Query psy4643
Match_columns 207
No_of_seqs 115 out of 438
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 22:03:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4643.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4643hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00168 pbsA heme oxygenase; 100.0 3.8E-53 8.2E-58 361.7 19.8 186 7-204 31-217 (238)
2 COG5398 Heme oxygenase [Inorga 100.0 1.5E-48 3.2E-53 322.6 16.1 189 7-207 29-217 (238)
3 PF01126 Heme_oxygenase: Heme 100.0 1.1E-39 2.3E-44 271.4 16.1 174 8-193 30-205 (205)
4 cd00232 HemeO Heme oxygenase c 100.0 7.2E-36 1.6E-40 248.1 20.1 175 7-194 28-202 (203)
5 KOG4480|consensus 99.8 4E-20 8.8E-25 159.5 13.8 173 9-200 43-218 (283)
6 COG3230 HemO Heme oxygenase [I 99.3 8.3E-11 1.8E-15 96.0 12.2 158 7-193 34-193 (196)
7 KOG4480|consensus 99.1 3.6E-09 7.9E-14 91.9 13.2 165 14-194 114-279 (283)
8 PF03070 TENA_THI-4: TENA/THI- 89.3 0.55 1.2E-05 38.4 4.2 165 8-183 23-196 (210)
9 PRK14713 multifunctional hydro 76.5 34 0.00073 32.7 10.9 155 8-178 347-509 (530)
10 COG5398 Heme oxygenase [Inorga 74.4 6.2 0.00013 33.8 4.7 109 12-127 4-122 (238)
11 PRK05157 pyrroloquinoline quin 62.7 1E+02 0.0023 26.8 10.2 107 84-197 119-230 (246)
12 TIGR02111 PQQ_syn_pqqC coenzym 62.1 97 0.0021 26.9 9.7 105 84-195 112-221 (239)
13 TIGR02792 PCA_ligA protocatech 60.5 5.7 0.00012 30.7 1.6 29 148-178 32-60 (117)
14 PRK13378 protocatechuate 4,5-d 58.7 6.6 0.00014 30.3 1.7 29 148-178 38-66 (117)
15 cd07924 PCA_45_Doxase_A The A 57.8 7 0.00015 30.4 1.7 29 148-178 35-63 (121)
16 cd07925 LigA_like_1 The A subu 57.3 7.7 0.00017 29.5 1.9 30 147-178 26-55 (106)
17 PRK13377 protocatechuate 4,5-d 56.7 7.2 0.00016 30.6 1.7 29 148-178 38-66 (129)
18 PRK09517 multifunctional thiam 56.3 1.7E+02 0.0037 29.4 11.6 153 8-178 573-733 (755)
19 PRK13379 protocatechuate 4,5-d 56.0 7.7 0.00017 30.1 1.7 29 148-178 39-67 (119)
20 cd07921 PCA_45_Doxase_A_like S 55.2 7.5 0.00016 29.6 1.5 29 148-178 27-55 (106)
21 PF12981 DUF3865: Domain of Un 49.4 1.5E+02 0.0033 25.4 8.6 130 52-196 92-228 (231)
22 cd07923 Gallate_dioxygenase_C 45.8 11 0.00023 28.1 1.0 28 149-178 20-47 (94)
23 cd07321 Extradiol_Dioxygenase_ 41.0 32 0.00069 24.4 2.9 27 150-178 19-45 (77)
24 COG5424 Pyrroloquinoline quino 40.5 2.5E+02 0.0054 24.5 9.4 102 81-198 113-215 (242)
25 KOG3028|consensus 38.2 2.8E+02 0.0061 25.1 8.9 91 87-193 91-181 (313)
26 PF06892 Phage_CP76: Phage reg 37.4 1.5E+02 0.0032 24.0 6.6 48 150-199 101-148 (162)
27 COG0819 TenA Putative transcri 36.2 71 0.0015 27.2 4.7 155 10-185 32-201 (218)
28 cd07356 HN_L-whirlin_R1_like F 35.9 1.4E+02 0.003 21.4 5.4 37 156-196 7-43 (78)
29 PF14246 TetR_C_7: AefR-like t 35.5 50 0.0011 20.9 3.0 22 164-185 31-52 (55)
30 PF11460 DUF3007: Protein of u 31.8 61 0.0013 24.6 3.2 14 167-180 89-102 (104)
31 PF07746 LigA: Aromatic-ring-o 30.6 52 0.0011 24.0 2.6 29 149-179 13-41 (88)
32 PF09702 Cas_Csa5: CRISPR-asso 28.5 80 0.0017 23.9 3.3 26 161-186 11-36 (105)
33 COG1101 PhnK ABC-type uncharac 27.3 43 0.00094 29.2 1.9 38 86-130 122-159 (263)
34 PF09921 DUF2153: Uncharacteri 27.2 1.9E+02 0.0041 22.6 5.3 41 158-198 13-53 (126)
35 PF02093 Gag_p30: Gag P30 core 27.1 92 0.002 26.5 3.9 30 152-184 40-69 (211)
36 PRK13372 pcmA protocatechuate 26.4 41 0.00089 31.8 1.8 29 148-178 38-66 (444)
37 PF01152 Bac_globin: Bacterial 26.1 2.4E+02 0.0051 20.7 5.7 59 112-178 46-108 (120)
38 PF14250 AbrB-like: AbrB-like 24.8 27 0.00058 24.7 0.2 22 99-120 35-56 (71)
39 PF06429 Flg_bbr_C: Flagellar 24.8 1.3E+02 0.0029 20.4 3.8 27 177-203 47-73 (74)
40 KOG0932|consensus 23.7 53 0.0011 32.2 2.0 57 138-198 343-400 (774)
41 PTZ00347 phosphomethylpyrimidi 23.6 3.7E+02 0.008 25.3 7.7 94 81-187 105-205 (504)
42 PRK13367 protocatechuate 4,5-d 23.4 53 0.0011 30.8 1.9 28 149-178 333-360 (420)
43 PF09539 DUF2385: Protein of u 22.6 3E+02 0.0065 20.5 5.4 51 148-200 26-76 (96)
44 PF04282 DUF438: Family of unk 22.2 2.5E+02 0.0055 19.7 4.8 18 147-164 12-29 (71)
45 cd07355 HN_L-delphilin-R2_like 21.9 1.9E+02 0.0042 20.8 4.1 28 155-185 6-33 (80)
46 COG1327 Predicted transcriptio 21.4 3.8E+02 0.0083 21.7 6.2 61 119-185 20-96 (156)
47 PHA02098 hypothetical protein 21.2 61 0.0013 21.2 1.3 35 151-188 4-38 (56)
48 COG2346 Truncated hemoglobins 21.1 1.9E+02 0.0042 22.8 4.4 30 152-183 90-119 (133)
49 PF15603 Imm45: Immunity prote 21.0 1.2E+02 0.0026 21.9 2.9 19 167-185 55-73 (82)
50 PF07309 FlaF: Flagellar prote 20.8 2.8E+02 0.006 21.0 5.1 47 149-195 50-96 (113)
51 PF15134 DUF4570: Domain of un 20.4 2.9E+02 0.0064 21.1 5.1 30 171-200 38-67 (109)
No 1
>CHL00168 pbsA heme oxygenase; Provisional
Probab=100.00 E-value=3.8e-53 Score=361.66 Aligned_cols=186 Identities=26% Similarity=0.426 Sum_probs=177.3
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHHHHHHHhhcCccccCCCCccccChHHHHHHHhHhhCCCCCCCCCCCCCccccCCCCh
Q psy4643 7 GAMSDTSIWIEGLLVFYEVFKFLESAMEEHKSNQYLQQFNISDMKRTEAFEADLEHYLGPDWKADYKPRPDWKADYKPRE 86 (207)
Q Consensus 7 ~~~~d~~~Y~~~L~~~y~vY~aLE~al~~~~~~p~l~~l~~~~L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~~~~~p 86 (207)
+|..+++.|+++|.+||+||.+||+++++++++|++++++.|+|+|+++|++||++|+|++|++ .++|+|
T Consensus 31 ~g~~~~~~Y~~ll~~ly~vY~aLE~~l~~~~~~~~~~~~~~peL~R~~aLe~DL~~l~G~~w~~----------~~~p~p 100 (238)
T CHL00168 31 GGVIDKKSYRKLVANLYFVYSAIEEEIEKNKEHPLIKPIYFQELNRKESLEKDLNYYYGDDWKS----------IIEPSP 100 (238)
T ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCcccccccchhhhhhHHHHHHHHHHcCCCccc----------cCCCCh
Confidence 4789999999999999999999999999999999999999999999999999999999999998 789999
Q ss_pred hHHHHHHHHHHhhccCcchHHHHHHHHHHhhhchhHHHHHHHHHhhccCc-CcccceeecCCCChHHHHHHHHHHHHhcc
Q psy4643 87 SVVNYLNHLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKKRQLSLMKSN-YQDQVLSFDPSVNVGQLKRQIKSILDDES 165 (207)
Q Consensus 87 a~~~yv~~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~-~g~~Fy~F~~~~~~~~~k~~yr~~ld~l~ 165 (207)
+++.||+||+++++++|++|+||+|||||||+||||||+++++++.++++ .|++||.|+++.+++.+|+.||++||++
T Consensus 101 a~~~Yv~rI~~~~~~~P~~LvAH~YvrYLGdlsGGQiI~k~l~r~~gl~~~~G~~Fy~F~~i~~~~~fk~~yr~~Ld~l- 179 (238)
T CHL00168 101 ATKIYVDRIHKISAKKPELLIAHAYTRYLGDLSGGQILKKIAQRAMNLSDSGGLAFYDFDNIEDDQEFKQIYKAALDNL- 179 (238)
T ss_pred HHHHHHHHHHHHhhcChHHHHHHHHHHHHHhccccHHHHHHHHHHhCCCCCcCccccCCCCcCcHHHHHHHHHHHHhcC-
Confidence 99999999999999999999999999999999999999998888888865 7999999997789999999999999998
Q ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy4643 166 TQFSRQTREQLLAESRKVFLLNNSIIKCVLELLEVLLKT 204 (207)
Q Consensus 166 ~~l~~~e~~~iv~EA~~aF~ln~~i~~eL~~~~~~~~~~ 204 (207)
++|++++++||+||+.+|++|++||.||++.....++.
T Consensus 180 -~l~e~e~~~iI~EA~~AF~lN~~vf~eL~~~~~~~~~~ 217 (238)
T CHL00168 180 -PLSDDQIQNIIAEANIAFNLNMKMFQELNSSFIKIITM 217 (238)
T ss_pred -CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999999999999999998877754
No 2
>COG5398 Heme oxygenase [Inorganic ion transport and metabolism]
Probab=100.00 E-value=1.5e-48 Score=322.62 Aligned_cols=189 Identities=26% Similarity=0.415 Sum_probs=181.7
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHHHHHHHhhcCccccCCCCccccChHHHHHHHhHhhCCCCCCCCCCCCCccccCCCCh
Q psy4643 7 GAMSDTSIWIEGLLVFYEVFKFLESAMEEHKSNQYLQQFNISDMKRTEAFEADLEHYLGPDWKADYKPRPDWKADYKPRE 86 (207)
Q Consensus 7 ~~~~d~~~Y~~~L~~~y~vY~aLE~al~~~~~~p~l~~l~~~~L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~~~~~p 86 (207)
+|.++...|++.+..+|+||.+||.+++.++++|+++++++|+|+|.+.|++||.+++|.+|++ .|.|+|
T Consensus 29 kg~V~~e~f~kl~~n~yf~ysaleaa~~~~~d~~~l~~i~fp~lnr~~tle~dl~~yyg~nwre----------~I~~sp 98 (238)
T COG5398 29 KGVVERESFRKLLANLYFVYSALEAATQIHKDNPILSSIYFPELNRKATLEKDLLYYYGNNWRE----------NIQPSP 98 (238)
T ss_pred cCcccHHHHHHHHHHHHHHHHHHHHHHHHhccCchhhhccchhhhhHHHhhcCHHHHhcccHHH----------hcCcCh
Confidence 4778999999999999999999999999999999999999999999999999999999999998 789999
Q ss_pred hHHHHHHHHHHhhccCcchHHHHHHHHHHhhhchhHHHHHHHHHhhccCcCcccceeecCCCChHHHHHHHHHHHHhccc
Q psy4643 87 SVVNYLNHLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKKRQLSLMKSNYQDQVLSFDPSVNVGQLKRQIKSILDDEST 166 (207)
Q Consensus 87 a~~~yv~~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~~g~~Fy~F~~~~~~~~~k~~yr~~ld~l~~ 166 (207)
+++.||.||+.++...|.+||||+|+|||||||||||+++..+.+.+++..|++||.|+..++.+.||+.||+.||++
T Consensus 99 ~t~~yv~rv~~iaa~ap~lLIah~ytRyLGdlsggq~l~ki~q~~~~L~~~gtaFy~F~dl~dek~fK~~YR~~ld~l-- 176 (238)
T COG5398 99 ATIAYVDRVRYIAATAPELLIAHNYTRYLGDLSGGQILKKIAQSALELSEGGTAFYEFEDLGDEKAFKDEYRQNLDSL-- 176 (238)
T ss_pred hHHHHHHHHHHHHhcCcchhHHHHHHHHHhcCCCcHHHHHHHHHHhccccccceeeeHhhcchhhhHHHHHHHHhhcc--
Confidence 999999999999999999999999999999999999999998888889888999999998889999999999999998
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCC
Q psy4643 167 QFSRQTREQLLAESRKVFLLNNSIIKCVLELLEVLLKTFDF 207 (207)
Q Consensus 167 ~l~~~e~~~iv~EA~~aF~ln~~i~~eL~~~~~~~~~~~~~ 207 (207)
+||++++++||+||+.||++|++||.+|++..+.+|.++-|
T Consensus 177 ~ldeAt~~rIvdeAn~aF~~N~~~~~eLE~n~~~aiG~~~F 217 (238)
T COG5398 177 ELDEATKLRIVDEANDAFDFNMQMFQELEGNLIKAIGKFSF 217 (238)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 89999999999999999999999999999999999987654
No 3
>PF01126 Heme_oxygenase: Heme oxygenase; InterPro: IPR016053 Haem oxygenase (1.14.99.3 from EC) (HO) [] is the microsomal enzyme that, in animals, carries out the oxidation of haem, it cleaves the haem ring at the alpha-methene bridge to form biliverdin and carbon monoxide []. Biliverdin is subsequently converted to bilirubin by biliverdin reductase. In mammals there are three isozymes of haem oxygenase: HO-1 to HO-3. The first two isozymes differ in their tissue expression and their inducibility: HO-1 is highly inducible by its substrate haem and by various non-haem substances, while HO-2 is non-inducible. It has been suggested [] that HO-2 could be implicated in the production of carbon monoxide in the brain where it is said to act as a neurotransmitter. In the genome of the chloroplast of red algae as well as in cyanobacteria, there is a haem oxygenase (gene pbsA) that is the key enzyme in the synthesis of the chromophoric part of the photosynthetic antennae []. A haem oxygenase is also present in the bacteria Corynebacterium diphtheriae (gene hmuO), where it is involved in the acquisition of iron from the host haem []. There is, in the central section of these enzymes, a well-conserved region centred on a histidine residue.; GO: 0004392 heme oxygenase (decyclizing) activity, 0006788 heme oxidation, 0055114 oxidation-reduction process; PDB: 1J77_A 1P3U_A 1P3V_A 1P3T_A 1WNW_B 1WNX_B 1IW1_B 1WNV_C 1V8X_A 1WZG_B ....
Probab=100.00 E-value=1.1e-39 Score=271.38 Aligned_cols=174 Identities=26% Similarity=0.467 Sum_probs=157.5
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHhhcCccccCCCCccccChHHHHHHHhHhhCCCCCCCCCCCCCccccCCCChh
Q psy4643 8 AMSDTSIWIEGLLVFYEVFKFLESAMEEHKSNQYLQQFNISDMKRTEAFEADLEHYLGPDWKADYKPRPDWKADYKPRES 87 (207)
Q Consensus 8 ~~~d~~~Y~~~L~~~y~vY~aLE~al~~~~~~p~l~~l~~~~L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~~~~~pa 87 (207)
+..|++.|+++|.+||+||.+||.+++++.++|.++.++.|++.|+++|++||++|.|++|.+ .++|+|+
T Consensus 30 ~~~~~~~Y~~~L~~~~~~y~~lE~~l~~~~~~~~~~~~~~~~l~R~~~L~~DL~~l~~~~~~~----------~~~~~~a 99 (205)
T PF01126_consen 30 GDLSRDDYARFLQAFYHVYRALEAALDRNRDDPALAPLYFPELRRSAALEADLAALGGPDWRD----------DIEPSPA 99 (205)
T ss_dssp TSSTHHHHHHHHHHHHHHHHHHHHHHHHTTTSTTTGGGS-GHHHTHHHHHHHHHHHHCTTHHH----------HCHHHHH
T ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHhhcccCCccccccCcchhHHHHHHHHHHHhhCCCccc----------ccCCChh
Confidence 568999999999999999999999999999999999999999999999999999999989987 6788999
Q ss_pred HHHHHHHHHHhhccCcchHHHHHHHHHHhhhchhHHHHHHHHHhhccCcC--cccceeecCCCChHHHHHHHHHHHHhcc
Q psy4643 88 VVNYLNHLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKKRQLSLMKSNY--QDQVLSFDPSVNVGQLKRQIKSILDDES 165 (207)
Q Consensus 88 ~~~yv~~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~~--g~~Fy~F~~~~~~~~~k~~yr~~ld~l~ 165 (207)
+.+|+++|++++.++|+.++||+||+|+|+|+|||||++.+....++++. |++||.|++..+.+.+|+.|++.||++
T Consensus 100 ~~~~~~~i~~~~~~~p~~~lg~~YV~egs~LgGg~ii~~~~~~~~~l~~~~~~~~f~~~~~~~~~~~~w~~f~~~l~~~- 178 (205)
T PF01126_consen 100 TQAYVPHIRELAESSPALLLGHAYVLEGSTLGGGQIIRRLLARHLGLPEGFGGLSFFSFGGIEDTGALWRAFRAALDAA- 178 (205)
T ss_dssp HHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHT-BTTBCSGGGGH-TTSSSHHHHHHHHHHHHHHS-
T ss_pred HHHHHHHHHHHHccCHHHHHHHHHHHHHHHhhHHHHHHHHHHHhcCCCCCcccccccCCCCcccHHHHHHHHHHHHhcC-
Confidence 99999999999999999999999999999999999999975556667654 899999996579999999999999998
Q ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 166 TQFSRQTREQLLAESRKVFLLNNSIIKC 193 (207)
Q Consensus 166 ~~l~~~e~~~iv~EA~~aF~ln~~i~~e 193 (207)
.+|++++++||+||+.+|++|++||+|
T Consensus 179 -~l~~~~~~~ii~~A~~~F~~~~~~~~~ 205 (205)
T PF01126_consen 179 -ALTEEERDEIIEEAKAAFRLNIAWFRE 205 (205)
T ss_dssp ----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred -CCCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 799999999999999999999999986
No 4
>cd00232 HemeO Heme oxygenase catalyzes the rate limiting step in the degradation of heme to bilirubin, it is essential for recycling of iron from heme. Heme is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This family includes bacterial HO, as well as the mammalian isoforms HO-1, and HO-2. Heme oxygenases play key roles in heme homeostasis, oxidative stress response, photosynthetic pigment formation in cyanobacteria, cellular signaling in mammals, and iron acquisition from host heme by bacterial pathogens.
Probab=100.00 E-value=7.2e-36 Score=248.05 Aligned_cols=175 Identities=27% Similarity=0.457 Sum_probs=161.2
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHHHHHHHhhcCccccCCCCccccChHHHHHHHhHhhCCCCCCCCCCCCCccccCCCCh
Q psy4643 7 GAMSDTSIWIEGLLVFYEVFKFLESAMEEHKSNQYLQQFNISDMKRTEAFEADLEHYLGPDWKADYKPRPDWKADYKPRE 86 (207)
Q Consensus 7 ~~~~d~~~Y~~~L~~~y~vY~aLE~al~~~~~~p~l~~l~~~~L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~~~~~p 86 (207)
.+..+.+.|+++|.++|.+|.++|.++++...+|.+..++.+++.|+++|++||++|.|+.|.. ..+|.+
T Consensus 28 ~~~~s~~~Y~~~L~~~~~~~~~lE~~l~~~~~~~~~~~~~~~~~~r~~~L~~DL~~lg~~~~~~----------~~~~~~ 97 (203)
T cd00232 28 KGFLSREGYARFLANLYLVYRALEALLEASKDNPYLAPLYLPELERAAALEKDLAYLGGSDWRV----------REPPLP 97 (203)
T ss_pred cCCcCHHHHHHHHHHHHHHHHHHHHHHHHccCCcccccccCccccchHHHHHHHHHHhCCCccc----------cCCCCh
Confidence 5678999999999999999999999999999888777788999999999999999998887765 445667
Q ss_pred hHHHHHHHHHHhhccCcchHHHHHHHHHHhhhchhHHHHHHHHHhhccCcCcccceeecCCCChHHHHHHHHHHHHhccc
Q psy4643 87 SVVNYLNHLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKKRQLSLMKSNYQDQVLSFDPSVNVGQLKRQIKSILDDEST 166 (207)
Q Consensus 87 a~~~yv~~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~~g~~Fy~F~~~~~~~~~k~~yr~~ld~l~~ 166 (207)
++ .|+++|+..+.++|..++||+||+|+|+|||||+|+++++....+++.|++||.|++..+.+.+|+.|+..||++
T Consensus 98 ~~-~~~~~~~~~~~~~~~~~lg~~YV~egs~l~GG~~i~~~l~~~~~~~~~~~~f~~~~g~~~~~~~w~~f~~~l~~~-- 174 (203)
T cd00232 98 AA-AYAARLREIAEENPALLLGHAYVRYGADLSGGQVLAKIAQRALLLEGKGLAFYAFHGIADRGLFKREFREALDAL-- 174 (203)
T ss_pred HH-HHHHHHHHHHhcCHHHHHHHHHHHHHHHhcccHHHHHHHHHHhCCCCccCccccCCCcCCHHHHHHHHHHHHhcC--
Confidence 77 999999999999999999999999999999999999997776677778999999995589999999999999998
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 167 QFSRQTREQLLAESRKVFLLNNSIIKCV 194 (207)
Q Consensus 167 ~l~~~e~~~iv~EA~~aF~ln~~i~~eL 194 (207)
.+|+++++++|+||+.+|++|.+||.++
T Consensus 175 ~~~~~~~~~~i~~A~~~F~~~~~~~~~~ 202 (203)
T cd00232 175 PLDEEERQRVVAEARAAFRLNGQVFREL 202 (203)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 7999999999999999999999999987
No 5
>KOG4480|consensus
Probab=99.84 E-value=4e-20 Score=159.48 Aligned_cols=173 Identities=18% Similarity=0.306 Sum_probs=152.7
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHHHHhhcCccccCCCCc---cccChHHHHHHHhHhhCCCCCCCCCCCCCccccCCCC
Q psy4643 9 MSDTSIWIEGLLVFYEVFKFLESAMEEHKSNQYLQQFNIS---DMKRTEAFEADLEHYLGPDWKADYKPRPDWKADYKPR 85 (207)
Q Consensus 9 ~~d~~~Y~~~L~~~y~vY~aLE~al~~~~~~p~l~~l~~~---~L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~~~~~ 85 (207)
-.++..........|..|..++.......++|.+.+.++| +++|.+++++|+++++|.+|++ .++..
T Consensus 43 n~t~~l~~~~t~a~~~~~~~y~~e~~~~~E~~~F~~~~f~~~~el~e~~a~~~d~~~~~~~~W~e----------~ie~~ 112 (283)
T KOG4480|consen 43 NVTPELVQLSTAALYFWYKAYPGETEGFKEEMRFVAMRFPSTEELHEKEALEQDPEEFFGENWEE----------TIEGE 112 (283)
T ss_pred CCchHHHHHHHHHHHHHHHhCcchhhhhhHHHhhHhhhcCCHHHHhHHhhhhcChhhhccccccc----------cccCC
Confidence 3456666677888999999999999999999988888776 7999999999999999999998 78889
Q ss_pred hhHHHHHHHHHHhhccCcchHHHHHHHHHHhhhchhHHHHHHHHHhhccCcCcccceeecCCCChHHHHHHHHHHHHhcc
Q psy4643 86 ESVVNYLNHLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKKRQLSLMKSNYQDQVLSFDPSVNVGQLKRQIKSILDDES 165 (207)
Q Consensus 86 pa~~~yv~~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~~g~~Fy~F~~~~~~~~~k~~yr~~ld~l~ 165 (207)
|+++.|+.|++-++++.|.+|++|+|+||||++||| +.+.-++...++..|.+||.|+........++.|+ .|.+
T Consensus 113 pa~~kyl~~~~~v~~t~e~ll~~s~~~~Y~g~~s~G--Lek~~q~~~dl~w~~~q~~~~pe~~~a~k~~~~y~--k~~~- 187 (283)
T KOG4480|consen 113 PAYQKYLVDSKLVADTEEELLVASAYTRYAGLLSGG--LEKAEQKELDLPWTGEQFYTFPELANAGKTYQKYL--KNNL- 187 (283)
T ss_pred HHHHHHHHHHHHHHHhhhHHHHHhhHHHHHHhhccH--HHHHHHHHhhcchhhhhccccCCCCcHHHHHHHHH--HHhh-
Confidence 999999999999999999999999999999999999 66665667777777899999997788999999999 6666
Q ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 166 TQFSRQTREQLLAESRKVFLLNNSIIKCVLELLEV 200 (207)
Q Consensus 166 ~~l~~~e~~~iv~EA~~aF~ln~~i~~eL~~~~~~ 200 (207)
.+++ +.+|.|+..+|-.|+++++.+......
T Consensus 188 -E~~p---q~~I~~~~~iyf~~~~~f~~~~~~v~~ 218 (283)
T KOG4480|consen 188 -ELDP---QRFICEFYNIYFAHIAGFQMLGRKVAE 218 (283)
T ss_pred -ccCh---hHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666 679999999999999999888766543
No 6
>COG3230 HemO Heme oxygenase [Inorganic ion transport and metabolism]
Probab=99.27 E-value=8.3e-11 Score=96.02 Aligned_cols=158 Identities=16% Similarity=0.172 Sum_probs=120.8
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHHHHHHHhhcCccccCCCCcc-ccChHHHHHHHhHhhCCCCCCCCCCCCCccccCCCC
Q psy4643 7 GAMSDTSIWIEGLLVFYEVFKFLESAMEEHKSNQYLQQFNISD-MKRTEAFEADLEHYLGPDWKADYKPRPDWKADYKPR 85 (207)
Q Consensus 7 ~~~~d~~~Y~~~L~~~y~vY~aLE~al~~~~~~p~l~~l~~~~-L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~~~~~ 85 (207)
..+.|+..|.+++...|.+-.+||..+... +.-..+..++ +.|..++++||..+ |...+.. +.|. ..
T Consensus 34 ~pf~sr~nyl~f~~~q~~f~~~Le~~~r~~---~l~~~lp~l~~r~r~~~l~~DLadl-G~~~~~~--d~p~------~~ 101 (196)
T COG3230 34 QPFLSRRNYLKFLKRQYLFHKPLEHILRDA---ELPKALPELEYRARYDALEQDLADL-GEEPPKF--DKPR------CE 101 (196)
T ss_pred CccccHHHHHHHHHHHHHHhhhHHHHHccc---cchhhcccHHHHHHHHHHHHHHHHh-CCCCCcc--cccc------cc
Confidence 357889999999999999999999998773 2223333334 88999999999998 7764431 1110 01
Q ss_pred hhHHHHHHHHHHhhccCcchHHHHHHHHHHhhhchhHHHHHHHHHhhcc-CcCcccceeecCCCChHHHHHHHHHHHHhc
Q psy4643 86 ESVVNYLNHLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKKRQLSLMK-SNYQDQVLSFDPSVNVGQLKRQIKSILDDE 164 (207)
Q Consensus 86 pa~~~yv~~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~~~~a~~l-~~~g~~Fy~F~~~~~~~~~k~~yr~~ld~l 164 (207)
|.. +-+...++..||+.++.| ||++|-|+..+ .++ +..|.+.+.-+ +.....-|+.|-+.||.+
T Consensus 102 ~~~------------t~~aea~GwlYV~EGstL-GaAfL~K~aa~-L~l~~e~garhLag~-~~grG~~WrsF~e~L~~~ 166 (196)
T COG3230 102 PPL------------TLAAEAFGWLYVAEGSTL-GAAFLFKHAAK-LGLNPEFGARHLAGY-GDGRGKRWRSFVEHLDAI 166 (196)
T ss_pred CCc------------hhHHHhhhhhhhccccch-HHHHHHHHHHH-hcCCcccchHhhcCC-CCCCCccHHHHHHHHHhc
Confidence 111 223356799999999998 99999998544 333 45699999988 556777788999999998
Q ss_pred ccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 165 STQFSRQTREQLLAESRKVFLLNNSIIKC 193 (207)
Q Consensus 165 ~~~l~~~e~~~iv~EA~~aF~ln~~i~~e 193 (207)
.+|+|+...+|+.|+.+|.....++.+
T Consensus 167 --~l~~E~e~~av~gA~~aF~~fr~~l~~ 193 (196)
T COG3230 167 --NLTPEAEAEAVAGARAAFAAFRRVLQE 193 (196)
T ss_pred --cCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 899999999999999999988887754
No 7
>KOG4480|consensus
Probab=99.05 E-value=3.6e-09 Score=91.90 Aligned_cols=165 Identities=16% Similarity=0.215 Sum_probs=134.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCccccCCCCccccChHHHHHHHhHhhCCCCCCCCCCCCCccccCCCChhHHHHHH
Q psy4643 14 IWIEGLLVFYEVFKFLESAMEEHKSNQYLQQFNISDMKRTEAFEADLEHYLGPDWKADYKPRPDWKADYKPRESVVNYLN 93 (207)
Q Consensus 14 ~Y~~~L~~~y~vY~aLE~al~~~~~~p~l~~l~~~~L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~~~~~pa~~~yv~ 93 (207)
.|.++|.+...||.+.|..+.++.- +....+...+|.|.+.++.||.++ |.-.-+ --.+.++.+.|..
T Consensus 114 a~~kyl~~~~~v~~t~e~ll~~s~~-~~Y~g~~s~GLek~~q~~~dl~w~-~~q~~~----------~pe~~~a~k~~~~ 181 (283)
T KOG4480|consen 114 AYQKYLVDSKLVADTEEELLVASAY-TRYAGLLSGGLEKAEQKELDLPWT-GEQFYT----------FPELANAGKTYQK 181 (283)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHhhH-HHHHHhhccHHHHHHHHHhhcchh-hhhccc----------cCCCCcHHHHHHH
Confidence 4999999999999999999998543 333445567799999999999998 421111 2346788889999
Q ss_pred HHHHhhccCcchHHHHHHHHHHhhhchhHHHHHHHHHhhc-cCcCcccceeecCCCChHHHHHHHHHHHHhcccCCCHHH
Q psy4643 94 HLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKKRQLSLM-KSNYQDQVLSFDPSVNVGQLKRQIKSILDDESTQFSRQT 172 (207)
Q Consensus 94 ~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~~~~a~~-l~~~g~~Fy~F~~~~~~~~~k~~yr~~ld~l~~~l~~~e 172 (207)
..++...-+|...|+|+|.-|.....|||++.+++ +.+ +...-..|+.++ ..-..+-+.+++.++..++.++.++
T Consensus 182 y~k~~~E~~pq~~I~~~~~iyf~~~~~f~~~~~~v--~~~ile~~~~ef~~~~--~~~~~~~~~v~ekln~~~~~~~r~~ 257 (283)
T KOG4480|consen 182 YLKNNLELDPQRFICEFYNIYFAHIAGFQMLGRKV--AEEILENKELEFDGWD--GRFSELLQNVREKLNKEGEAWTREE 257 (283)
T ss_pred HHHHhhccChhHHHHHHHHHHHHHHHHHHHHHHHH--HHHHhccCcccccccc--hhhhHHHHHHHHHhhhccccchhHH
Confidence 99999999999999999999999999999999983 333 444456666655 3567788899999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q psy4643 173 REQLLAESRKVFLLNNSIIKCV 194 (207)
Q Consensus 173 ~~~iv~EA~~aF~ln~~i~~eL 194 (207)
+.+++.+-..+|.+-..|+..+
T Consensus 258 ~~~~L~~~~l~fif~~~iv~~~ 279 (283)
T KOG4480|consen 258 KNACLLETSLAFIFVGEIVRLI 279 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999888764
No 8
>PF03070 TENA_THI-4: TENA/THI-4/PQQC family; InterPro: IPR004305 Proteins containing this domain are found in all the three major phyla of life: archaebacteria, eubacteria, and eukaryotes. In Bacillus subtilis, TENA is one of a number of proteins that enhance the expression of extracellular enzymes, such as alkaline protease, neutral protease and levansucrase []. The THI-4 protein, which is involved in thiamine biosynthesis, also contains this domain. The C-terminal part of these proteins consistently show significant sequence similarity to TENA proteins. This similarity was first noted with the Neurospora crassa THI-4 []. The exact molecular function of this domain is uncertain.; PDB: 2RD3_D 3RM5_B 1UDD_D 1Z72_B 3HML_A 3HLX_A 3HNH_A 3DDE_B 3OQL_A 2A6B_A ....
Probab=89.34 E-value=0.55 Score=38.43 Aligned_cols=165 Identities=16% Similarity=0.152 Sum_probs=87.9
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHhhc-CccccC---C---CCccccChHHHHHHHhHhhCCCCCCCCCCCCCccc
Q psy4643 8 AMSDTSIWIEGLLVFYEVFKFLESAMEEHKS-NQYLQQ---F---NISDMKRTEAFEADLEHYLGPDWKADYKPRPDWKA 80 (207)
Q Consensus 8 ~~~d~~~Y~~~L~~~y~vY~aLE~al~~~~~-~p~l~~---l---~~~~L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~ 80 (207)
|-.++..+..+|.+=|+.-...=.++..... .|.... + ..........+-.++..-+|-++.+ +.
T Consensus 23 GtL~~~~f~~Yl~QD~~yl~~~~r~~a~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~gi~~~~--------~~ 94 (210)
T PF03070_consen 23 GTLPKEAFRYYLIQDYHYLKHFARALALLASKAPDPEEQRELLSRLIQEIEEELELHEDFAEELGISRED--------LE 94 (210)
T ss_dssp TESEHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHH--------HH
T ss_pred CCCCHHHHHHHHHhhHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHH--------HH
Confidence 4467788888988888777777776665432 111000 0 0011111122223332223544332 12
Q ss_pred cCCCChhHHHHHHHHHHhhcc-CcchHHHHHHHHHHhhhchhHHHHHHHHHhhccCcC-cccceeecCCCChHHHHHHHH
Q psy4643 81 DYKPRESVVNYLNHLEDLKQT-NDTLLIAYVYHMYLGVLSGGQIINKKRQLSLMKSNY-QDQVLSFDPSVNVGQLKRQIK 158 (207)
Q Consensus 81 ~~~~~pa~~~yv~~i~~~~~~-~P~~LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~~-g~~Fy~F~~~~~~~~~k~~yr 158 (207)
.++|+|+|..|++++..++.+ ++...++-.+.-+.+=..=|+.+....+ ...+. -..+.+.++.++-...-....
T Consensus 95 ~~~~~p~~~~y~~~l~~~a~~~~~~~~l~al~pc~~~Y~~~~~~~~~~~~---~~~~~~y~~wi~~y~~~~f~~~~~~~~ 171 (210)
T PF03070_consen 95 NIEPSPATRAYTDFLLSLAQTGSLAEGLAALLPCEWIYAEIGKRLAEKLR---APEDNPYQEWIDMYASEEFEAFVEWLE 171 (210)
T ss_dssp HSTC-HHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHHCS---TTSSHHHHHHHHHHHSHHHHHHHHHHH
T ss_pred hhhhhhHHHHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHhcccc---CCCCccHHHHHHhcCCHHHHHHHHHHH
Confidence 468999999999999998764 4555667767666666555665554421 11110 112222232224445566777
Q ss_pred HHHHhcccCCCHHHHHHHHHHHHHH
Q psy4643 159 SILDDESTQFSRQTREQLLAESRKV 183 (207)
Q Consensus 159 ~~ld~l~~~l~~~e~~~iv~EA~~a 183 (207)
+.+|.+....++++++++.+--..+
T Consensus 172 ~~~~~~~~~~~~~~~~~~~~~f~~~ 196 (210)
T PF03070_consen 172 ELLDELAAEASDEERERLEEIFRRS 196 (210)
T ss_dssp HHHHHHHHTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 7888876566666655444443333
No 9
>PRK14713 multifunctional hydroxymethylpyrimidine phosphokinase/4-amino-5-aminomethyl-2-methylpyrimidine hydrolase; Provisional
Probab=76.51 E-value=34 Score=32.67 Aligned_cols=155 Identities=12% Similarity=0.063 Sum_probs=78.2
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHhhcC-ccccC--CCCccccChHHHHHHHhHhhCCCCCCCCCCCCCccccCCC
Q psy4643 8 AMSDTSIWIEGLLVFYEVFKFLESAMEEHKSN-QYLQQ--FNISDMKRTEAFEADLEHYLGPDWKADYKPRPDWKADYKP 84 (207)
Q Consensus 8 ~~~d~~~Y~~~L~~~y~vY~aLE~al~~~~~~-p~l~~--l~~~~L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~~~~ 84 (207)
|-.+++.+..+|.+=|.....+-.++...... |.... +....+...-.-|.++-.=+-..|.. ..++
T Consensus 347 GtL~~~~F~~Yl~QD~~yL~~~~r~~a~~~aka~~~e~~~~~~~~~~~~~~~E~~~h~~~~~~~~~----------~~~~ 416 (530)
T PRK14713 347 GTLPEEAFEFYLAQDALYLNGYSRALARLAALAPDPAEQVFWAQSAQACLEVESELHRSWLGDRDA----------DTAP 416 (530)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc----------cCCC
Confidence 45688889999888777777666666554321 10000 00000000000111111000112322 4578
Q ss_pred ChhHHHHHHHHHHhhccCcc-h---HHHHHHHHHHhhhchhHHHHHHHHHhhccCcC-cccceeecCCCChHHHHHHHHH
Q psy4643 85 RESVVNYLNHLEDLKQTNDT-L---LIAYVYHMYLGVLSGGQIINKKRQLSLMKSNY-QDQVLSFDPSVNVGQLKRQIKS 159 (207)
Q Consensus 85 ~pa~~~yv~~i~~~~~~~P~-~---LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~~-g~~Fy~F~~~~~~~~~k~~yr~ 159 (207)
.|++.+|++++.+.+.+... . .|.-|+..|.-- |+-+... ....++. =..+.+++.+++-.+.=+.+++
T Consensus 417 ~p~~~aY~~~l~~~a~~~~~~~~l~AllPC~~~Y~~i---g~~l~~~---~~~~~~~~Y~~WI~~Y~~~~f~~~v~~~~~ 490 (530)
T PRK14713 417 SPVTLAYTDFLLARAAGGSYAVGAAAVLPCFWLYAEV---GAELHAR---AGNPDDHPYAEWLQTYADPEFAAATRRAIA 490 (530)
T ss_pred ChHHHHHHHHHHHHHhcCCHHHHHHHHHhHHHHHHHH---HHHHHhh---ccCCCCChHHHHHHHhCCHHHHHHHHHHHH
Confidence 99999999999998655333 2 334455555432 3333221 0011111 0122333433344555667888
Q ss_pred HHHhcccCCCHHHHHHHHH
Q psy4643 160 ILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 160 ~ld~l~~~l~~~e~~~iv~ 178 (207)
.+|+++..+++++++++.+
T Consensus 491 ~ld~~~~~~s~~~~~~~~~ 509 (530)
T PRK14713 491 FVDRAFRAASPAERAAMAR 509 (530)
T ss_pred HHHHHHhhCCHHHHHHHHH
Confidence 8898887889999875443
No 10
>COG5398 Heme oxygenase [Inorganic ion transport and metabolism]
Probab=74.39 E-value=6.2 Score=33.75 Aligned_cols=109 Identities=13% Similarity=0.029 Sum_probs=79.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhcCcc--------c--cCCCCccccChHHHHHHHhHhhCCCCCCCCCCCCCcccc
Q psy4643 12 TSIWIEGLLVFYEVFKFLESAMEEHKSNQY--------L--QQFNISDMKRTEAFEADLEHYLGPDWKADYKPRPDWKAD 81 (207)
Q Consensus 12 ~~~Y~~~L~~~y~vY~aLE~al~~~~~~p~--------l--~~l~~~~L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~ 81 (207)
...|+.|....|.+.+..+ -++.....|+ + ..++.++|+++-..-+|..-+.+-.+++ +. -++.
T Consensus 4 a~~lR~gt~~ah~~aEnv~-fmkcfLkg~V~~e~f~kl~~n~yf~ysaleaa~~~~~d~~~l~~i~fp~----ln-r~~t 77 (238)
T COG5398 4 AFKLRQGTQKAHTVAENVG-FMKCFLKGVVERESFRKLLANLYFVYSALEAATQIHKDNPILSSIYFPE----LN-RKAT 77 (238)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHHHHHcCcccHHHHHHHHHHHHHHHHHHHHHHHHhccCchhhhccchh----hh-hHHH
Confidence 4689999999999999999 6666655442 1 1234578888888888888776654432 00 0112
Q ss_pred CCCChhHHHHHHHHHHhhccCcchHHHHHHHHHHhhhchhHHHHHH
Q psy4643 82 YKPRESVVNYLNHLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKK 127 (207)
Q Consensus 82 ~~~~pa~~~yv~~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~ 127 (207)
.+. +.+.-|-+.+++..+..|...+-++.++|++...||..|++.
T Consensus 78 le~-dl~~yyg~nwre~I~~sp~t~~yv~rv~~iaa~ap~lLIah~ 122 (238)
T COG5398 78 LEK-DLLYYYGNNWRENIQPSPATIAYVDRVRYIAATAPELLIAHN 122 (238)
T ss_pred hhc-CHHHHhcccHHHhcCcChhHHHHHHHHHHHHhcCcchhHHHH
Confidence 232 334455588898888889999999999999999999999987
No 11
>PRK05157 pyrroloquinoline quinone biosynthesis protein PqqC; Provisional
Probab=62.70 E-value=1e+02 Score=26.75 Aligned_cols=107 Identities=10% Similarity=-0.019 Sum_probs=68.4
Q ss_pred CChhHHHHHHHHHHhhccCcc-hHHHHHHHHHHhhhchhHHHHHHHHHhhccCc----CcccceeecCCCChHHHHHHHH
Q psy4643 84 PRESVVNYLNHLEDLKQTNDT-LLIAYVYHMYLGVLSGGQIINKKRQLSLMKSN----YQDQVLSFDPSVNVGQLKRQIK 158 (207)
Q Consensus 84 ~~pa~~~yv~~i~~~~~~~P~-~LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~----~g~~Fy~F~~~~~~~~~k~~yr 158 (207)
++|.|+..|+.-...++..|. .-+|-.|+ -+.=-+|.+.++.-..++++ .|+.||.---.....+..-...
T Consensus 119 ~lP~tr~aVday~~~~r~~~~~eavas~lt----E~~~P~I~~~ri~gl~~~Y~~~~~e~l~yF~~h~~~a~~Dvehal~ 194 (246)
T PRK05157 119 VLPGVRFAVDAYVNFARRAPWLEAVASSLT----ELFAPQIHQERLAGWPEHYPWIDPEGLAYFRSRLTQAPRDVEHGLA 194 (246)
T ss_pred CChHHHHHHHHHHHHHccCCHHHHHHHHHH----HHhhhHHHHHHHHHHHHHCCCCCHHHHHHHHHHhhccchhHHHHHH
Confidence 679999999998888877774 46676666 22356677776544444433 4888888762223344444444
Q ss_pred HHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 159 SILDDESTQFSRQTREQLLAESRKVFLLNNSIIKCVLEL 197 (207)
Q Consensus 159 ~~ld~l~~~l~~~e~~~iv~EA~~aF~ln~~i~~eL~~~ 197 (207)
--++.+ -|+++++++++.+...=+.--..++.|...
T Consensus 195 ~~l~~~---~t~e~q~~al~al~~k~d~Lw~~LDai~~a 230 (246)
T PRK05157 195 YVLDHA---TTREQQERALEALQFKLDVLWSMLDALYMA 230 (246)
T ss_pred HHHHHc---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455544 477889888888766666555566655443
No 12
>TIGR02111 PQQ_syn_pqqC coenzyme PQQ biosynthesis protein C. This model describes the coenzyme PQQ (pyrrolo-quinoline-quinone) biosynthesis protein PqqC.In contrast to the broader model pfam05312, this model does not include related proteins likely to be functionally distinct from PqqC, such as homologs found in the Chlamydias.
Probab=62.09 E-value=97 Score=26.87 Aligned_cols=105 Identities=11% Similarity=0.006 Sum_probs=63.0
Q ss_pred CChhHHHHHHHHHHhhccCcch-HHHHHHHHHHhhhchhHHHHHHHHHhhccCc----CcccceeecCCCChHHHHHHHH
Q psy4643 84 PRESVVNYLNHLEDLKQTNDTL-LIAYVYHMYLGVLSGGQIINKKRQLSLMKSN----YQDQVLSFDPSVNVGQLKRQIK 158 (207)
Q Consensus 84 ~~pa~~~yv~~i~~~~~~~P~~-LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~----~g~~Fy~F~~~~~~~~~k~~yr 158 (207)
.+|.|+..|+--...++..|.+ -+|-.|| -+.==+|.+.++.-..++++ .|+.||+---.....+.--.+.
T Consensus 112 ~lP~trfaVday~~f~r~~~~~eavasslT----E~f~P~I~~~ri~gl~~~Y~~~~~e~l~yF~~r~~qa~rd~e~~l~ 187 (239)
T TIGR02111 112 VLPGTRFAVDAYVHFVREKSLLEAIASSLT----ELFAPQIHSERVAGMLQHYDFIDDAALAYFRKRLTQAPRDVEFGLD 187 (239)
T ss_pred CCHHHHHHHHHHHHHHhcCCHHHHHHHHHH----HHHhHHHHHHHHHhHHHHCCCCCHHHHHHHHHHHhhhHHHHHHHHH
Confidence 3798988888888888777776 7777777 22345666666433333333 3666666541222334433444
Q ss_pred HHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 159 SILDDESTQFSRQTREQLLAESRKVFLLNNSIIKCVL 195 (207)
Q Consensus 159 ~~ld~l~~~l~~~e~~~iv~EA~~aF~ln~~i~~eL~ 195 (207)
-.++.+ -|+++++++++.+.-.=+.--..++.|.
T Consensus 188 ~~l~~~---~t~e~Q~~~l~al~fk~dvLw~~LDal~ 221 (239)
T TIGR02111 188 YVLDHA---TTREKQEAALEALTFKCDVLWAQLDALY 221 (239)
T ss_pred HHHHHc---CCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446554 4778888888886655554445555544
No 13
>TIGR02792 PCA_ligA protocatechuate 4,5-dioxygenase, alpha subunit. Protocatechuate (PCA) 4,5-dioxygenase is the first enzyme in the PCA 4,5-cleavage pathway that is an alternative to PCA 3,4-cleavage and PCA 2,3 cleavage pathways. PCA is an intermediate in the breakdown of lignin (hence the gene symbol ligA) and other compounds. Members of this family are the alpha chain of PCA 4,5-dioxygenase, or the equivalent domain of a fusion protein.
Probab=60.48 E-value=5.7 Score=30.69 Aligned_cols=29 Identities=21% Similarity=0.306 Sum_probs=24.9
Q ss_pred CChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 148 VNVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 148 ~~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
++.+.||.+-++.+|+. +||++||+.|.+
T Consensus 32 ~nRerF~ade~Ay~d~~--~Lt~eqk~av~~ 60 (117)
T TIGR02792 32 ENRERFKADESAYLDEW--NLTPAQKQAVLA 60 (117)
T ss_pred HHHHHHHhCHHHHHHHc--CCCHHHHHHHHh
Confidence 35678898999999998 899999998765
No 14
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=58.72 E-value=6.6 Score=30.35 Aligned_cols=29 Identities=7% Similarity=0.072 Sum_probs=24.7
Q ss_pred CChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 148 VNVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 148 ~~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
++.+.|+.+-++.+++. +||++||+.|.+
T Consensus 38 ~nRe~F~ade~Ay~~~~--~Lteeqk~aV~~ 66 (117)
T PRK13378 38 ANRAAFLADEAAYCRKY--GLNEEQKEAIRN 66 (117)
T ss_pred HHHHHHHhCHHHHHHHc--CCCHHHHHHHHh
Confidence 35678888889999998 899999998765
No 15
>cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=57.85 E-value=7 Score=30.38 Aligned_cols=29 Identities=21% Similarity=0.333 Sum_probs=24.8
Q ss_pred CChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 148 VNVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 148 ~~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
++.+.|+.+-++.+++. +||++||+.|++
T Consensus 35 ~nRerF~ade~Ay~~~~--~Lteeqr~aV~~ 63 (121)
T cd07924 35 ENRERFKADERAYLDKW--PMTEEQKQAVLA 63 (121)
T ss_pred HHHHHHHhCHHHHHHHc--CCCHHHHHHHHH
Confidence 35678888889999998 899999998765
No 16
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=57.33 E-value=7.7 Score=29.48 Aligned_cols=30 Identities=3% Similarity=0.066 Sum_probs=25.2
Q ss_pred CCChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 147 SVNVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 147 ~~~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
.++.+.|+.+-.+.+++. +||++||+.|.+
T Consensus 26 ~~nRe~F~aD~~Ay~~~~--~Lteeqr~av~~ 55 (106)
T cd07925 26 AANREAFLADEEAYCEKF--GLTPEQKQAVRN 55 (106)
T ss_pred HHHHHHHHhCHHHHHHHc--CCCHHHHHHHHH
Confidence 346778888889999998 899999998765
No 17
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=56.65 E-value=7.2 Score=30.60 Aligned_cols=29 Identities=21% Similarity=0.358 Sum_probs=24.8
Q ss_pred CChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 148 VNVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 148 ~~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
++.+.|+.+-++.+|+. +||++||+.|.+
T Consensus 38 ~nRerF~ade~Ay~de~--~Lteeqr~aV~~ 66 (129)
T PRK13377 38 ENRERFKADERAYLDEW--PMTEEQKQAVLA 66 (129)
T ss_pred HHHHHHHhCHHHHHHHc--CCCHHHHHHHHh
Confidence 35678888889999998 899999998765
No 18
>PRK09517 multifunctional thiamine-phosphate pyrophosphorylase/synthase/phosphomethylpyrimidine kinase; Provisional
Probab=56.27 E-value=1.7e+02 Score=29.36 Aligned_cols=153 Identities=12% Similarity=0.020 Sum_probs=76.7
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHhhcC-cccc--CCCCccccChHHHHHHHhHhhCCCCCCCCCCCCCccccCCC
Q psy4643 8 AMSDTSIWIEGLLVFYEVFKFLESAMEEHKSN-QYLQ--QFNISDMKRTEAFEADLEHYLGPDWKADYKPRPDWKADYKP 84 (207)
Q Consensus 8 ~~~d~~~Y~~~L~~~y~vY~aLE~al~~~~~~-p~l~--~l~~~~L~R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~~~~ 84 (207)
|-.+++.+..+|.+=|.....+=.++...... |... ......+...-.=|.++-.=+-..|.. ..++
T Consensus 573 GtL~~e~F~~YL~QD~~YL~~yar~~a~~~aka~~~~~~~~~~~~~~~~~~~E~~~h~~~~~~~~~----------~~~~ 642 (755)
T PRK09517 573 GTLRRPEFDFYIDQDAQYLRQYSRALARLSSIAPDSHAQVEWAQSAAECIVVEAELHRSYLSGKEA----------PSAP 642 (755)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc----------CCCC
Confidence 45678888888888887777776666554321 1000 000000000000111111101112332 4578
Q ss_pred ChhHHHHHHHHHHhhccCcc-hHHH---HHHHHHHhhhchhHHHHHHHHHhhccCcCc-ccceeecCCCChHHHHHHHHH
Q psy4643 85 RESVVNYLNHLEDLKQTNDT-LLIA---YVYHMYLGVLSGGQIINKKRQLSLMKSNYQ-DQVLSFDPSVNVGQLKRQIKS 159 (207)
Q Consensus 85 ~pa~~~yv~~i~~~~~~~P~-~LlA---h~Yv~YlgdlsGGqii~~~~~~a~~l~~~g-~~Fy~F~~~~~~~~~k~~yr~ 159 (207)
+|++.+|.++|-+.+.+... .+++ -|+..|.- =|+.+... . -++.. -.+-+++.+++-...=+.+++
T Consensus 643 ~p~~~aYt~~l~~~a~~g~~~~~laAllPC~w~Y~~---ig~~l~~~---~--~~~~~Y~~WI~~Y~~~~f~~~v~~~~~ 714 (755)
T PRK09517 643 SPVTMAYTDFLIARTYTEDYVVGVAAVLPCYWLYAE---IGLMLAEQ---N--HDEHPYKDWLNTYSGEEFIAGTRAAIA 714 (755)
T ss_pred ChHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH---HHHHHHhc---c--CCCchHHHHHHHhCCHHHHHHHHHHHH
Confidence 99999999999998765433 2333 44444432 23333221 1 01110 122233422333445567788
Q ss_pred HHHhcccCCCHHHHHHHHH
Q psy4643 160 ILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 160 ~ld~l~~~l~~~e~~~iv~ 178 (207)
.+|+++..+|+++++++.+
T Consensus 715 ~ld~~~~~~s~~~~~~l~~ 733 (755)
T PRK09517 715 RVEKALENAGPEQRVDAAR 733 (755)
T ss_pred HHHHHHhhCCHHHHHHHHH
Confidence 8998887888988875543
No 19
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=56.02 E-value=7.7 Score=30.06 Aligned_cols=29 Identities=10% Similarity=0.236 Sum_probs=24.5
Q ss_pred CChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 148 VNVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 148 ~~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
...++||.+-++.+++. +||+|||+.|.+
T Consensus 39 ~~RerF~aDe~ay~~~~--~Lt~eqk~aV~~ 67 (119)
T PRK13379 39 PWRDRFLQDAEALMQEA--GLTEQEKELIRA 67 (119)
T ss_pred HHHHHHHhCHHHHHHHc--CCCHHHHHHHHh
Confidence 35678888889999998 899999987764
No 20
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=55.22 E-value=7.5 Score=29.58 Aligned_cols=29 Identities=14% Similarity=0.202 Sum_probs=24.2
Q ss_pred CChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 148 VNVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 148 ~~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
...++||.+-...+++. +||+||++.|.+
T Consensus 27 ~~Re~F~aD~eAy~~~~--gLTeEe~~AV~~ 55 (106)
T cd07921 27 ENREAFKADEEAYCDKF--GLTEEQKQAVLD 55 (106)
T ss_pred HHHHHHHhCHHHHHHHc--CCCHHHHHHHHh
Confidence 35678888888999988 899999998765
No 21
>PF12981 DUF3865: Domain of Unknown Function with PDB structure (DUF3865); InterPro: IPR024477 This entry represents a family of proteins of unknown function. The Nostoc punctiforme protein (D0VWS1 from SWISSPROT) has been structurally characterised and adopts a heme oxygenase-like fold similar to that of the Chlamydia trachomatis death domain-binding CADD protein. The proposed active sites of the Nostoc and Chlamydia sequences are identical, suggesting similar functions.; PDB: 3B5P_A 3B5O_A.
Probab=49.38 E-value=1.5e+02 Score=25.45 Aligned_cols=130 Identities=12% Similarity=0.108 Sum_probs=73.5
Q ss_pred ChHHHHHHHhHhhCCCCCCCCCCCCCccccCCCChhHHHHHHHHHHhhccCcchHHHHHHHHHHhhhchhHHHHHH-HHH
Q psy4643 52 RTEAFEADLEHYLGPDWKADYKPRPDWKADYKPRESVVNYLNHLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKK-RQL 130 (207)
Q Consensus 52 R~~~L~~DL~~l~g~~w~~~~~~~~~~~~~~~~~pa~~~yv~~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~-~~~ 130 (207)
-..-+.+=+....|.+-. ...|+++|..+...+..+-..++...+|-+|...-.-+.==+.|+.. .+.
T Consensus 92 Hy~~~~~~l~~~~~~~v~-----------~~~Ps~aT~~fl~sv~~L~t~~~s~vlGa~YAtE~~AIpEl~ll~ei~~~l 160 (231)
T PF12981_consen 92 HYVVFRKALHTYFGFDVN-----------NRMPSVATTHFLDSVLALFTWDSSEVLGACYATEAAAIPELQLLYEIVNEL 160 (231)
T ss_dssp HHHHHHHHHHHHHS---T-----------T----HHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred hHHHHHHHHHHHhCCccc-----------ccCCcHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455555554454432 56789999999999999998889899999998877665444444442 111
Q ss_pred hh--cc--CcCcccceeecCCCC-hHHHHHHHHHHHHhcccCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 131 SL--MK--SNYQDQVLSFDPSVN-VGQLKRQIKSILDDESTQFSRQT-REQLLAESRKVFLLNNSIIKCVLE 196 (207)
Q Consensus 131 a~--~l--~~~g~~Fy~F~~~~~-~~~~k~~yr~~ld~l~~~l~~~e-~~~iv~EA~~aF~ln~~i~~eL~~ 196 (207)
+. ++ +..-++||+.. ..+ ..+=+++.++.++.- +++++ ...+++....+-.....|-.+|..
T Consensus 161 a~rk~~~~~~s~l~F~d~H-lDg~E~~H~d~L~~~l~~~---i~~e~q~~~f~~Gf~~mI~~m~~wW~~L~~ 228 (231)
T PF12981_consen 161 AQRKGLHNSWSQLDFYDWH-LDGTEQEHKDGLRQFLASY---IDTEEQMPLFKDGFLAMIDIMEDWWKELNK 228 (231)
T ss_dssp ---HHHHH------HHHHH-CS----HHHHHHHHHHHTT-----GGG-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hcccCCCcchhhhHHHHHh-cchHHHHHHHHHHHHHHHH---cCcchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11 11 11124677665 333 345677888888764 44444 667788877777777777777654
No 22
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=45.82 E-value=11 Score=28.14 Aligned_cols=28 Identities=7% Similarity=0.249 Sum_probs=22.3
Q ss_pred ChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 149 NVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 149 ~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
..+.||.+-...+++. +||+||++.|.+
T Consensus 20 ~RerF~~D~ea~~~e~--gLt~Ee~~av~~ 47 (94)
T cd07923 20 HRERFLEDPEALFDEA--GLTEEERTLIRN 47 (94)
T ss_pred HHHHHHhCHHHHHHHc--CCCHHHHHHHHc
Confidence 4567777778889888 899999987754
No 23
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=41.05 E-value=32 Score=24.35 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=21.5
Q ss_pred hHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 150 VGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 150 ~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
.++|+.+=...+++. +||++|++.|.+
T Consensus 19 re~f~~dp~a~~~~~--~Lt~eE~~al~~ 45 (77)
T cd07321 19 KERFKADPEAVLAEY--GLTPEEKAALLA 45 (77)
T ss_pred HHHHHhCHHHHHHHc--CCCHHHHHHHHc
Confidence 456677777888887 899999998765
No 24
>COG5424 Pyrroloquinoline quinone (Coenzyme PQQ) biosynthesis protein C [Coenzyme metabolism]
Probab=40.55 E-value=2.5e+02 Score=24.46 Aligned_cols=102 Identities=13% Similarity=0.081 Sum_probs=57.1
Q ss_pred cCCCChhHHHHHHHHHHhhccCcch-HHHHHHHHHHhhhchhHHHHHHHHHhhccCcCcccceeecCCCChHHHHHHHHH
Q psy4643 81 DYKPRESVVNYLNHLEDLKQTNDTL-LIAYVYHMYLGVLSGGQIINKKRQLSLMKSNYQDQVLSFDPSVNVGQLKRQIKS 159 (207)
Q Consensus 81 ~~~~~pa~~~yv~~i~~~~~~~P~~-LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~~g~~Fy~F~~~~~~~~~k~~yr~ 159 (207)
..+|+|+++.-|.--...+.+.+.+ -+|-.|+..+ --+||...+++ ....||-|. + ..-++.||.
T Consensus 113 s~eplp~~~~av~~~~~~a~~~s~~~~~aslyt~El---~apri~~~ki~-------gl~~~~~~~---~-~a~~~yf~~ 178 (242)
T COG5424 113 SHEPLPSTRFAVDTWVRFATEKSWLEGAASLYTYEL---VAPRISVEKIS-------GLPYFNGFS---D-AAAYAYFRE 178 (242)
T ss_pred hcCCCHHHHHHHHHHHHHhcchhHHHHHHHHHHHHh---hccHHHHHHcc-------CchhhcCcc---h-HHHHHHHHH
Confidence 3468999988888877777665553 4455555433 35676666532 134555554 2 566667777
Q ss_pred HHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 160 ILDDESTQFSRQTREQLLAESRKVFLLNNSIIKCVLELL 198 (207)
Q Consensus 160 ~ld~l~~~l~~~e~~~iv~EA~~aF~ln~~i~~eL~~~~ 198 (207)
.+..- .-..+|..++|.+.-..=+.--++.+.++...
T Consensus 179 h~eaD--~~Ha~Ealkiv~~~~~t~E~~~~~~~~~~~~~ 215 (242)
T COG5424 179 HLEAD--VRHAEEALKIVLELAGTRELQDQVLDALQKSL 215 (242)
T ss_pred HHHHh--hhhHHHHHHHHHHHHhchhhHHHHHHHHHHHH
Confidence 77443 44555555566555444333333333333333
No 25
>KOG3028|consensus
Probab=38.20 E-value=2.8e+02 Score=25.06 Aligned_cols=91 Identities=15% Similarity=0.196 Sum_probs=59.4
Q ss_pred hHHHHHHHHHHhhccCcchHHHHHHHHHHhhhchhHHHHHHHHHhhccCcCcccceeecCCCChHHHHHHHHHHHHhccc
Q psy4643 87 SVVNYLNHLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKKRQLSLMKSNYQDQVLSFDPSVNVGQLKRQIKSILDDEST 166 (207)
Q Consensus 87 a~~~yv~~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~~~~a~~l~~~g~~Fy~F~~~~~~~~~k~~yr~~ld~l~~ 166 (207)
.+.+|.+-|..- +.=|..|++|+..-.=+-+.++.-.+ .-+.+.+|+.+. .+.+..++++....
T Consensus 91 ~~~a~~sll~~~------l~~a~~~t~~v~~~Ny~e~Tkk~yak---~l~fP~n~~~p~------~l~~qAk~rl~l~~- 154 (313)
T KOG3028|consen 91 DTLAFMSLLEEN------LEPALLYTFWVDTENYNEVTKKWYAK---ALPFPLNYILPG------KLQRQAKERLQLTL- 154 (313)
T ss_pred HHHHHHHHHHHH------HHHHHHHHHHhcccchhhHhHHHHHh---cCCCchhhcchh------hhHHHHHHHHHHHh-
Confidence 344455555443 44477888888866556666665222 223467777776 77888888886554
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 167 QFSRQTREQLLAESRKVFLLNNSIIKC 193 (207)
Q Consensus 167 ~l~~~e~~~iv~EA~~aF~ln~~i~~e 193 (207)
+-.++..++|..+|+.|+..-...+.+
T Consensus 155 g~~~~~e~~i~~~Aska~~~LS~~Lgs 181 (313)
T KOG3028|consen 155 GELTEREDQIYKDASKALNLLSTLLGS 181 (313)
T ss_pred CCchhhHHHHHHHHHHHHHHHHHHhcC
Confidence 334456778999999999987776543
No 26
>PF06892 Phage_CP76: Phage regulatory protein CII (CP76); InterPro: IPR009679 This entry is represented by Bacteriophage 186, CII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage regulatory protein CII (CP76) sequences which are thought to be DNA binding proteins which are involved in the establishment of lysogeny [].
Probab=37.45 E-value=1.5e+02 Score=23.96 Aligned_cols=48 Identities=23% Similarity=0.325 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 150 VGQLKRQIKSILDDESTQFSRQTREQLLAESRKVFLLNNSIIKCVLELLE 199 (207)
Q Consensus 150 ~~~~k~~yr~~ld~l~~~l~~~e~~~iv~EA~~aF~ln~~i~~eL~~~~~ 199 (207)
..++-....+.+.. ..+|..||..|+++++.+-+....++.+++...+
T Consensus 101 ~Gela~~a~ea~~d--grit~~er~~i~~~a~~ai~~l~ll~~~ve~R~~ 148 (162)
T PF06892_consen 101 VGELAREALEALSD--GRITRSERNRIIKEANAAIRSLALLINDVEARTQ 148 (162)
T ss_pred HHHHHHHHHHHhcC--CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 34444444555543 3899999999999999999999999999988765
No 27
>COG0819 TenA Putative transcription activator [Transcription]
Probab=36.18 E-value=71 Score=27.18 Aligned_cols=155 Identities=17% Similarity=0.132 Sum_probs=73.0
Q ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHhhcCccccCCCCccccChHHHHHHHh-----------HhhCCCCCCCCCCCCCc
Q psy4643 10 SDTSIWIEGLLVFYEVFKFLESAMEEHKSNQYLQQFNISDMKRTEAFEADLE-----------HYLGPDWKADYKPRPDW 78 (207)
Q Consensus 10 ~d~~~Y~~~L~~~y~vY~aLE~al~~~~~~p~l~~l~~~~L~R~~~L~~DL~-----------~l~g~~w~~~~~~~~~~ 78 (207)
..++.+.-+|.+=|.....+-+++....... .. .+.+.+.......+. --+|-+-+ -
T Consensus 32 L~~~~F~~YL~QDy~YL~~~~ra~~~~~~ka--~~--~~~~~~~~~~~~~~~~~E~~~h~~~~~~lgis~~--------~ 99 (218)
T COG0819 32 LPREKFQFYLVQDYLYLVNFARALALLASKA--PD--LELMEELAKIIQFLVEGEMELHERLAEELGISLD--------E 99 (218)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHH--------H
Confidence 4566777777777777777777766553211 00 112222222222221 11233211 0
Q ss_pred cccCCCChhHHHHHHHHHHhhccCcc--hHHHHHHHHHHhhhchhHHHHHHHHH-hhccCcCc-ccceeecCCCChHHHH
Q psy4643 79 KADYKPRESVVNYLNHLEDLKQTNDT--LLIAYVYHMYLGVLSGGQIINKKRQL-SLMKSNYQ-DQVLSFDPSVNVGQLK 154 (207)
Q Consensus 79 ~~~~~~~pa~~~yv~~i~~~~~~~P~--~LlAh~Yv~YlgdlsGGqii~~~~~~-a~~l~~~g-~~Fy~F~~~~~~~~~k 154 (207)
+...+|+|++.+|+++|-..+..... .+.|-.=..+ |=..|++++.. ....++.. -..-+++.+.+=.+.=
T Consensus 100 ~~~~~~~~~~~aYt~ym~~~~~~g~~~~~~aAl~PC~~-----~Y~eig~~~~~~~~~~~~~~Y~~Wi~~Y~s~ef~~~v 174 (218)
T COG0819 100 LLKTEPSPANKAYTRYLLDTAYSGSFAELLAALLPCLW-----GYAEIGKRLKAKPRASPNPPYQEWIDTYASEEFQEAV 174 (218)
T ss_pred HHhcCCCchHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-----HHHHHHHHHHhccccCCCCcHHHHHHHcCCHHHHHHH
Confidence 11457889999999999998865533 2222211111 11223333111 11011100 1111223122334445
Q ss_pred HHHHHHHHhcccCCCHHHHHHHHHHHHHHHH
Q psy4643 155 RQIKSILDDESTQFSRQTREQLLAESRKVFL 185 (207)
Q Consensus 155 ~~yr~~ld~l~~~l~~~e~~~iv~EA~~aF~ 185 (207)
+..++.||+++...++++.++ .+.+|.
T Consensus 175 ~~~~~~ld~~~~~~~~~~~~~----l~~iF~ 201 (218)
T COG0819 175 EELEALLDSLAENSSEEELEK----LKQIFL 201 (218)
T ss_pred HHHHHHHHHHHhcCCHHHHHH----HHHHHH
Confidence 567788888876667776664 445554
No 28
>cd07356 HN_L-whirlin_R1_like First harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains. This subgroup contains the first of two harmonin_N_like domains of the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. This first harmonin_N_like domain precedes PDZ1, and is a putative protein-binding module based on its sequence similarity to the N-terminal domain of harmonin. This first harmonin_N_like domain has been assayed for interaction with the cytoplasmic domain of cadherin 23 (a component of the Usher network and an interacting partner of the harmonin N-domain), however no interaction could be detected. Th
Probab=35.94 E-value=1.4e+02 Score=21.40 Aligned_cols=37 Identities=14% Similarity=0.256 Sum_probs=27.6
Q ss_pred HHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 156 QIKSILDDESTQFSRQTREQLLAESRKVFLLNNSIIKCVLE 196 (207)
Q Consensus 156 ~yr~~ld~l~~~l~~~e~~~iv~EA~~aF~ln~~i~~eL~~ 196 (207)
.+...|+.+ ||++||+.++. +...++-|.++.+=+..
T Consensus 7 ~lh~~l~~l---Ls~~Er~~f~h-~Ln~Y~~~RnV~~Lv~s 43 (78)
T cd07356 7 RLHNALTKL---LSEAEREEFIH-CLNDYHAKRNVYDLVQS 43 (78)
T ss_pred HHHHHHHHH---ccHHHHHHHHH-HHHHHHhcccHHHHHHH
Confidence 566788876 99999999875 56778877777655443
No 29
>PF14246 TetR_C_7: AefR-like transcriptional repressor, C-terminal region; PDB: 3BHQ_B 3CDL_A.
Probab=35.50 E-value=50 Score=20.90 Aligned_cols=22 Identities=18% Similarity=0.264 Sum_probs=15.3
Q ss_pred cccCCCHHHHHHHHHHHHHHHH
Q psy4643 164 ESTQFSRQTREQLLAESRKVFL 185 (207)
Q Consensus 164 l~~~l~~~e~~~iv~EA~~aF~ 185 (207)
.....|++|.+++|++|..+|-
T Consensus 31 ~~~~~s~~e~~~~v~~aV~~FL 52 (55)
T PF14246_consen 31 LAPPPSAEEIERIVESAVDMFL 52 (55)
T ss_dssp TS----HHHHHHHHHHHHHHHH
T ss_pred CCCCcCHHHHHHHHHHHHHHHH
Confidence 3346789999999999999984
No 30
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=31.81 E-value=61 Score=24.57 Aligned_cols=14 Identities=36% Similarity=0.344 Sum_probs=11.0
Q ss_pred CCCHHHHHHHHHHH
Q psy4643 167 QFSRQTREQLLAES 180 (207)
Q Consensus 167 ~l~~~e~~~iv~EA 180 (207)
.|||+|.+++.+|-
T Consensus 89 ~l~~eE~~~L~~ei 102 (104)
T PF11460_consen 89 ELSPEELEALQAEI 102 (104)
T ss_pred hCCHHHHHHHHHHh
Confidence 47899998887763
No 31
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=30.62 E-value=52 Score=24.01 Aligned_cols=29 Identities=17% Similarity=0.312 Sum_probs=19.6
Q ss_pred ChHHHHHHHHHHHHhcccCCCHHHHHHHHHH
Q psy4643 149 NVGQLKRQIKSILDDESTQFSRQTREQLLAE 179 (207)
Q Consensus 149 ~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~E 179 (207)
..++|+++=...+++. +||++|++.|.+-
T Consensus 13 ~r~~F~~D~~a~~~~~--~Lt~eer~av~~r 41 (88)
T PF07746_consen 13 NRERFLADPEAYLDEY--GLTEEERQAVLDR 41 (88)
T ss_dssp HHHHHHH-HHHHHHCC--T--HHHHHHHHCT
T ss_pred HHHHHHHCHHHHHHHc--CCCHHHHHHHHcC
Confidence 3456777777888887 8999999987653
No 32
>PF09702 Cas_Csa5: CRISPR-associated protein (Cas_Csa5); InterPro: IPR010157 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a minor family of Cas protein found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus.
Probab=28.46 E-value=80 Score=23.94 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=21.4
Q ss_pred HHhcccCCCHHHHHHHHHHHHHHHHH
Q psy4643 161 LDDESTQFSRQTREQLLAESRKVFLL 186 (207)
Q Consensus 161 ld~l~~~l~~~e~~~iv~EA~~aF~l 186 (207)
+|.++..||+|.-...|-||..+|+.
T Consensus 11 vDRiaNALs~E~v~~aL~dAlR~~~s 36 (105)
T PF09702_consen 11 VDRIANALSPEAVEVALYDALRIFRS 36 (105)
T ss_pred HHHHHhhcCHHHHHHHHHHHHHHHHH
Confidence 34445569999999999999999984
No 33
>COG1101 PhnK ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=27.31 E-value=43 Score=29.17 Aligned_cols=38 Identities=26% Similarity=0.344 Sum_probs=27.7
Q ss_pred hhHHHHHHHHHHhhccCcchHHHHHHHHHHhhhchhHHHHHHHHH
Q psy4643 86 ESVVNYLNHLEDLKQTNDTLLIAYVYHMYLGVLSGGQIINKKRQL 130 (207)
Q Consensus 86 pa~~~yv~~i~~~~~~~P~~LlAh~Yv~YlgdlsGGqii~~~~~~ 130 (207)
.....|.++|..+ |..|--+.-.+ +|.||||| |..+++
T Consensus 122 ~~~~~f~~~l~~l----~lgLenrL~~~-iglLSGGQ--RQalsL 159 (263)
T COG1101 122 RRRSSFRERLARL----GLGLENRLSDR-IGLLSGGQ--RQALSL 159 (263)
T ss_pred HHHHHHHHHHhhc----ccchhhhhcCh-hhhccchH--HHHHHH
Confidence 4566777788777 66787887777 99999998 444443
No 34
>PF09921 DUF2153: Uncharacterized protein conserved in archaea (DUF2153); InterPro: IPR014450 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=27.17 E-value=1.9e+02 Score=22.64 Aligned_cols=41 Identities=17% Similarity=0.188 Sum_probs=30.6
Q ss_pred HHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 158 KSILDDESTQFSRQTREQLLAESRKVFLLNNSIIKCVLELL 198 (207)
Q Consensus 158 r~~ld~l~~~l~~~e~~~iv~EA~~aF~ln~~i~~eL~~~~ 198 (207)
.+-+.+.+.......|.++|=-|+.+|.+....++..+.=+
T Consensus 13 l~~~~~~e~~~~~~DRL~LIl~sr~afqhm~RTlKaFd~WL 53 (126)
T PF09921_consen 13 LETFKKHEKNVESADRLDLILSSRAAFQHMMRTLKAFDQWL 53 (126)
T ss_pred HHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333444445678888999999999999999998877644
No 35
>PF02093 Gag_p30: Gag P30 core shell protein; InterPro: IPR003036 P30 is essential for viral assembly []. Cleavage of P70 in vitro can be accompanied by a shift from a concentrically coiled internal strand ("immature") to a collapsed ("mature") form of the virus core [].; GO: 0019068 virion assembly; PDB: 3BP9_U 1U7K_D 2Y4Z_A 1BM4_A.
Probab=27.14 E-value=92 Score=26.53 Aligned_cols=30 Identities=27% Similarity=0.435 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHH
Q psy4643 152 QLKRQIKSILDDESTQFSRQTREQLLAESRKVF 184 (207)
Q Consensus 152 ~~k~~yr~~ld~l~~~l~~~e~~~iv~EA~~aF 184 (207)
.=|++...-|..+ +|.|||+.|..||+..-
T Consensus 40 pTWdDcqqLL~~L---fT~EEr~rI~~~Ark~v 69 (211)
T PF02093_consen 40 PTWDDCQQLLQTL---FTTEERERILQEARKYV 69 (211)
T ss_dssp --HHHHHHHHHHH---S-HHHHHHHHHHHHHT-
T ss_pred CCHHHHHHHHHHH---cCHHHHHHHHHHHHHHh
Confidence 3477888888876 99999999999999854
No 36
>PRK13372 pcmA protocatechuate 4,5-dioxygenase; Provisional
Probab=26.40 E-value=41 Score=31.76 Aligned_cols=29 Identities=21% Similarity=0.294 Sum_probs=25.0
Q ss_pred CChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 148 VNVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 148 ~~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
.+.++||.+-+..+++. +||++||+.|.+
T Consensus 38 ~~R~~f~~d~~ay~~~~--~lt~eq~~~v~~ 66 (444)
T PRK13372 38 DNRARFKADEGAYLDEW--ALNEAQKQAVLA 66 (444)
T ss_pred HHHHHHhhCHHHHHHHc--CCCHHHHHHHHh
Confidence 36788999999999998 899999998765
No 37
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=26.10 E-value=2.4e+02 Score=20.73 Aligned_cols=59 Identities=22% Similarity=0.294 Sum_probs=33.9
Q ss_pred HHHHhhhchhHHHHHHHH----HhhccCcCcccceeecCCCChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 112 HMYLGVLSGGQIINKKRQ----LSLMKSNYQDQVLSFDPSVNVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 112 v~YlgdlsGGqii~~~~~----~a~~l~~~g~~Fy~F~~~~~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
+.|+..+.||.-.=.-.. +...+.+.+.+=..|+ .+...+++.|++. ..+++.++++++
T Consensus 46 ~~fl~~~~GGp~~Y~~~~G~p~m~~~H~~l~it~~~f~------~~~~~~~~al~~~--~v~~~~~~~~~~ 108 (120)
T PF01152_consen 46 AEFLSQLLGGPPLYTGRDGHPMMREAHAHLGITEEHFD------RWLELLKQALDEL--GVPEELIDELLA 108 (120)
T ss_dssp HHHHHHHTTSSSHHHHHHSSH-HHHHHTTS-BBHHHHH------HHHHHHHHHHHHT--TCTHHHHHHHHH
T ss_pred HHHHHHHhCCCCCCcccCCCchHHHHHhCCCCCHHHHH------HHHHHHHHHHHHh--CCCHHHHHHHHH
Confidence 445666666654332111 1112334455555555 8888999999998 677777766553
No 38
>PF14250 AbrB-like: AbrB-like transcriptional regulator
Probab=24.83 E-value=27 Score=24.65 Aligned_cols=22 Identities=36% Similarity=0.539 Sum_probs=18.1
Q ss_pred hccCcchHHHHHHHHHHhhhch
Q psy4643 99 KQTNDTLLIAYVYHMYLGVLSG 120 (207)
Q Consensus 99 ~~~~P~~LlAh~Yv~YlgdlsG 120 (207)
.+.|..+||+++||.-|++--|
T Consensus 35 Vq~NGnLLIG~AYT~~m~L~PG 56 (71)
T PF14250_consen 35 VQGNGNLLIGSAYTKQMGLKPG 56 (71)
T ss_pred EecCCCEEEcHHHHHHhCCCCC
Confidence 4578899999999999987533
No 39
>PF06429 Flg_bbr_C: Flagellar basal body rod FlgEFG protein C-terminal; InterPro: IPR010930 This entry consists of a number of C-terminal domains of unknown function. This domain seems to be specific to flagellar basal-body rod and flagellar hook proteins in which IPR001444 from INTERPRO is often present at the extreme N terminus.; GO: 0019861 flagellum; PDB: 2D4Y_A 2BGY_A 1WLG_B 2BGZ_A 3A69_A.
Probab=24.78 E-value=1.3e+02 Score=20.41 Aligned_cols=27 Identities=22% Similarity=0.441 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy4643 177 LAESRKVFLLNNSIIKCVLELLEVLLK 203 (207)
Q Consensus 177 v~EA~~aF~ln~~i~~eL~~~~~~~~~ 203 (207)
+=++..+|+.|..++...+.....++.
T Consensus 47 li~~qr~y~a~~kvi~~~d~m~~~~i~ 73 (74)
T PF06429_consen 47 LIEAQRAYEANAKVIQTADEMLQTAIN 73 (74)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 447889999999999999998887764
No 40
>KOG0932|consensus
Probab=23.75 E-value=53 Score=32.22 Aligned_cols=57 Identities=21% Similarity=0.188 Sum_probs=37.5
Q ss_pred cccceeecCCCChHHHHHHHHHHHHhcccCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q psy4643 138 QDQVLSFDPSVNVGQLKRQIKSILDDESTQFSRQTREQL-LAESRKVFLLNNSIIKCVLELL 198 (207)
Q Consensus 138 g~~Fy~F~~~~~~~~~k~~yr~~ld~l~~~l~~~e~~~i-v~EA~~aF~ln~~i~~eL~~~~ 198 (207)
=++||+|. +-.+..--+.|-+++.=. +-| .||++| ..-++.-|+||-.+|..+++..
T Consensus 343 YL~fF~Fs-g~tlD~ALR~Flka~~L~--GET-qeRERvL~hFS~Ry~~CNP~~~~S~DgvH 400 (774)
T KOG0932|consen 343 YLSFFQFS-GMTLDQALREFLKALELM--GET-QERERVLRHFSRRYFQCNPDIFDSEDGVH 400 (774)
T ss_pred HHHHhhcc-CccHHHHHHHHHHHhhhc--cch-HHHHHHHHHHHHHhhccCccccccccchh
Confidence 48999998 444444444555555322 223 444444 6789999999999999887653
No 41
>PTZ00347 phosphomethylpyrimidine kinase; Provisional
Probab=23.65 E-value=3.7e+02 Score=25.33 Aligned_cols=94 Identities=14% Similarity=0.174 Sum_probs=48.1
Q ss_pred cCCCChhHHHHHHHHHHhhccCcc---hH---HHHHHHHHHhhhchhHHHHHHHHHhhccCcC-cccceeecCCCChHHH
Q psy4643 81 DYKPRESVVNYLNHLEDLKQTNDT---LL---IAYVYHMYLGVLSGGQIINKKRQLSLMKSNY-QDQVLSFDPSVNVGQL 153 (207)
Q Consensus 81 ~~~~~pa~~~yv~~i~~~~~~~P~---~L---lAh~Yv~YlgdlsGGqii~~~~~~a~~l~~~-g~~Fy~F~~~~~~~~~ 153 (207)
..++.|++.+|++++..++.+... .+ +.-|+-.|.= . |+.+.... ... ++. =..+.+++.+++-.+.
T Consensus 105 ~~~~~p~~~aY~~~l~~~a~~g~~~~~~~l~Al~pC~~~Y~~-i--g~~l~~~~--~~~-~~~~y~~Wi~~y~~~~f~~~ 178 (504)
T PTZ00347 105 AAGPEAACRKYVDFLLASGNADTLGPSVVIAAVIPCARLYAW-V--GQELTNEV--ELT-ESHPFRRWLLSYSDEPINTS 178 (504)
T ss_pred ccCCCHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHH-H--HHHHHhcc--CCC-CCChHHHHHHhcCCHHHHHH
Confidence 456789999999999998765432 23 3344444443 1 33332210 000 010 0123333423334455
Q ss_pred HHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHH
Q psy4643 154 KRQIKSILDDESTQFSRQTREQLLAESRKVFLLN 187 (207)
Q Consensus 154 k~~yr~~ld~l~~~l~~~e~~~iv~EA~~aF~ln 187 (207)
=.++++.+|+++. .++ +++...+|.-.
T Consensus 179 ~~~~~~~ld~~~~---~~~----~~~~~~~F~~~ 205 (504)
T PTZ00347 179 VEQLESLLDKYIR---PGE----FSEVAQAYRRA 205 (504)
T ss_pred HHHHHHHHHHHhc---hhh----HHHHHHHHHHH
Confidence 5677777887632 233 34456677643
No 42
>PRK13367 protocatechuate 4,5-dioxygenase; Provisional
Probab=23.38 E-value=53 Score=30.84 Aligned_cols=28 Identities=11% Similarity=0.195 Sum_probs=23.1
Q ss_pred ChHHHHHHHHHHHHhcccCCCHHHHHHHHH
Q psy4643 149 NVGQLKRQIKSILDDESTQFSRQTREQLLA 178 (207)
Q Consensus 149 ~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~ 178 (207)
+.++||.+-+..+++. +||++||+.|.+
T Consensus 333 ~R~~f~~d~~a~~~~~--~lt~eq~~~v~~ 360 (420)
T PRK13367 333 WRERFLADPEALYDEA--GLSEEERDLIRR 360 (420)
T ss_pred HHHHHHhCHHHHHHHc--CCCHHHHHHHHh
Confidence 4567788888899998 899999998764
No 43
>PF09539 DUF2385: Protein of unknown function (DUF2385); InterPro: IPR012645 Members of this uncharacterised protein family are found in a number of alphaproteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus (Caulobacter vibrioides), and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulphide bond. The function is unknown.
Probab=22.58 E-value=3e+02 Score=20.51 Aligned_cols=51 Identities=14% Similarity=0.169 Sum_probs=35.0
Q ss_pred CChHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 148 VNVGQLKRQIKSILDDESTQFSRQTREQLLAESRKVFLLNNSIIKCVLELLEV 200 (207)
Q Consensus 148 ~~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~EA~~aF~ln~~i~~eL~~~~~~ 200 (207)
.+.+.+++...+-|+.- .-++..|+.+++.=|.-|+-..............
T Consensus 26 ~~~~~WR~~M~~Ll~~E--~p~~~rR~rl~~aFN~GYr~~~~~Y~~Ct~~A~~ 76 (96)
T PF09539_consen 26 NEDQYWRDRMQALLDAE--APDEARRARLIAAFNRGYRAFSSVYRTCTPAARE 76 (96)
T ss_pred CCcchHHHHHHHHHHhc--CCCHHHHHHHHHHHHHHHHHHhHhhccCCHHHHH
Confidence 35556666666666543 5688899999998888888777776655444433
No 44
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=22.22 E-value=2.5e+02 Score=19.65 Aligned_cols=18 Identities=17% Similarity=0.359 Sum_probs=15.1
Q ss_pred CCChHHHHHHHHHHHHhc
Q psy4643 147 SVNVGQLKRQIKSILDDE 164 (207)
Q Consensus 147 ~~~~~~~k~~yr~~ld~l 164 (207)
+.+++.+|.+|.+.+..+
T Consensus 12 G~~~e~vk~~F~~~~~~V 29 (71)
T PF04282_consen 12 GEDPEEVKEEFKKLFSDV 29 (71)
T ss_pred CCCHHHHHHHHHHHHCCC
Confidence 458899999999999765
No 45
>cd07355 HN_L-delphilin-R2_like Second harmonin_N_like domain (repeat 2) of L-delphilin, and related domains. This subgroup contains the second of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin), and related domains. Delphilin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain in L-delphilin follows the second PDZ protein-binding domain, PDZ2; it is also found in the shorter C-terminal isoforms (S-delphilin/delphilin alpha and delphilin beta). It is a putative protein-binding module based on its sequence similarity to the harmonin N-domain. The first harmonin_N_like domain of L-delphilin belongs to a different subgroup and is missing from S-delphilin.
Probab=21.86 E-value=1.9e+02 Score=20.82 Aligned_cols=28 Identities=14% Similarity=0.204 Sum_probs=21.3
Q ss_pred HHHHHHHHhcccCCCHHHHHHHHHHHHHHHH
Q psy4643 155 RQIKSILDDESTQFSRQTREQLLAESRKVFL 185 (207)
Q Consensus 155 ~~yr~~ld~l~~~l~~~e~~~iv~EA~~aF~ 185 (207)
+.|++.|+.+ ||+.||..|.+.=+.-|+
T Consensus 6 Rtf~~~mehl---Lt~~ER~~i~qaL~~y~~ 33 (80)
T cd07355 6 RTFKQQMEHL---LTPPERYGIKKALEDYFQ 33 (80)
T ss_pred hhHHHHHHHh---CCHHHHHHHHHHHHHHHH
Confidence 5788899887 999999887765555444
No 46
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=21.44 E-value=3.8e+02 Score=21.72 Aligned_cols=61 Identities=13% Similarity=0.277 Sum_probs=42.1
Q ss_pred chhHHHHHHHHHhhccCcCcccceeecCCC----------------ChHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHH
Q psy4643 119 SGGQIINKKRQLSLMKSNYQDQVLSFDPSV----------------NVGQLKRQIKSILDDESTQFSRQTREQLLAESRK 182 (207)
Q Consensus 119 sGGqii~~~~~~a~~l~~~g~~Fy~F~~~~----------------~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~EA~~ 182 (207)
..|+.|+|.+. =+.+|-+|.+|+... +.+.+.+.+..++..- +.+.++-+.+|..-..
T Consensus 20 edg~aIRRRRe----C~~C~~RFTTfE~~El~~~~VvKkdg~Re~F~r~Kl~~gl~~A~~KR--pVs~e~ie~~v~~ie~ 93 (156)
T COG1327 20 EEGNAIRRRRE----CLECGERFTTFERAELRPLIVVKKDGRREPFDREKLRRGLIRACEKR--PVSSEQIEEAVSHIER 93 (156)
T ss_pred cccchhhhhhc----ccccccccchhheeeeccceEECcCCCcCCCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHHHH
Confidence 35777777532 234688999986442 4577888888888766 8999998888876554
Q ss_pred HHH
Q psy4643 183 VFL 185 (207)
Q Consensus 183 aF~ 185 (207)
--+
T Consensus 94 ~Lr 96 (156)
T COG1327 94 QLR 96 (156)
T ss_pred HHH
Confidence 443
No 47
>PHA02098 hypothetical protein
Probab=21.18 E-value=61 Score=21.17 Aligned_cols=35 Identities=17% Similarity=0.112 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHH
Q psy4643 151 GQLKRQIKSILDDESTQFSRQTREQLLAESRKVFLLNN 188 (207)
Q Consensus 151 ~~~k~~yr~~ld~l~~~l~~~e~~~iv~EA~~aF~ln~ 188 (207)
...|+.|+=+.++. -+.+.+++|-+.|-+.|.+|-
T Consensus 4 ~lykrgykwa~~a~---~~g~s~~~ie~~adnsfdfnd 38 (56)
T PHA02098 4 DLYKRGYKWANKAY---QDGDTLQDIEDKADNSFDFND 38 (56)
T ss_pred HHHHHhhHHHHHHh---hccchHHHHHHhccccCCccc
Confidence 45688888888765 466788889999999999884
No 48
>COG2346 Truncated hemoglobins [General function prediction only]
Probab=21.06 E-value=1.9e+02 Score=22.76 Aligned_cols=30 Identities=20% Similarity=0.362 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhcccCCCHHHHHHHHHHHHHH
Q psy4643 152 QLKRQIKSILDDESTQFSRQTREQLLAESRKV 183 (207)
Q Consensus 152 ~~k~~yr~~ld~l~~~l~~~e~~~iv~EA~~a 183 (207)
.+-..|..+||++ .++++.+..|.+-+..+
T Consensus 90 ~WL~~~~~al~ei--~~~~e~~~~i~~~~~~~ 119 (133)
T COG2346 90 AWLGLFADALDEI--GLPEELREEILARAERI 119 (133)
T ss_pred HHHHHHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 5556788999998 68999999888876654
No 49
>PF15603 Imm45: Immunity protein 45
Probab=20.95 E-value=1.2e+02 Score=21.93 Aligned_cols=19 Identities=16% Similarity=0.329 Sum_probs=17.1
Q ss_pred CCCHHHHHHHHHHHHHHHH
Q psy4643 167 QFSRQTREQLLAESRKVFL 185 (207)
Q Consensus 167 ~l~~~e~~~iv~EA~~aF~ 185 (207)
++|+.|++.||++...-|.
T Consensus 55 ~it~~e~q~II~aI~~~~~ 73 (82)
T PF15603_consen 55 PITIAERQKIIEAIEKYFS 73 (82)
T ss_pred ccCHHHHHHHHHHHHHHHh
Confidence 7999999999999988775
No 50
>PF07309 FlaF: Flagellar protein FlaF; InterPro: IPR010845 This family consists of several bacterial FlaF flagellar proteins. FlaF and FlaG are trans-acting, regulatory factors that modulate flagellin synthesis during flagellum biogenesis [].
Probab=20.80 E-value=2.8e+02 Score=21.00 Aligned_cols=47 Identities=11% Similarity=0.069 Sum_probs=39.8
Q ss_pred ChHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 149 NVGQLKRQIKSILDDESTQFSRQTREQLLAESRKVFLLNNSIIKCVL 195 (207)
Q Consensus 149 ~~~~~k~~yr~~ld~l~~~l~~~e~~~iv~EA~~aF~ln~~i~~eL~ 195 (207)
...++|..|+.-+-+-..+|.++-|+.++.=+.-+++....+...-.
T Consensus 50 ~N~rLW~~~~~dl~~~~n~LP~~LRa~LisL~~fv~~~t~~~~~~~~ 96 (113)
T PF07309_consen 50 FNRRLWTIFAADLASPDNPLPDELRANLISLGLFVLRETSKVLRGPA 96 (113)
T ss_pred HHHHHHHHHHHHHcCccCCCCHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence 45689999999998777899999999999999998888888876544
No 51
>PF15134 DUF4570: Domain of unknown function (DUF4570)
Probab=20.37 E-value=2.9e+02 Score=21.08 Aligned_cols=30 Identities=7% Similarity=0.008 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4643 171 QTREQLLAESRKVFLLNNSIIKCVLELLEV 200 (207)
Q Consensus 171 ~e~~~iv~EA~~aF~ln~~i~~eL~~~~~~ 200 (207)
.++....+.+..|++.|-.|+.+|+..-..
T Consensus 38 ~~kk~~~~a~~~A~kRN~~LLqDie~~eks 67 (109)
T PF15134_consen 38 TEKKSQQQASEAAKKRNKQLLQDIEAAEKS 67 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345567889999999999999999876544
Done!