E-value=19 Score=23.56 Aligned_cols=14 Identities=50% Similarity=0.653 Sum_probs=12.1
Q ss_pred CC-eEEecccceeee
Q psy9708 12 QG-AWVENKGPLLTF 25 (99)
Q Consensus 12 ~g-~~vgnhG~el~~ 25 (99)
.| +|+|++.++++-
T Consensus 32 GgVawvg~kS~~~tK 46 (92)
T PF15475_consen 32 GGVAWVGSKSLELTK 46 (92)
T ss_pred cceEEEcccceEEEE
Confidence 36 899999999984
No 47
>PRK11702 hypothetical protein; Provisional
Probab=38.63 E-value=37 Score=22.98 Aligned_cols=33 Identities=21% Similarity=0.344 Sum_probs=26.7
Q ss_pred CCeeeEeecC-CCCCchHHHHHH-HHHHHHHhCcc
Q psy9708 61 GPLLTFHYTN-TPVELRPEMVSL-ATQLIESAGFK 93 (99)
Q Consensus 61 ~~~~a~HyR~-v~~~~~~~v~~~-~~~~~~~~G~~ 93 (99)
+|.++.+|.+ ++.+..+..++. ..++++..||-
T Consensus 22 GF~v~~~~~~~~~~e~~D~~vD~fIde~Ie~ngL~ 56 (108)
T PRK11702 22 GFSVNWRFPEGTSEEQIDATVDAFIDEVIEPNGLA 56 (108)
T ss_pred eeEEEEEECCCCCHHHHHHHHHHHHHHHHhcCCce
Confidence 5889999988 788888888877 45789998864
No 48
>TIGR02631 xylA_Arthro xylose isomerase, Arthrobacter type. This model describes a D-xylose isomerase that is also active as a D-glucose isomerase. It is tetrameric and dependent on a divalent cation Mg2+, Co2+ or Mn2+ as characterized in Arthrobacter. Members of this family differ substantially from the D-xylose isomerases of family TIGR02630.
Probab=38.25 E-value=88 Score=25.04 Aligned_cols=22 Identities=18% Similarity=0.347 Sum_probs=17.5
Q ss_pred CchHHHHHHHHHHHHHhCcccc
Q psy9708 74 ELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 74 ~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
..++..++..++.++++||+++
T Consensus 64 ~e~~~~~~~lk~~L~~~GL~v~ 85 (382)
T TIGR02631 64 QERDQIVRRFKKALDETGLKVP 85 (382)
T ss_pred hHHHHHHHHHHHHHHHhCCeEE
Confidence 4445667889999999999964
No 49
>cd08510 PBP2_Lactococcal_OppA_like The substrate binding component of an ABC-type lactococcal OppA-like transport system contains. This family represents the substrate binding domain of an ATP-binding cassette (ABC)-type oligopeptide import system from Lactococcus lactis and other gram-positive bacteria, as well as its closet homologs from gram-negative bacteria. Oligopeptide-binding protein (OppA) from Lactococcus lactis can bind peptides of length from 4 to at least 35 residues without sequence preference. The oligopeptide import system OppABCDEF is consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in sev
Probab=37.78 E-value=1.1e+02 Score=24.71 Aligned_cols=55 Identities=20% Similarity=0.274 Sum_probs=34.0
Q ss_pred HHHHHHHHHhCCCC----ceEE--eecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKA----GAWV--ENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~----G~~V--E~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|... |.+. +.||+.+++-+.. .......+....++-.++.|+++.
T Consensus 344 ~~Ak~lL~eaG~~~~~~dg~~~~~~G~~l~i~l~~~~-~~~~~~~~a~~i~~~l~~~Gi~v~ 404 (516)
T cd08510 344 EKAKKLLDEAGYKDVDGDGFREDPDGKPLTINFAAMS-GSETAEPIAQYYIQQWKKIGLNVE 404 (516)
T ss_pred HHHHHHHHHcCCEEcCCCeeEECCCCcEEEEEEEecC-CCccHHHHHHHHHHHHHHcCceEE
Confidence 56788889888642 3444 3455666666543 223445555566666677898874
No 50
>cd08514 PBP2_AppA_like The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold. This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains correspondin
Probab=37.61 E-value=1e+02 Score=24.36 Aligned_cols=55 Identities=18% Similarity=0.290 Sum_probs=34.6
Q ss_pred HHHHHHHHHhCCCCc--e-EEe--ecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAG--A-WVE--NKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G--~-~VE--~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|...+ - +.+ .|++.+++.|..- ......+....++-.++.|++++
T Consensus 312 ~~Ak~lL~eaG~~~~~~~~~~~~~G~~l~l~l~~~~~-~~~~~~~a~~i~~~l~~~Gi~v~ 371 (483)
T cd08514 312 DKAKELLAEAGWVDGDDDGILDKDGKPFSFTLLTNQG-NPVREQAATIIQQQLKEIGIDVK 371 (483)
T ss_pred HHHHHHHHHcCCCcCCCCceecCCCCEEEEEEEecCC-CchHHHHHHHHHHHHHhcCcEEE
Confidence 567888888886542 1 233 2456777877642 23345566666777777898874
No 51
>PF14226 DIOX_N: non-haem dioxygenase in morphine synthesis N-terminal; PDB: 3OOX_A 1BK0_A 1IPS_B 1QIQ_A 1OC1_A 2Y86_A 2Y60_A 1W03_A 2VE1_A 1QJF_A ....
Probab=36.73 E-value=49 Score=20.94 Aligned_cols=35 Identities=17% Similarity=0.210 Sum_probs=22.0
Q ss_pred hHHHhhhCCCC-eEEecccceeeeeccCCccchhHHHHHHHHHHH
Q psy9708 3 KWIERHYCKQG-AWVENKGPLLTFHYTNTPVELRPEMVSLATQLI 46 (99)
Q Consensus 3 ~dl~~~v~~~g-~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~ 46 (99)
++|.+-..-.| .|+-|||+. .+....+-+.++++.
T Consensus 18 ~~l~~A~~~~GFf~l~nhGi~---------~~l~~~~~~~~~~fF 53 (116)
T PF14226_consen 18 EQLRDACEEWGFFYLVNHGIP---------QELIDRVFAAAREFF 53 (116)
T ss_dssp HHHHHHHHHTSEEEEESSSSS---------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCEEEEeccccc---------chhhHHHHHHHHHHH
Confidence 44555455568 899999865 355666666665544
No 52
>TIGR01893 aa-his-dipept aminoacyl-histidine dipeptidase.
Probab=36.20 E-value=1.8e+02 Score=23.49 Aligned_cols=40 Identities=10% Similarity=0.094 Sum_probs=33.5
Q ss_pred EEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 56 WVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 56 ~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
..+.....+.+..|.+|....+++.+..++.++.+|+.+.
T Consensus 346 ~~~~~~~~~~i~~R~~~~~~~~~i~~~i~~~~~~~~~~v~ 385 (477)
T TIGR01893 346 KTKENKVIFTFLIRSSVESDKDYVTEKIESIAKLAGARVE 385 (477)
T ss_pred EEcCCEEEEEEEeCCCCchhHHHHHHHHHHHhhhcCeEEE
Confidence 4566678889999999999999999999999988777653
No 53
>cd08496 PBP2_NikA_DppA_OppA_like_9 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most
Probab=33.33 E-value=1.4e+02 Score=23.49 Aligned_cols=46 Identities=22% Similarity=0.317 Sum_probs=30.9
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|+.. ++.+++.|.. .....+....++-.++.|+.++
T Consensus 301 ~~A~~lL~~aG~~~-------g~~l~i~~~~---~~~~~~a~~i~~~l~~iGi~v~ 346 (454)
T cd08496 301 EKAKELLAEAGYPN-------GFSLTIPTGA---QNADTLAEIVQQQLAKVGIKVT 346 (454)
T ss_pred HHHHHHHHHcCCCC-------CceEEEEecC---CchhHHHHHHHHHHHHcCceEE
Confidence 56678888888653 4677787765 2344555566666677898774
No 54
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the C-terminal region of DltD.; PDB: 3BMA_C.
Probab=33.11 E-value=23 Score=24.34 Aligned_cols=28 Identities=29% Similarity=0.432 Sum_probs=21.8
Q ss_pred eecCCCCCchHHHHHHHHHHHHHhCccc
Q psy9708 67 HYTNTPVELRPEMVSLATQLIESAGFKA 94 (99)
Q Consensus 67 HyR~v~~~~~~~v~~~~~~~~~~~G~~~ 94 (99)
=|-+.+.+.+.+..+..+.+++++||++
T Consensus 65 dytG~~~~~r~~~y~kI~~~~~~~gf~v 92 (130)
T PF04914_consen 65 DYTGLSKEMRQEYYKKIKYQLKSQGFNV 92 (130)
T ss_dssp HHTT--HHHHHHHHHHHHHHHHTTT--E
T ss_pred HHhCCCHHHHHHHHHHHHHHHHHCCCEE
Confidence 3677899999999999999999999976
No 55
>PF14606 Lipase_GDSL_3: GDSL-like Lipase/Acylhydrolase family; PDB: 3SKV_B.
Probab=32.93 E-value=1.3e+02 Score=21.73 Aligned_cols=63 Identities=14% Similarity=0.052 Sum_probs=37.6
Q ss_pred ccCCccchhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHh
Q psy9708 27 YTNTPVELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESA 90 (99)
Q Consensus 27 ~~~~p~e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~ 90 (99)
.|..+.++.+++....+.|++.++.+|=..||.=+.... .+++-..+...+..+..++.+++.
T Consensus 69 ~N~~~~~~~~~~~~fv~~iR~~hP~tPIllv~~~~~~~~-~~~~~~~~~~~~~~~~~r~~v~~l 131 (178)
T PF14606_consen 69 PNMSPEEFRERLDGFVKTIREAHPDTPILLVSPIPYPAG-YFDNSRGETVEEFREALREAVEQL 131 (178)
T ss_dssp HHCCTTTHHHHHHHHHHHHHTT-SSS-EEEEE----TTT-TS--TTS--HHHHHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHHHHHHhCCCCCEEEEecCCcccc-ccCchHHHHHHHHHHHHHHHHHHH
Confidence 445678999999999999999999788778886554444 333323344445556666666654
No 56
>cd08512 PBP2_NikA_DppA_OppA_like_7 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=32.16 E-value=1.8e+02 Score=22.86 Aligned_cols=48 Identities=27% Similarity=0.435 Sum_probs=31.4
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|... +..+++-+..-. .....+....++-.++.|+++.
T Consensus 319 ~~A~~lL~eaG~~~-------g~~l~l~~~~~~-~~~~~~a~~i~~~l~~~Gi~v~ 366 (476)
T cd08512 319 EKAKELLAEAGYPN-------GFKLTLSYNSGN-EPREDIAQLLQASLAQIGIKVE 366 (476)
T ss_pred HHHHHHHHHcCCCC-------CcEEEEEeCCCC-cchHHHHHHHHHHHHHhCCeEE
Confidence 56688888888653 455666666533 2345566666666777898764
No 57
>cd08492 PBP2_NikA_DppA_OppA_like_15 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=32.09 E-value=2.1e+02 Score=22.51 Aligned_cols=55 Identities=20% Similarity=0.315 Sum_probs=33.6
Q ss_pred HHHHHHHHHhCCC-C--ceEEee--cCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFK-A--GAWVEN--KGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~-~--G~~VE~--K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|+. . +-+.+. |++.+++-+..- ......+....++-.++.|+.+.
T Consensus 317 ~~A~~lL~~aG~~~~~~~g~~~~~g~~l~l~~~~~~~-~~~~~~~a~~i~~~l~~iGi~v~ 376 (484)
T cd08492 317 EKAKKLLDEAGWTARGADGIRTKDGKRLTLTFLYSTG-QPQSQSVLQLIQAQLKEVGIDLQ 376 (484)
T ss_pred HHHHHHHHHcCCCcCCCCceecCCCcEEEEEEecCCC-CchHHHHHHHHHHHHHhhCeEEE
Confidence 5678888888875 2 224453 345555555432 23455666667777788898864
No 58
>cd08515 PBP2_NikA_DppA_OppA_like_10 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=32.05 E-value=1.8e+02 Score=22.85 Aligned_cols=49 Identities=14% Similarity=0.167 Sum_probs=29.3
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|+..| ..+++.+.........++.+..++-.++.|++++
T Consensus 309 ~~A~~lL~~aG~~~g-------~~l~l~~~~~~~~~~~~~a~~i~~~l~~~Gi~v~ 357 (460)
T cd08515 309 EKAKALLAEAGYPDG-------FEIDYYAYRGYYPNDRPVAEAIVGMWKAVGINAE 357 (460)
T ss_pred HHHHHHHHHcCCCCC-------ceEEEEecCCCCCchHHHHHHHHHHHHHhCceEE
Confidence 456788888876543 3455555432222344555666666677898764
No 59
>cd08518 PBP2_NikA_DppA_OppA_like_19 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=31.17 E-value=1.7e+02 Score=23.01 Aligned_cols=55 Identities=20% Similarity=0.357 Sum_probs=34.7
Q ss_pred HHHHHHHHHhCCCCce--EEee--cCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGA--WVEN--KGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~--~VE~--K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|...|. +.+. |++.+++-|..-. .....+....++-.++.|+.+.
T Consensus 300 ~~Ak~lL~eaG~~~~~~g~~~~~g~~l~l~l~~~~~~-~~~~~~a~~i~~~l~~iGi~v~ 358 (464)
T cd08518 300 EKAKKILEEAGWKDGDDGGREKDGQKAEFTLYYPSGD-QVRQDLAVAVASQAKKLGIEVK 358 (464)
T ss_pred HHHHHHHHHcCCCcCCCCeeccCCcEEEEEEEeCCCC-HHHHHHHHHHHHHHHHhCCeEE
Confidence 6678888988876432 3332 4567777776532 2344555666666677898764
No 60
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=30.92 E-value=1.2e+02 Score=18.13 Aligned_cols=39 Identities=8% Similarity=-0.052 Sum_probs=30.8
Q ss_pred EEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 56 WVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 56 ~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
.++...|..-+.+.. |....+.+.+....+.+++|+.++
T Consensus 35 ~~~~~~F~m~~~~~~-~~~~~~~l~~~l~~~~~~~~l~i~ 73 (77)
T cd04893 35 AILGTEFALTMLVEG-SWDAIAKLEAALPGLARRLDLTLM 73 (77)
T ss_pred eEEcCEEEEEEEEEe-ccccHHHHHHHHHHHHHHcCCEEE
Confidence 667777788888884 555678888889999999999874
No 61
>PF03778 DUF321: Protein of unknown function (DUF321) ; InterPro: IPR005529 This entry represents a group of tandem repeats, found in Arabidopsis species, whose sequence is distantly related to the FARP (FMRFamide) group of neuropeptides (IPR002544 from INTERPRO). The function of these repeats is not known, being mostly found in uncharacterised proetins, but they are also present in the nuclear migration protein NUM1 [].
Probab=30.44 E-value=35 Score=16.40 Aligned_cols=12 Identities=33% Similarity=0.495 Sum_probs=8.9
Q ss_pred eEEecccceeee
Q psy9708 14 AWVENKGPLLTF 25 (99)
Q Consensus 14 ~~vgnhG~el~~ 25 (99)
-|-+||||....
T Consensus 3 FwreN~gftFla 14 (20)
T PF03778_consen 3 FWRENHGFTFLA 14 (20)
T ss_pred cceeecCEEEEe
Confidence 378999998543
No 62
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=29.24 E-value=38 Score=18.84 Aligned_cols=18 Identities=33% Similarity=0.377 Sum_probs=13.6
Q ss_pred HHHHHHHHhCcccccccC
Q psy9708 82 LATQLIESAGFKAGECEL 99 (99)
Q Consensus 82 ~~~~~~~~~G~~~~~~~~ 99 (99)
..-.++.++||..|..||
T Consensus 31 e~~~lA~~~Gy~ft~~el 48 (49)
T PF07862_consen 31 EVVALAREAGYDFTEEEL 48 (49)
T ss_pred HHHHHHHHcCCCCCHHHh
Confidence 345578999999987664
No 63
>PRK12677 xylose isomerase; Provisional
Probab=28.79 E-value=1.8e+02 Score=23.28 Aligned_cols=21 Identities=10% Similarity=0.238 Sum_probs=16.7
Q ss_pred chHHHHHHHHHHHHHhCcccc
Q psy9708 75 LRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 75 ~~~~v~~~~~~~~~~~G~~~~ 95 (99)
.++..++..++.++++||++.
T Consensus 64 ~~~~~~~~lk~~l~~~GL~v~ 84 (384)
T PRK12677 64 ERDRIIKRFKKALDETGLVVP 84 (384)
T ss_pred hhHHHHHHHHHHHHHcCCeeE
Confidence 344567889999999999965
No 64
>TIGR03212 uraD_N-term-dom putative urate catabolism protein. This model represents a protein that is predominantly found just upstream of the UraD protein (OHCU decarboxylase) and in a number of instances as a N-terminal fusion with it. UraD itself catalyzes the last step in the catabolism of urate to allantoate. The function of this protein is presently unknown. It shows homology with the pfam01522 polysaccharide deacetylase domain family.
Probab=28.75 E-value=94 Score=24.02 Aligned_cols=44 Identities=11% Similarity=-0.001 Sum_probs=26.0
Q ss_pred hhhCCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhC
Q psy9708 7 RHYCKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG 50 (99)
Q Consensus 7 ~~v~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~ 50 (99)
+.+--.|+=+||||..-.....-.+.+.+..|.+..+.|.+..|
T Consensus 110 ~~i~~~GHEIg~Hg~~H~~~~~ls~~~e~~~i~~s~~~i~~~tG 153 (297)
T TIGR03212 110 AAMKEAGWEIASHGLRWIDYQDMDEAQEREHIAEAIRLHTEVTG 153 (297)
T ss_pred HHHHHcCCEEeeccccCcccccCCHHHHHHHHHHHHHHHHHHhC
Confidence 33445679999999974433322334556666555555544445
No 65
>PF02971 FTCD: Formiminotransferase domain; InterPro: IPR013802 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. In humans, deficiency of this enzyme results in a disease phenotype []. This entry represents the C-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 1QD1_B 2PFD_C.
Probab=28.16 E-value=1.5e+02 Score=21.08 Aligned_cols=44 Identities=14% Similarity=0.168 Sum_probs=27.1
Q ss_pred EEeecCCe-eeEeecCCCCCchHHHHHHHHHHHHHhCcccccccC
Q psy9708 56 WVENKGPL-LTFHYTNTPVELRPEMVSLATQLIESAGFKAGECEL 99 (99)
Q Consensus 56 ~VE~K~~~-~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~~~~~ 99 (99)
++|.++.+ ++.---+....-.-.+-+.++..++++|..++.+|+
T Consensus 45 ~l~~~~~aQVSmNltd~~~Tpl~~vfe~v~~eA~~~Gv~v~gsEl 89 (145)
T PF02971_consen 45 YLEERGIAQVSMNLTDYEKTPLHRVFEEVKREAARYGVPVVGSEL 89 (145)
T ss_dssp EETTTTEEEEEEEES-TTTS-HHHHHHHHHHHHHCTT--EEEEEE
T ss_pred eeccCCeeEEEEeeecCCCCcHHHHHHHHHHHHHHhCCCccceEE
Confidence 88888655 344333333333445667889999999999988874
No 66
>cd08519 PBP2_NikA_DppA_OppA_like_20 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=27.36 E-value=2.3e+02 Score=22.39 Aligned_cols=49 Identities=24% Similarity=0.326 Sum_probs=31.4
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhC-ccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG-FKA 94 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G-~~~ 94 (99)
+.|++|.++.|...| |+..+.+.|..--+ ....+.....+-.++.| +.+
T Consensus 310 ~kA~~lL~~aG~~~G-----~~l~l~~~~~~~~~-~~~~~a~~i~~~l~~~G~i~v 359 (469)
T cd08519 310 EKARQLLQQAGYSAE-----NPLKLELWYRSNHP-ADKLEAATLKAQLEADGLFKV 359 (469)
T ss_pred HHHHHHHHHhCCCCC-----CCceEEEEecCCCC-chhHHHHHHHHHHHhccceEE
Confidence 667888888886654 77888898864322 22444555555566667 454
No 67
>cd08498 PBP2_NikA_DppA_OppA_like_2 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most si
Probab=27.00 E-value=2.4e+02 Score=22.29 Aligned_cols=49 Identities=22% Similarity=0.339 Sum_probs=30.0
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|... ++.+++-+.+-.......+....++-.++.|+.+.
T Consensus 315 ~kAk~lL~~aG~~~-------g~~l~l~~~~~~~~~~~~~a~~i~~~l~~~Gi~v~ 363 (481)
T cd08498 315 EKAKKLLAEAGYPD-------GFELTLHCPNDRYVNDEAIAQAVAGMLARIGIKVN 363 (481)
T ss_pred HHHHHHHHHcCCCC-------CceEEEEEcCCCCCcchHHHHHHHHHHHHhCceEE
Confidence 56688888888653 45666666553322233455555666677898763
No 68
>COG3317 NlpB Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=25.80 E-value=1e+02 Score=24.80 Aligned_cols=44 Identities=16% Similarity=0.306 Sum_probs=37.7
Q ss_pred hCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 49 AGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 49 ~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
++.+.|...|.-+=...+=|-+-|++ .+-..++++++++||++-
T Consensus 84 L~~Isg~r~erdGd~~~lv~~~~~~~---~~Wpqv~~~~qE~gf~i~ 127 (342)
T COG3317 84 LALISGSRAERDGDTRWLVVENQPAA---YLWPQVRRFLQENGFRIA 127 (342)
T ss_pred hhhcccchheecCCeeEEEEeCCchH---HhHHHHHHHHHHcCCccc
Confidence 66788999999999999999885555 788899999999999873
No 69
>cd08513 PBP2_thermophilic_Hb8_like The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold. This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium, and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporter
Probab=25.74 E-value=2.7e+02 Score=21.94 Aligned_cols=55 Identities=25% Similarity=0.336 Sum_probs=33.3
Q ss_pred HHHHHHHHHhCCCC---ceEEe--ecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKA---GAWVE--NKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~---G~~VE--~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|... |-+.+ .|++.+++-|..-. .....+...+++-.++.|+++.
T Consensus 310 ~kAk~lL~eaG~~~~~~g~~~~~~g~~l~l~l~~~~~~-~~~~~~a~~i~~~l~~iGi~v~ 369 (482)
T cd08513 310 EKAKQLLDEAGWKLGPDGGIREKDGTPLSFTLLTTSGN-AVRERVAELIQQQLAKIGIDVE 369 (482)
T ss_pred HHHHHHHHHcCCccCCCCcEEcCCCcEEEEEEEeCCCC-hHHHHHHHHHHHHHHHcCCEEE
Confidence 56788888888652 22554 34566666665421 2334555566666677898764
No 70
>PHA03307 transcriptional regulator ICP4; Provisional
Probab=25.55 E-value=25 Score=32.92 Aligned_cols=19 Identities=26% Similarity=0.548 Sum_probs=17.4
Q ss_pred ChhHHHhhhCCCC--eEEecc
Q psy9708 1 MLKWIERHYCKQG--AWVENK 19 (99)
Q Consensus 1 ~l~dl~~~v~~~g--~~vgnh 19 (99)
||+.|-+++|.+. +|+||=
T Consensus 1060 LLAAL~NRLc~p~ShAWAGnW 1080 (1352)
T PHA03307 1060 LLAALGNRLCLPDSHAWAGNW 1080 (1352)
T ss_pred HHHHHhccccCCcchhhhcCC
Confidence 6899999999999 899994
No 71
>cd08499 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling
Probab=25.33 E-value=2.4e+02 Score=22.16 Aligned_cols=47 Identities=19% Similarity=0.289 Sum_probs=30.2
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|... ++.+++-+.+-+ ....+...+++-.++.|+++.
T Consensus 304 ~~A~~lL~eaG~~~-------~~~l~l~~~~~~--~~~~~a~~i~~~l~~~GI~v~ 350 (474)
T cd08499 304 EKAKELLAEAGYPD-------GFETTLWTNDNR--ERIKIAEFIQQQLAQIGIDVE 350 (474)
T ss_pred HHHHHHHHHcCCCC-------CceEEEEecCCC--chhHHHHHHHHHHHHcCceEE
Confidence 56678888887653 456677666543 334455566666677898764
No 72
>cd08520 PBP2_NikA_DppA_OppA_like_21 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=25.21 E-value=2.5e+02 Score=22.15 Aligned_cols=54 Identities=17% Similarity=0.261 Sum_probs=33.3
Q ss_pred HHHHHHHHHhCCCC--ceEE-eecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKA--GAWV-ENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~--G~~V-E~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|... |.+. +.|++.+++-|.+-+ ...++...+++-.++.|+++.
T Consensus 305 ~kAk~lL~eaG~~~~~~~~~~~g~~l~l~l~~~~~~--~~~~~a~~i~~~l~~iGi~v~ 361 (468)
T cd08520 305 EKAKELLKGLGYTDNGGDGEKDGEPLSLELLTSSSG--DEVRVAELIKEQLERVGIKVN 361 (468)
T ss_pred HHHHHHHHHcCCcccCCCCCcCCceEEEEEEecCCc--hHHHHHHHHHHHHHHcCceEE
Confidence 56688888887632 2221 235566777665533 345566667777777898874
No 73
>PRK15104 oligopeptide ABC transporter substrate-binding protein OppA; Provisional
Probab=25.09 E-value=2.6e+02 Score=22.84 Aligned_cols=49 Identities=20% Similarity=0.350 Sum_probs=30.8
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHH-hCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIES-AGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~-~G~~~~ 95 (99)
+.|++|.++.|...| |++++++-|..-+ ....+....++...+ .|++++
T Consensus 368 ~kAk~LL~eAG~~~g-----~~l~i~l~~~~~~--~~~~~a~~i~~~~~~~iGI~v~ 417 (543)
T PRK15104 368 EEAKKLLAEAGYTAD-----KPLTFNLLYNTSD--LHKKLAIAAASIWKKNLGVNVK 417 (543)
T ss_pred HHHHHHHHhcCCCCC-----CCceEEEEeCCCC--chHHHHHHHHHHHHHhcCceEE
Confidence 667889999886644 6777888775322 223444455554444 798764
No 74
>cd08511 PBP2_NikA_DppA_OppA_like_5 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is mos
Probab=24.71 E-value=2e+02 Score=22.50 Aligned_cols=46 Identities=17% Similarity=0.289 Sum_probs=29.4
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|... ..+++=|++ .....++...+++-.++.|+.++
T Consensus 305 ~~A~~lL~~aG~~~--------~~l~i~~~~--~~~~~~~a~~i~~~l~~~Gi~v~ 350 (467)
T cd08511 305 AKAKALLAEAGVPT--------VTFELTTAN--TPTGRQLAQVIQAMAAEAGFTVK 350 (467)
T ss_pred HHHHHHHHHcCCCC--------ceEEEEecC--CCchhHHHHHHHHHHHhcCcEeE
Confidence 56788888887532 344444443 23345666777777888998875
No 75
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=24.64 E-value=2.7e+02 Score=20.05 Aligned_cols=60 Identities=8% Similarity=0.051 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHhCCCCce---EE-eecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 36 PEMVSLATQLIESAGFKAGA---WV-ENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 36 ~~l~~~a~~L~e~~~~~~G~---~V-E~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
++-.+...+..+++|++|+. .+ =.|.-++++=.......--.++.....+.++++|+.+.
T Consensus 6 ~~Tr~rV~~~a~elgY~pn~~a~~l~~~~~~~ig~v~~~~~~~~~~~~~~gi~~~~~~~g~~~~ 69 (309)
T PRK11041 6 QATRQRVEQAVLEVGYSPQSLGRNLKRNESRTILVIVPDICDPFFSEIIRGIEVTAAEHGYLVL 69 (309)
T ss_pred HHHHHHHHHHHHHHCCCcCHHHHHhhcCCCcEEEEEeCCCcCccHHHHHHHHHHHHHHCCCEEE
Confidence 33344445566777777765 11 22444555555555566778888889999999998764
No 76
>PF08608 Wyosine_form: Wyosine base formation; InterPro: IPR013917 The proteins in this entry appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that it participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW []. ; PDB: 2YX0_A 2Z2U_A.
Probab=23.99 E-value=65 Score=19.41 Aligned_cols=41 Identities=22% Similarity=0.258 Sum_probs=24.4
Q ss_pred EEeecCCe--eeEeecCC--CCCchHHHHHHHHHHHHHhCccccc
Q psy9708 56 WVENKGPL--LTFHYTNT--PVELRPEMVSLATQLIESAGFKAGE 96 (99)
Q Consensus 56 ~VE~K~~~--~a~HyR~v--~~~~~~~v~~~~~~~~~~~G~~~~~ 96 (99)
.||-|+++ -.--.|.+ +....++|.+=+++|.+..||.++.
T Consensus 6 fVEvKa~~~~G~s~~rLt~~nmp~h~eV~~F~~~l~~~~~y~i~~ 50 (62)
T PF08608_consen 6 FVEVKAYMHVGYSRNRLTMGNMPWHEEVLDFAEELAELLGYEITD 50 (62)
T ss_dssp EEEEEE------------GGGS--HHHHHHHHHHHHTTSTEEEEE
T ss_pred EEEEecCcccccccCccccCCCCcHHHHHHHHHHHHhhcCCEEEe
Confidence 68999888 21123343 4577888999999999999988753
No 77
>TIGR02884 spore_pdaA delta-lactam-biosynthetic de-N-acetylase. Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores in the peptidoglycan wall, or spore cortex. The proteins in this family are PdaA (yfjS), a member of a larger family of polysaccharide deacetylases, and are specificially involved in delta-lactam biosynthesis. PdaA acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation. PdaA may also perform the following transpeptidation for lactam ring formation, as heterologous expression in E. coli of CwlD and PdaA together is sufficient for delta-lactam production.
Probab=23.54 E-value=1.2e+02 Score=22.05 Aligned_cols=42 Identities=12% Similarity=0.165 Sum_probs=25.3
Q ss_pred hCCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhC
Q psy9708 9 YCKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG 50 (99)
Q Consensus 9 v~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~ 50 (99)
+--.|.-+|||+..=.....-.+.++...|.+..+.|.+..|
T Consensus 85 i~~~GheIgnHt~~H~~~~~ls~~~~~~ei~~~~~~i~~~~G 126 (224)
T TIGR02884 85 MVDEGHIVGNHSVHHPSLTAVNDEKFKEELTGVEEEFKKVTG 126 (224)
T ss_pred HHHcCCEeeecCccCcCcccCCHHHHHHHHHHHHHHHHHHhC
Confidence 445678899999863222122344667777766556655554
No 78
>cd08506 PBP2_clavulanate_OppA2 The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold. Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the precursors, glyceraldehyde-3-phosphate and arginine. CA possesses a characteristic (3R,5R) stereochemistry essential for reaction with penicillin-binding proteins and beta-lactamases. Two genes (oppA1 and oppA2) in the clavulanic acid gene cluster encode oligopeptide-binding proteins that are required for CA biosynthesis. OppA1/2 is involved in the binding and transport of peptides across the cell membrane of Streptomyces clavuligerus. Most of other periplasmic binding proteins are comprised of only two globular subdomains cor
Probab=23.54 E-value=2.6e+02 Score=21.95 Aligned_cols=46 Identities=26% Similarity=0.396 Sum_probs=30.6
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|.. +..+++=|++.+. ...+...+.+-.++.|+++.
T Consensus 305 ekAk~lL~~aG~~--------g~~l~~~~~~~~~--~~~~a~~i~~~l~~iGI~v~ 350 (466)
T cd08506 305 DKAKELLAEAGVP--------GLKLTLAYRDTAV--DKKIAEALQASLARAGIDVT 350 (466)
T ss_pred HHHHHHHHHcCCC--------CceEEEEeCCCch--HHHHHHHHHHHHHHcCCeEE
Confidence 6668888888864 3555555555432 55666667777788998764
No 79
>COG3171 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.52 E-value=87 Score=21.53 Aligned_cols=35 Identities=20% Similarity=0.281 Sum_probs=26.3
Q ss_pred CCeeeEeecC-CCCCchHHHHHH-HHHHHHHhCcccc
Q psy9708 61 GPLLTFHYTN-TPVELRPEMVSL-ATQLIESAGFKAG 95 (99)
Q Consensus 61 ~~~~a~HyR~-v~~~~~~~v~~~-~~~~~~~~G~~~~ 95 (99)
+|++.++|-+ |+.+..++.+++ ..++|+.+||.-.
T Consensus 30 gF~v~~~~~eg~~ae~~dea~drFidevI~~Ngl~~~ 66 (119)
T COG3171 30 GFSVQWSFHEGTSAEDVDEAVDRFIDEVIAPNGLAFA 66 (119)
T ss_pred heeeEEEecCCccHHHHHHHHHHHHHHHHccCceeEc
Confidence 4788888865 667888887755 7789998888643
No 80
>cd08503 PBP2_NikA_DppA_OppA_like_17 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most s
Probab=23.51 E-value=3e+02 Score=21.64 Aligned_cols=47 Identities=15% Similarity=0.169 Sum_probs=31.2
Q ss_pred HHHHHHHHHhCCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|.. + ..+++-|..-. .....+...+.+-+++.|+.+.
T Consensus 308 ~~A~~lL~eaG~~-~-------~~l~l~~~~~~-~~~~~~a~~i~~~l~~~Gi~v~ 354 (460)
T cd08503 308 DKAKALLAEAGLP-D-------LEVELVTSDAA-PGAVDAAVLFAEQAAQAGININ 354 (460)
T ss_pred HHHHHHHHHcCCC-C-------ceEEEEecCCC-ccHHHHHHHHHHHHHhhCCEEE
Confidence 5678888888753 2 56777775533 2456666666676778898764
No 81
>PF04320 DUF469: Protein with unknown function (DUF469); InterPro: IPR007416 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.
Probab=23.22 E-value=1.1e+02 Score=20.37 Aligned_cols=34 Identities=21% Similarity=0.269 Sum_probs=28.1
Q ss_pred CCeeeEeecC-CCCCchHHHHHHHHHHHHHhCccc
Q psy9708 61 GPLLTFHYTN-TPVELRPEMVSLATQLIESAGFKA 94 (99)
Q Consensus 61 ~~~~a~HyR~-v~~~~~~~v~~~~~~~~~~~G~~~ 94 (99)
+|.++..|.. ++++..+..++.-=+.++..||-.
T Consensus 16 GF~v~~~~~~~~~~e~~D~~~D~fId~Ie~~gL~~ 50 (101)
T PF04320_consen 16 GFEVSCRFAEGTSEEQIDAFVDAFIDVIEPNGLAF 50 (101)
T ss_pred EEEEEEEECCCCCHHHHHHHHHHHHHHHHhCCCEE
Confidence 5788899988 888999998888666999998754
No 82
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=23.18 E-value=67 Score=20.19 Aligned_cols=23 Identities=22% Similarity=0.341 Sum_probs=17.0
Q ss_pred CchHHHHHHHHHHHHHhCccccc
Q psy9708 74 ELRPEMVSLATQLIESAGFKAGE 96 (99)
Q Consensus 74 ~~~~~v~~~~~~~~~~~G~~~~~ 96 (99)
..+.++++.++++++.+||.+.+
T Consensus 20 ~e~~~~~~~i~~~~~~~Gis~~e 42 (93)
T PF00816_consen 20 QEREEAIAEIRELMAEYGISPEE 42 (93)
T ss_dssp HCCHHHHHHHHHHHHHTT--HHH
T ss_pred HHHHHHHHHHHHHHHHhCCCHHH
Confidence 34677889999999999998754
No 83
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=22.83 E-value=3.1e+02 Score=20.05 Aligned_cols=62 Identities=3% Similarity=0.083 Sum_probs=39.7
Q ss_pred CccchhHHHHHHHHHHHHHhCCCCce---EE-eecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 30 TPVELRPEMVSLATQLIESAGFKAGA---WV-ENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 30 ~p~e~~~~l~~~a~~L~e~~~~~~G~---~V-E~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
++.+-+.++.+ ..+++|++|+. .+ -.|..++++-.......--.++.+...+.++++|+.+.
T Consensus 30 Vs~~tr~rV~~----~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~l~~gi~~~~~~~g~~~~ 95 (328)
T PRK11303 30 VSDKTVEKVMA----VVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTSYARIAKYLERQARQRGYQLL 95 (328)
T ss_pred cCHHHHHHHHH----HHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCchHHHHHHHHHHHHHHcCCEEE
Confidence 44555555544 45666777765 22 33456677766554555667788888888899998763
No 84
>PF10250 O-FucT: GDP-fucose protein O-fucosyltransferase; InterPro: IPR019378 This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and Caenorhabditis elegans. Both features are characteristic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese []. ; PDB: 3ZY6_A 3ZY3_A 3ZY5_A 3ZY2_A 3ZY4_A.
Probab=22.74 E-value=1.3e+02 Score=22.68 Aligned_cols=32 Identities=25% Similarity=0.474 Sum_probs=21.4
Q ss_pred chhHHHHHHHHHHHHHhCCCCceEEeecCCeeeEeecCC
Q psy9708 33 ELRPEMVSLATQLIESAGFKAGAWVENKGPLLTFHYTNT 71 (99)
Q Consensus 33 e~~~~l~~~a~~L~e~~~~~~G~~VE~K~~~~a~HyR~v 71 (99)
.+.+.|.++|..+.+++. ..+++-+++|.|.=
T Consensus 174 ~~~~~i~~~a~~~i~~~~-------~~~~~yiavHlR~~ 205 (351)
T PF10250_consen 174 RFSPEIRELADKFIKRLL-------AGGGPYIAVHLRRG 205 (351)
T ss_dssp -B-HHHHHHHHHHHHHH-----------SSEEEEEE--S
T ss_pred ecCHHHHHHHHHHHHHhh-------cccCceEEEeeccc
Confidence 557888899999999884 78899999999995
No 85
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=22.43 E-value=1.3e+02 Score=17.99 Aligned_cols=39 Identities=18% Similarity=0.110 Sum_probs=30.6
Q ss_pred EEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 56 WVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 56 ~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
.+=...++..++... |++..+++.+...++.++.|+.+.
T Consensus 36 ~~~~~~f~~~~~v~~-~~~~~~~l~~~L~~l~~~~~l~v~ 74 (76)
T PF13740_consen 36 AVLGGRFTLIMLVSI-PEDSLERLESALEELAEELGLDVS 74 (76)
T ss_dssp EEETTEEEEEEEEEE-SHHHHHHHHHHHHHHHHHTT-EEE
T ss_pred EEEcCeEEEEEEEEe-CcccHHHHHHHHHHHHHHCCcEEE
Confidence 455567888888887 566888899999999999998763
No 86
>PF12077 DUF3556: Transmembrane protein of unknown function (DUF3556); InterPro: IPR021941 This family of transmembrane proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 576 to 592 amino acids in length.
Probab=22.30 E-value=95 Score=26.64 Aligned_cols=34 Identities=24% Similarity=0.439 Sum_probs=28.5
Q ss_pred HHHHHHHHHhCCCCce----EEeecCCe-eeEeecCCCC
Q psy9708 40 SLATQLIESAGFKAGA----WVENKGPL-LTFHYTNTPV 73 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G~----~VE~K~~~-~a~HyR~v~~ 73 (99)
++.++++++-+|.||. |+|.-|.- .+-|||-++.
T Consensus 503 ~lIaAvQ~rC~FePGE~rvv~~esQPih~~~Q~YrlvDA 541 (574)
T PF12077_consen 503 QLIAAVQRRCGFEPGEVRVVWLESQPIHRQTQEYRLVDA 541 (574)
T ss_pred HHHHHHHHHcCCCCCeEEEEEEecccccccceeEEEeec
Confidence 5667799999999998 99999984 6788998754
No 87
>cd08489 PBP2_NikA The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides,
Probab=22.22 E-value=3.8e+02 Score=21.17 Aligned_cols=55 Identities=18% Similarity=0.273 Sum_probs=34.1
Q ss_pred HHHHHHHHHhCCCCc---eEEee--cCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 40 SLATQLIESAGFKAG---AWVEN--KGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 40 ~~a~~L~e~~~~~~G---~~VE~--K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+.|++|.++.|...+ -+.+. ++.++++-|.. .......+.....+-.++.|+++.
T Consensus 307 ~~A~~lL~~aG~~~~~~~g~~~~~g~~~~~~l~~~~-~~~~~~~~a~~i~~~l~~~Gi~v~ 366 (488)
T cd08489 307 EKANALLDEAGWTLNEGDGIREKDGKPLSLELVYQT-DNALQKSIAEYLQSELKKIGIDLN 366 (488)
T ss_pred HHHHHHHHHcCCCcCCCCceEccCCceEEEEEEecC-CCchHHHHHHHHHHHHHHcCcEEE
Confidence 667888888887532 13343 34556666643 223455666677777788899864
No 88
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=21.87 E-value=2e+02 Score=17.46 Aligned_cols=47 Identities=23% Similarity=0.256 Sum_probs=30.5
Q ss_pred HHHHHHhCCCCce----EEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhC
Q psy9708 43 TQLIESAGFKAGA----WVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAG 91 (99)
Q Consensus 43 ~~L~e~~~~~~G~----~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G 91 (99)
+++.+++|..+|- -+++...+++-. +. |.+...++.+.+.+++.+++
T Consensus 16 k~i~~~lgl~~Gd~v~v~~~~~~iii~~~-~~-~~~~~~~~~~~~~~~~~~y~ 66 (74)
T TIGR02609 16 KEVLESLGLKEGDTLYVDEEEGGLKLKRF-DE-GKELEKKMQMAVERAMSKYD 66 (74)
T ss_pred HHHHHHcCcCCCCEEEEEEECCEEEEEEC-CC-CccHHHHHHHHHHHHHHHHH
Confidence 4677888888887 334444555432 22 34666677778888888775
No 89
>PRK08652 acetylornithine deacetylase; Provisional
Probab=21.62 E-value=1.6e+02 Score=22.03 Aligned_cols=36 Identities=8% Similarity=-0.019 Sum_probs=30.1
Q ss_pred ecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCccc
Q psy9708 59 NKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKA 94 (99)
Q Consensus 59 ~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~ 94 (99)
.--..+.+-.|..|.+..+++.+.++++++..++++
T Consensus 219 P~~~~~~~diR~~~~~~~~~v~~~i~~~~~~~~v~~ 254 (347)
T PRK08652 219 PALCRLRLDARIPPEVEVEDVLDEIDPILDEYTVKY 254 (347)
T ss_pred CCcEEEEEEEEcCCCCCHHHHHHHHHHHHHhcCceE
Confidence 345567889999999999999999999999887655
No 90
>PRK14648 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional
Probab=21.56 E-value=2.4e+02 Score=22.70 Aligned_cols=54 Identities=22% Similarity=0.223 Sum_probs=41.4
Q ss_pred HHHHHHHHhCCC----CceEEeecCCeeeEeecCCCCCchHHHHHHHHH-HHHHhCccc
Q psy9708 41 LATQLIESAGFK----AGAWVENKGPLLTFHYTNTPVELRPEMVSLATQ-LIESAGFKA 94 (99)
Q Consensus 41 ~a~~L~e~~~~~----~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~-~~~~~G~~~ 94 (99)
.|..|+|+.|++ -|+.|=.|=.-.=+-+-++..+.+-.+++.+++ +.+++|+.+
T Consensus 276 ~AG~LIe~~GLKG~riG~A~VS~kHAnfIVN~G~Ata~Dvl~Li~~v~~~V~ekfGI~L 334 (354)
T PRK14648 276 PSGILIEEAGLRGTSCGAAQVAPWHGNLIINTGNATAHQVRTLLRVVRQRVFETHGVWL 334 (354)
T ss_pred cHHHHHHHcCCCCCccCCEEEccccCcEEEECCCCCHHHHHHHHHHHHHHHHHHHCCee
Confidence 357788888754 234777787788888888888888888888776 888899876
No 91
>PF12936 Kri1_C: KRI1-like family C-terminal; InterPro: IPR024626 The yeast member of the Kri1-like family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus []. This entry represents the C-terminal domain of this protein family.
Probab=21.55 E-value=43 Score=21.90 Aligned_cols=14 Identities=21% Similarity=0.346 Sum_probs=10.4
Q ss_pred CeeeEeecCCCCCc
Q psy9708 62 PLLTFHYTNTPVEL 75 (99)
Q Consensus 62 ~~~a~HyR~v~~~~ 75 (99)
.-.-|.||+|+|+.
T Consensus 25 ~p~RFkYr~V~p~~ 38 (93)
T PF12936_consen 25 MPTRFKYREVPPNS 38 (93)
T ss_pred CCCceeeeecCccc
Confidence 33459999999853
No 92
>PF02288 Dehydratase_MU: Dehydratase medium subunit; InterPro: IPR003208 This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances.; PDB: 2D0P_B 2D0O_D 1IWP_E 1MMF_B 1NBW_B 3AUJ_B 1UC5_B 1IWB_B 1EEX_E 1DIO_B ....
Probab=21.53 E-value=2.3e+02 Score=18.95 Aligned_cols=24 Identities=25% Similarity=0.523 Sum_probs=16.6
Q ss_pred CCCCceEEeecCCeeeEeecCCCCC
Q psy9708 50 GFKAGAWVENKGPLLTFHYTNTPVE 74 (99)
Q Consensus 50 ~~~~G~~VE~K~~~~a~HyR~v~~~ 74 (99)
+.--|..|-.|+ .+.+||++.|++
T Consensus 56 ~lgVGIGi~~~G-~~vih~~~L~~~ 79 (112)
T PF02288_consen 56 RLGVGIGIQSKG-TIVIHYKDLPPL 79 (112)
T ss_dssp TTSEEEEE-TTS-EEEEEETTS-TT
T ss_pred CcceeEEEcCCC-cEEEEcCCCCCC
Confidence 345566887777 788999999874
No 93
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=21.45 E-value=78 Score=21.29 Aligned_cols=23 Identities=17% Similarity=0.112 Sum_probs=19.9
Q ss_pred CCchHHHHHHHHHHHHHhCcccc
Q psy9708 73 VELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 73 ~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+..++.|++.+.+++.+.||..+
T Consensus 7 ~~rr~~Il~aA~~lf~~~G~~~~ 29 (189)
T TIGR03384 7 PIRRAELIDATIESIGERGSLDV 29 (189)
T ss_pred hHHHHHHHHHHHHHHHhcCcccC
Confidence 46778899999999999999764
No 94
>TIGR00259 thylakoid_BtpA membrane complex biogenesis protein, BtpA family. Members of this family are found in C. elegans, Synechocystis sp., E. coli, and several of the Archaea. Members in Cyanobacteria have been shown to play a role in protein complex biogenesis, and designated BtpA (biogenesis of thylakoid protein). Homologs in non-photosynthetic species, where thylakoid intracytoplasmic membranes are lacking, are likely to act elsewhere in membrane protein biogenesis.
Probab=21.29 E-value=1.8e+02 Score=22.34 Aligned_cols=45 Identities=18% Similarity=0.042 Sum_probs=35.1
Q ss_pred hCCCCeEEecccceeeeeccCCccchhHHHHHHHHHHHHHhCCCCce
Q psy9708 9 YCKQGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAGA 55 (99)
Q Consensus 9 v~~~g~~vgnhG~el~~h~~~~p~e~~~~l~~~a~~L~e~~~~~~G~ 55 (99)
=|+||..++|.|=--... .++.+-...|...+.+++..++...|+
T Consensus 40 ~GvD~viveN~~d~P~~~--~~~p~tva~m~~i~~~v~~~~~~p~Gv 84 (257)
T TIGR00259 40 GGVDAVMFENFFDAPFLK--EVDPETVAAMAVIAGQLKSDVSIPLGI 84 (257)
T ss_pred CCCCEEEEecCCCCCCcC--CCCHHHHHHHHHHHHHHHHhcCCCeee
Confidence 588889999987433222 688889999999999999999655666
No 95
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=21.14 E-value=3.5e+02 Score=20.05 Aligned_cols=62 Identities=15% Similarity=0.056 Sum_probs=41.3
Q ss_pred CccchhHHHHHHHHHHHHHhCCCCce---E-EeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 30 TPVELRPEMVSLATQLIESAGFKAGA---W-VENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 30 ~p~e~~~~l~~~a~~L~e~~~~~~G~---~-VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
+..+-+.++.+ ..+++|++|+. . --.|.-++++-.....+.--..+...+.+.++++|+.+.
T Consensus 28 Vs~~tr~rV~~----~a~elgY~pn~~ar~l~~~~~~~Igvi~~~~~~~f~~~~~~gi~~~~~~~g~~~~ 93 (343)
T PRK10727 28 ASEASRLAVHS----AMESLSYHPNANARALAQQSTETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFLL 93 (343)
T ss_pred CCHHHHHHHHH----HHHHHCCCCCHHHHhhhhCCCCeEEEEeCCCCcchHHHHHHHHHHHHHHcCCEEE
Confidence 44455555544 45566777776 1 223455677777666666778888899999999998653
No 96
>PF02873 MurB_C: UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; InterPro: IPR011601 This entry represents a C-terminal conserved region of UDP-N-acetylenolpyruvoylglucosamine reductase 1.1.1.158 from EC, which is also called UDP-N-acetylmuramate dehydrogenase. It is a part of the pathway for the biosynthesis of the UDP-N-acetylmuramoyl-pentapeptide, which is a precursor of bacterial peptidoglycan. ; GO: 0008762 UDP-N-acetylmuramate dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 1MBB_A 2Q85_A 2MBR_A 1UXY_A 1MBT_A 1HSK_A 2GQU_A 2GQT_A 3I99_A 3TX1_A.
Probab=21.05 E-value=2.6e+02 Score=18.38 Aligned_cols=54 Identities=24% Similarity=0.241 Sum_probs=35.6
Q ss_pred HHHHHHHHhCCC----CceEEeecCCeeeEeecCCCCCchHHHHHHHHH-HHHHhCccc
Q psy9708 41 LATQLIESAGFK----AGAWVENKGPLLTFHYTNTPVELRPEMVSLATQ-LIESAGFKA 94 (99)
Q Consensus 41 ~a~~L~e~~~~~----~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~-~~~~~G~~~ 94 (99)
-|..|+++.|++ -|+.|=.|=+-.=+-+.++....+-++++.+++ +.+++|+.+
T Consensus 39 ~Ag~LIe~aGlKG~~iG~a~vS~kHanfivN~g~Ata~dv~~Li~~v~~~V~~~~Gi~L 97 (105)
T PF02873_consen 39 SAGWLIEQAGLKGFRIGGAQVSEKHANFIVNHGGATAADVLALIEEVRERVKEKFGIEL 97 (105)
T ss_dssp -HHHHHHHTT-TT-EETTEEE-SSSTTEEEE-SS--HHHHHHHHHHHHHHHHHHHS--B
T ss_pred hHHHHHHHcCCCCCeeCcCEechhhCCeEEECCCCCHHHHHHHHHHHHHHHHHHHCCee
Confidence 667899999753 244788887777777888887788888877766 888899876
No 97
>cd07051 BMC_like_1_repeat1 Bacterial Micro-Compartment (BMC)-like domain 1 repeat 1. BMC-like domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of the carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view. Proteins in this CD contain two tandem BMC domains. This CD includes repeat 1 (the first BMC domain of BMC like 1 proteins).
Probab=20.95 E-value=2.8e+02 Score=18.84 Aligned_cols=47 Identities=19% Similarity=0.370 Sum_probs=37.1
Q ss_pred HHHHhCCCCce-EEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccccc
Q psy9708 45 LIESAGFKAGA-WVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAGEC 97 (99)
Q Consensus 45 L~e~~~~~~G~-~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~~~ 97 (99)
|+.. ..++|. .||.-==++-+|+|+ ..++.+..+.+.+..|.+...|
T Consensus 53 LKa~-~Vrpg~~vVER~fG~leiH~~~-----q~~V~~AG~aiL~~lg~~~~dr 100 (111)
T cd07051 53 LKAA-NVRPGVQVVERQFGLLELHSRS-----QSEVLAAGDAVLDALGLTEEDR 100 (111)
T ss_pred HHhc-cccccceeehhhcceEEEEcCC-----HHHHHHHHHHHHHHcCCCHHHc
Confidence 4443 479999 889888899999998 5677788888999999876543
No 98
>PF03437 BtpA: BtpA family; InterPro: IPR005137 Photosystem I (PSI) is a large protein complex embedded within the photosynthetic thylakoid membrane. It consists of 11 subunits, ~100 chlorophyll a molecules, 2 phylloquinones, and 3 Fe4S4-clusters. The three dimensional structure of the PSI complex has been resolved at 2.5 A [], which allows the precise localisation of each cofactor. PSI together with photosystem II (PSII) catalyses the light-induced steps in oxygenic photosynthesis - a process found in cyanobacteria, eukaryotic algae (e.g. red algae, green algae) and higher plants. To date, three thylakoid proteins involved in the stable accumulation of PSI have been identified: BtpA [], Ycf3 [, ], and Ycf4 (IPR003359 from INTERPRO) []. Because translation of the psaA and psaB mRNAs encoding the two reaction centre polypeptides, of PSI and PSII respectively, is not affected in mutant strains lacking functional ycf3 and ycf4, the products of these two genes appear to act at a post-translational step of PSI biosynthesis. These gene products are therefore involved either in the stabilisation or in the assembly of the PSI complex. However, their exact roles remain unknown. The BtpA protein appears to act at the level of PSI stabilisation []. It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane [, ]. Homologs of BtpA are found in the crenarchaeota and euryarchaeota, where their function remains unknown. The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane domain []. Ycf4 co-fractionates with a protein complex larger than PSI upon sucrose density gradient centrifugation of solubilised thylakoids []. The Ycf3 protein is loosely associated with the thylakoid membrane and can be released from the membrane with sodium carbonate. This suggests that Ycf3 is not part of a stable complex and that it probably interacts transiently with its partners []. Ycf3 contains a number of tetratrico peptide repeats (TPR, IPR001440 from INTERPRO); TPR is a structural motif present in a wide range of proteins, which mediates protein-protein interactions.
Probab=20.81 E-value=3.6e+02 Score=20.55 Aligned_cols=43 Identities=21% Similarity=0.225 Sum_probs=30.0
Q ss_pred CCCCceEEeecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCccc
Q psy9708 50 GFKAGAWVENKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKA 94 (99)
Q Consensus 50 ~~~~G~~VE~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~ 94 (99)
+..+|..|||=.-.- | .+.++++.++.|-..++++.+..++.+
T Consensus 41 ~GvDgiiveN~~D~P-y-~~~~~~etvaaM~~i~~~v~~~~~~p~ 83 (254)
T PF03437_consen 41 GGVDGIIVENMGDVP-Y-PKRVGPETVAAMARIAREVRREVSVPV 83 (254)
T ss_pred CCCCEEEEecCCCCC-c-cCCCCHHHHHHHHHHHHHHHHhCCCCE
Confidence 459999999832211 1 233788889988888888888876544
No 99
>PLN02750 oxidoreductase, 2OG-Fe(II) oxygenase family protein
Probab=20.78 E-value=1.2e+02 Score=23.72 Aligned_cols=20 Identities=30% Similarity=0.099 Sum_probs=14.7
Q ss_pred hHHHhhhCCCC-eEEecccce
Q psy9708 3 KWIERHYCKQG-AWVENKGPL 22 (99)
Q Consensus 3 ~dl~~~v~~~g-~~vgnhG~e 22 (99)
++|++-..-.| .|+-|||+.
T Consensus 45 ~~l~~Ac~~~GFf~v~nHGi~ 65 (345)
T PLN02750 45 SKIGEACKKWGFFQVINHGVP 65 (345)
T ss_pred HHHHHHHHhCCEEEEEcCCCC
Confidence 45566566678 899999974
No 100
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=20.49 E-value=3.5e+02 Score=19.79 Aligned_cols=62 Identities=8% Similarity=0.112 Sum_probs=40.3
Q ss_pred CccchhHHHHHHHHHHHHHhCCCCce---EEe-ecCCeeeEeecCCCCCchHHHHHHHHHHHHHhCcccc
Q psy9708 30 TPVELRPEMVSLATQLIESAGFKAGA---WVE-NKGPLLTFHYTNTPVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 30 ~p~e~~~~l~~~a~~L~e~~~~~~G~---~VE-~K~~~~a~HyR~v~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
++.+-+.++ .+..+++|++|+. .+- .|..++.|=.......--.++.....+.++++|+.+.
T Consensus 29 vs~~tr~rV----~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~ 94 (327)
T TIGR02417 29 ISQETVERV----MAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLL 94 (327)
T ss_pred cCHHHHHHH----HHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEE
Confidence 444555554 4455667777765 222 3455666666555556677888889999999998864
No 101
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=20.17 E-value=79 Score=21.70 Aligned_cols=24 Identities=25% Similarity=0.250 Sum_probs=20.6
Q ss_pred CCCchHHHHHHHHHHHHHhCcccc
Q psy9708 72 PVELRPEMVSLATQLIESAGFKAG 95 (99)
Q Consensus 72 ~~~~~~~v~~~~~~~~~~~G~~~~ 95 (99)
++..++.|++.+.+++.+.||.-+
T Consensus 6 ~~~~R~~Il~aA~~lf~e~G~~~t 29 (192)
T PRK14996 6 RDERREVILQAAMRVALAEGFAAM 29 (192)
T ss_pred HHHHHHHHHHHHHHHHHhcChhhc
Confidence 557788899999999999999754
No 102
>cd02641 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA.
Probab=20.12 E-value=1.3e+02 Score=17.64 Aligned_cols=23 Identities=26% Similarity=0.364 Sum_probs=18.4
Q ss_pred CCCchHHHHHHHHHHHHHhCccc
Q psy9708 72 PVELRPEMVSLATQLIESAGFKA 94 (99)
Q Consensus 72 ~~~~~~~v~~~~~~~~~~~G~~~ 94 (99)
|+++-+.=...++++++++||+-
T Consensus 23 ~p~ls~~eR~~vH~lA~~~gL~s 45 (60)
T cd02641 23 PPTLSSHDRLLVHELAEELGLRH 45 (60)
T ss_pred CCCCCHHHHHHHHHHHHHcCCce
Confidence 56666666788999999999874
No 103
>PF00120 Gln-synt_C: Glutamine synthetase, catalytic domain; InterPro: IPR008146 Glutamine synthetase (6.3.1.2 from EC) (GS) [] plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. There seem to be three different classes of GS [, , ]: Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of 12 identical subunits. The activity of GSI-type enzyme is controlled by the adenylation of a tyrosine residue. The adenylated enzyme is inactive (see IPR001637 from INTERPRO). Class II enzymes (GSII) are found in eukaryotes and in bacteria belonging to the Rhizobiaceae, Frankiaceae, and Streptomycetaceae families (these bacteria have also a class-I GS). GSII are octamer of identical subunits. Plants have two or more isozymes of GSII, one of the isozymes is translocated into the chloroplast. Class III enzymes (GSIII) have been found in Bacteroides fragilis. in Butyrivibrio fibrisolvens. It is a hexamer of identical chains and in some protozoa. It is much larger (about 700 amino acids) than the GSI (450 to 470 amino acids) or GSII (350 to 420 amino acids) enzymes. While the three classes of GS's are clearly structurally related, the sequence similarities are not so extensive.; GO: 0004356 glutamate-ammonia ligase activity, 0006807 nitrogen compound metabolic process; PDB: 2J9I_E 3ZXV_D 1HTQ_D 1HTO_F 2BVC_F 2WGS_G 3ZXR_B 2WHI_D 3NG0_A 1LGR_C ....
Probab=20.10 E-value=84 Score=23.36 Aligned_cols=61 Identities=16% Similarity=0.196 Sum_probs=34.7
Q ss_pred chhHHHHHHHHHHHHHhCCCC-ceEEeecC--CeeeEeecCCCCCchHHHH---HHHHHHHHHhCcccc
Q psy9708 33 ELRPEMVSLATQLIESAGFKA-GAWVENKG--PLLTFHYTNTPVELRPEMV---SLATQLIESAGFKAG 95 (99)
Q Consensus 33 e~~~~l~~~a~~L~e~~~~~~-G~~VE~K~--~~~a~HyR~v~~~~~~~v~---~~~~~~~~~~G~~~~ 95 (99)
...+-+.+..+.| ++.|+.. +.-=|.-| +-+++-|.. +-.+.|.++ ..++++++++|+.+|
T Consensus 66 ~~~~~~~~i~~~l-~~~Gi~ve~~h~E~gpgQ~Ei~~~~~~-~l~aaD~~~~~k~~ik~vA~~~Gl~at 132 (259)
T PF00120_consen 66 AGEDFLEEIVDAL-EQAGIPVEQIHHEVGPGQYEINLGPCD-PLEAADNLVLFKEIIKEVARKHGLTAT 132 (259)
T ss_dssp TTHHHHHHHHHHH-HHCT--EEEEEEESSTTEEEEEEEEEE-CHHHHHHHHHHHHHHHHHHHHTTEEEE
T ss_pred HHHHHHHHHHHHH-HHhhccccccccccchHhhccccccCc-HHHHHHHHHHHHHHHHHHHHHcCCcee
Confidence 3344454554555 3343222 11334443 234555555 557777763 679999999999886
Done!