RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13497
(262 letters)
>gnl|CDD|234168 TIGR03328, salvage_mtnB, methylthioribulose-1-phosphate
dehydratase. Members of this family are the
methylthioribulose-1-phosphate dehydratase of the
methionine salvage pathway. This pathway allows
methylthioadenosine, left over from polyamine
biosynthesis, to be recycled to methionine [Amino acid
biosynthesis, Aspartate family].
Length = 193
Score = 224 bits (574), Expect = 2e-74
Identities = 80/236 (33%), Positives = 109/236 (46%), Gaps = 45/236 (19%)
Query: 21 IPELCKQFYHLGWVTGTGGGMTIKL-GDEIYIAPSGVQKERLTSKDLFVQDMEGKDLQLP 79
+ E + Y GWV GTGG ++ +L DEI I PSGV K RLT +D V D++GK +
Sbjct: 1 LIEAGRDLYKRGWVPGTGGNLSARLDEDEILITPSGVDKGRLTPEDFLVVDLQGKPVS-- 58
Query: 80 EDKTLKKSQCTPLFMCSYTLR-NAGAVIHTHSKAAVLVTMLYPGNVSIELVSSYLGNIFQ 138
LK S T L Y L AGAV+HTHS A +++ LYP N
Sbjct: 59 --GGLKPSAETLLHTQLYRLTPGAGAVLHTHSVEATVLSRLYPSN--------------- 101
Query: 139 LKFFVQFTYNWYLVAYCWSNVFRIAYQEMIKGTWNSTLGRYNRYDEELVVPIIENTPQEK 198
F + EM+K L ++++L +PI ENT
Sbjct: 102 -------------------GAFELEGYEMLKA-----LPGITTHEDKLTIPIFENTQDIA 137
Query: 199 DLRDSLERALVEFPSTSAVLVRRHGVYVWGGDWKSTKTQTECYDYLFELAVSMKQL 254
L DS+ L +P VL+R HG+Y WG DW+ K E ++LFE + M +L
Sbjct: 138 RLADSVAPYLEAYPDVPGVLIRGHGLYAWGRDWEEAKRHLEALEFLFECELEMLKL 193
>gnl|CDD|214970 smart01007, Aldolase_II, Class II Aldolase and Adducin N-terminal
domain. This family includes class II aldolases and
adducins which have not been ascribed any enzymatic
function.
Length = 185
Score = 126 bits (320), Expect = 2e-36
Identities = 58/232 (25%), Positives = 84/232 (36%), Gaps = 50/232 (21%)
Query: 21 IPELCKQFYHLGWVTGTGGGMTIKLGDE--IYIAPSGVQKERLTSKDLFVQDMEGKDLQL 78
+ C+ G V GTGG ++ ++G+E I PSGV LT+ DL V D++G +
Sbjct: 1 LAAACRLLARRGLVEGTGGNISARVGEEDLFLITPSGVDFGELTASDLVVVDLDGN--VV 58
Query: 79 PEDKTLKKSQCTPLFMCSYTLR-NAGAVIHTHSKAAVLVTMLYPGNVSIELVSSYLGNIF 137
K S TPL + Y R + GAV+HTHS A + L
Sbjct: 59 EGGGGPKPSSETPLHLAIYRARPDVGAVVHTHSPYATALAALG----------------- 101
Query: 138 QLKFFVQFTYNWYLVAYCWSNVFRIAYQEMIKGTWNSTLGRYNRYDEELVVPIIENTPQE 197
+ E G Y P E +
Sbjct: 102 --------------------KPLPLLPTEQAAAFL----GGEIPYA-PYAGPGTELAEEG 136
Query: 198 KDLRDSLERALVEFPSTSAVLVRRHGVYVWGGDWKSTKTQTECYDYLFELAV 249
+L ++L AL P AVL+R HG+ VWG + E + E+ +
Sbjct: 137 AELAEALAEAL---PDRPAVLLRNHGLLVWGKTLEEAFDLAEELEEAAEIQL 185
>gnl|CDD|216015 pfam00596, Aldolase_II, Class II Aldolase and Adducin N-terminal
domain. This family includes class II aldolases and
adducins which have not been ascribed any enzymatic
function.
Length = 181
Score = 125 bits (317), Expect = 7e-36
Identities = 56/231 (24%), Positives = 86/231 (37%), Gaps = 54/231 (23%)
Query: 21 IPELCKQFYHLGWVTGTGGGMTIKLGDEIYIAPSGVQKERLTSKDLFVQDMEGKDLQLPE 80
+ C+ G V GTGG ++ + D I PSGV LT++DL V D++G ++
Sbjct: 3 LAAACRLLARRGLVEGTGGNISARDPDHFLITPSGVDFGELTAEDLVVVDLDGNVVEGG- 61
Query: 81 DKTLKKSQCTPLFMCSYTLR-NAGAVIHTHSKAAVLVTMLYPGNVSIELVSSYLGNIFQL 139
+ K S TPL Y R + GAV+HTHS A ++ L G I
Sbjct: 62 EGGGKPSSETPLHAAIYRARPDVGAVVHTHSPYATALSALKEGLPPI------------- 108
Query: 140 KFFVQFTYNWYLVAYCWSNVFRIAYQEMIKGTWNSTLGRYNRYDEELVVPIIEN-TPQEK 198
+ E +P++ P +
Sbjct: 109 ---------------------------------TQEAAAFYLGGE---IPVVPYYRPGTE 132
Query: 199 DLRDSLERALVEFPSTSAVLVRRHGVYVWGGDWKSTKTQTECYDYLFELAV 249
+L + L AL AVL+R HG+ VWG + + E + E+ +
Sbjct: 133 ELGERLAEALGG--DRKAVLLRNHGLLVWGKTLEEAFDRAEVLERAAEIQL 181
>gnl|CDD|223313 COG0235, AraD, Ribulose-5-phosphate 4-epimerase and related
epimerases and aldolases [Carbohydrate transport and
metabolism].
Length = 219
Score = 105 bits (265), Expect = 8e-28
Identities = 58/252 (23%), Positives = 91/252 (36%), Gaps = 57/252 (22%)
Query: 14 PEHPRNLIPELCKQFYHLGWVTGTGGGMTIKLGDE--IYIAPSGVQKERLTSKDLFVQDM 71
E R + + + G V GT G ++++L + I PSGV LT+ DL V D+
Sbjct: 5 LEKLRQELAKAARLLARRGLVEGTAGNISVRLPEGGLFLITPSGVPFGELTADDLVVVDL 64
Query: 72 EGKDLQLPEDKTLKKSQCTPLFMCSYTLR-NAGAVIHTHSKAAVLVTMLYPGNVSIELVS 130
+G+ + K S TP+ + Y R +AGAV+HTHS A ++ L + +
Sbjct: 65 DGE----VVEGGKKPSSETPIHLAIYRARPDAGAVVHTHSPYATALSTL---GEPLPPLG 117
Query: 131 SYLGNIFQLKFFVQFTYNWYLVAYCWSNVFRIAYQEMIKGTWNSTLGRYNRYDEELVVPI 190
+ LK+F Y V +
Sbjct: 118 TEH-----LKYFGG-------------------------------GIPCAPYAGPGSVEL 141
Query: 191 IENTPQEKDLRDSLERALVEFPSTSAVLVRRHGVYVWGGDWKSTKTQTECYDYLFELAVS 250
E + DL +++ L+R HGV WG E + L +L +
Sbjct: 142 AEALAEAADLAEAV-----------LKLLRNHGVVAWGKTLAEAVHLAEVLEELAKLQLK 190
Query: 251 MKQLGLNPLSPP 262
LG L+ P
Sbjct: 191 ALSLGKPLLTAP 202
>gnl|CDD|180679 PRK06754, mtnB, methylthioribulose-1-phosphate dehydratase;
Reviewed.
Length = 208
Score = 89.7 bits (223), Expect = 8e-22
Identities = 60/237 (25%), Positives = 95/237 (40%), Gaps = 50/237 (21%)
Query: 23 ELCKQFYHLGWVTGTGGGMTIKLGDE---IYIAPSGVQKERLTSKDLFVQDMEGKDLQLP 79
E+ K+ W T G ++IK+ D+ + SG K + T +D + D +GK P
Sbjct: 13 EIKKELAARDWFPATSGNLSIKVSDDPLTFLVTASGKDKRKTTPEDFLLVDHDGK----P 68
Query: 80 EDKT-LKKSQCTPLFMCSYTLRNAGAVIHTHSKAAVLVTMLYPGNVSIELVSSYLGNIFQ 138
++T LK S T L Y NAG V+H H+ +++ LY +
Sbjct: 69 VEETELKPSAETLLHTHIYNNTNAGCVLHVHTVDNNVISELYGDD--------------- 113
Query: 139 LKFFVQFTYNWYLVAYCWSNVFRIAYQEMIKGTWNSTLGRYNRYDEELVVPIIENTPQEK 198
QE+IK LG + + E+ +PIIEN
Sbjct: 114 -------------------GAVTFQGQEIIKA-----LGIWEE-NAEIHIPIIENHADIP 148
Query: 199 DLRDSLERALVEFPSTSAVLVRRHGVYVWGGDWKSTKTQTECYDYLFELAVSMKQLG 255
L + + + + AVL+R HG+ VWG D K E Y++LF + + +
Sbjct: 149 TLAEEFAKHIQ--GDSGAVLIRNHGITVWGRDAFEAKKHLEAYEFLFSYHIKLLSIQ 203
>gnl|CDD|238232 cd00398, Aldolase_II, Class II Aldolase and Adducin head
(N-terminal) domain. Aldolases are ubiquitous enzymes
catalyzing central steps of carbohydrate metabolism.
Based on enzymatic mechanisms, this superfamily has been
divided into two distinct classes (Class I and II).
Class II enzymes are further divided into two
sub-classes A and B. This family includes class II A
aldolases and adducins which has not been ascribed any
enzymatic function. Members of this class are primarily
bacterial and eukaryotic in origin and include
L-fuculose-1-phosphate, L-rhamnulose-1-phosphate
aldolases and L-ribulose-5-phosphate 4-epimerases. They
all share the ability to promote carbon-carbon bond
cleavage and stabilize enolate intermediates using
divalent cations.
Length = 209
Score = 86.7 bits (215), Expect = 1e-20
Identities = 43/108 (39%), Positives = 55/108 (50%), Gaps = 8/108 (7%)
Query: 15 EHPRNLIPELCKQFYHLGWVTGTGGGMTIKLGDEIY--IAPSGVQKERLTSKDLFVQDME 72
E + I C GWVTGTGG ++ + D Y I PSGV E +T+ DL V D +
Sbjct: 1 EKLKRKIIAACLLLDLYGWVTGTGGNVSARDRDRGYFLITPSGVDYEEMTASDLVVVDAQ 60
Query: 73 GKDLQLPEDKTLKKSQCTPLFMCSYTLRN-AGAVIHTHSKAAVLVTML 119
GK + E K K S TPL + Y R G ++HTHS A V+ L
Sbjct: 61 GK---VVEGK--KPSSETPLHLALYRARPDIGCIVHTHSTHATAVSQL 103
Score = 41.2 bits (97), Expect = 2e-04
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 188 VPIIEN-TPQEKDLRDSLERALVEFPSTSAVLVRRHGVYVWGGDWKSTKTQTECYDYLFE 246
+P TP+ + +RAL FP++ AVL+R HG++ WG + E
Sbjct: 123 IPCTPYMTPETGEDEIGTQRAL-GFPNSKAVLLRNHGLFAWGPTLDEAFHLAVVLEVAAE 181
Query: 247 LAVSMKQLG--LNPLSPP 262
+ + +G L P+S
Sbjct: 182 IQLKALSMGGQLPPISLE 199
>gnl|CDD|236415 PRK09220, PRK09220, methylthioribulose-1-phosphate dehydratase;
Provisional.
Length = 204
Score = 79.2 bits (196), Expect = 6e-18
Identities = 55/237 (23%), Positives = 86/237 (36%), Gaps = 46/237 (19%)
Query: 20 LIPELCKQFYHLGWVTGTGGGMTIKLGD-EIYIAPSGVQKERLTSKDLFVQDMEGKDLQL 78
+ + GWV T G M+++L + I SG K LT++D D+ G +
Sbjct: 9 QLIAAGRWIGARGWVPATSGNMSVRLDEQHCAITVSGKDKGSLTAEDFLQVDIAGNAVPS 68
Query: 79 PEDKTLKKSQCTPLFMCSYTLRN-AGAVIHTHSKAAVLVTMLYPGNVSIELVSSYLGNIF 137
K S T L Y L GAV+HTHS A +++ + + ++ L Y
Sbjct: 69 G----RKPSAETLLHTQLYRLFPEIGAVLHTHSVNATVLSRVEKSD-ALVL-EGY----- 117
Query: 138 QLKFFVQFTYNWYLVAYCWSNVFRIAYQEMIKGTWNSTLGRYNRYDEELVVPIIENTPQE 197
E+ K ++ +VVPI +N
Sbjct: 118 ----------------------------ELQK-----AFAGQTTHETAVVVPIFDNDQDI 144
Query: 198 KDLRDSLERALVEFPSTSAVLVRRHGVYVWGGDWKSTKTQTECYDYLFELAVSMKQL 254
L + L P L+R HG+Y WG D + E ++LFE + + L
Sbjct: 145 ARLAARVAPYLDAQPLRYGYLIRGHGLYCWGRDMAEARRHLEGLEFLFECELERRLL 201
>gnl|CDD|181241 PRK08130, PRK08130, putative aldolase; Validated.
Length = 213
Score = 43.3 bits (103), Expect = 3e-05
Identities = 29/104 (27%), Positives = 43/104 (41%), Gaps = 7/104 (6%)
Query: 18 RNLIPELCKQFYHLGWVTGTGGGMTIKLGDE-IYIAPSGVQKERLTSKDLFVQDMEGKDL 76
R I L + + G+ G+ G ++ +L D + P+G RL L D +G
Sbjct: 7 REEIVRLGRSLFQRGYTVGSAGNISARLDDGGWLVTPTGSCLGRLDPARLSKVDADGN-- 64
Query: 77 QLPEDKTLKKSQCTPLFMCSYTLR-NAGAVIHTHSKAAVLVTML 119
L DK K+ PL Y GAV+H HS ++ L
Sbjct: 65 WLSGDKPSKEV---PLHRAIYRNNPECGAVVHLHSTHLTALSCL 105
>gnl|CDD|183870 PRK13145, araD, L-ribulose-5-phosphate 4-epimerase; Provisional.
Length = 234
Score = 42.9 bits (101), Expect = 7e-05
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 5/67 (7%)
Query: 49 IYIAPSGVQKERLTSKDLFVQDMEGKDLQLPEDKTLKKSQCTPLFMCSY-TLRNAGAVIH 107
I I PSGV + LT +++ V D++G ++ L S P + Y G ++H
Sbjct: 40 IVIKPSGVDYDELTPENMVVTDLDGNVVE----GDLNPSSDLPTHVELYKAWPEVGGIVH 95
Query: 108 THSKAAV 114
THS AV
Sbjct: 96 THSTEAV 102
>gnl|CDD|188107 TIGR01086, fucA, L-fuculose phosphate aldolase. Members of this
family are L-fuculose phosphate aldolase from various
Proteobacteria, encoded in fucose utilization operons.
Homologs in other bacteria given similar annotation but
scoring below the trusted cutoff may share extensive
sequence similarity but are not experimenally
characterized and are not found in apparent fucose
utilization operons; we consider their annotation as
L-fuculose phosphate aldolase to be tenuous. This model
has been narrowed in scope from the previous version
[Energy metabolism, Sugars].
Length = 214
Score = 42.2 bits (99), Expect = 7e-05
Identities = 28/99 (28%), Positives = 48/99 (48%), Gaps = 4/99 (4%)
Query: 21 IPELCKQFYHLGWVTGTGGGMTIKLGDEIYIAPSGVQKERLTSKDLFVQDMEGKDLQLPE 80
I + C + LG GT G ++++ D + I P+G+ E+LT++ + D GK E
Sbjct: 9 IIDTCLEMTRLGLNQGTAGNVSVRYKDGMLITPTGIPYEKLTTEHIVYVDGNGKH----E 64
Query: 81 DKTLKKSQCTPLFMCSYTLRNAGAVIHTHSKAAVLVTML 119
+ L S+ T +A AV+H H+ V++L
Sbjct: 65 EGKLPSSEWQFHLSVYQTRPDANAVVHNHAIHCAAVSIL 103
>gnl|CDD|181226 PRK08087, PRK08087, L-fuculose phosphate aldolase; Provisional.
Length = 215
Score = 42.4 bits (100), Expect = 8e-05
Identities = 28/99 (28%), Positives = 46/99 (46%), Gaps = 4/99 (4%)
Query: 21 IPELCKQFYHLGWVTGTGGGMTIKLGDEIYIAPSGVQKERLTSKDLFVQDMEGKDLQLPE 80
I + C + LG GT G ++++ D + I P+G+ E+LT + D GK E
Sbjct: 10 IIDTCLEMTRLGLNQGTAGNVSVRYQDGMLITPTGIPYEKLTESHIVFVDGNGK----HE 65
Query: 81 DKTLKKSQCTPLFMCSYTLRNAGAVIHTHSKAAVLVTML 119
+ L S+ T +A AV+H H+ V++L
Sbjct: 66 EGKLPSSEWRFHMAAYQTRPDANAVVHNHAVHCTAVSIL 104
>gnl|CDD|183460 PRK12348, sgaE, L-ribulose-5-phosphate 4-epimerase; Reviewed.
Length = 228
Score = 40.2 bits (94), Expect = 5e-04
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 49 IYIAPSGVQKERLTSKDLFVQDMEGKDLQLPEDKTLKKSQCTPLFMCSY-TLRNAGAVIH 107
+ I PSGV E + + D+ V DM GK + + + S T + Y + G ++H
Sbjct: 38 VVIKPSGVAYETMKADDMVVVDMSGKVV----EGEYRPSSDTATHLELYRRYPSLGGIVH 93
Query: 108 THSKAA 113
THS A
Sbjct: 94 THSTHA 99
>gnl|CDD|236181 PRK08193, araD, L-ribulose-5-phosphate 4-epimerase; Reviewed.
Length = 231
Score = 39.8 bits (94), Expect = 7e-04
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 51 IAPSGVQKERLTSKDLFVQDMEGKDLQLPEDKTLKKSQCTPLFMCSY-TLRNAGAVIHTH 109
I PSGV +++T++D+ V D+EG + + LK S TP + Y G ++HTH
Sbjct: 41 IKPSGVDYDKMTAEDMVVVDLEGNVV----EGKLKPSSDTPTHLVLYKAFPEIGGIVHTH 96
Query: 110 SKAAV 114
S+ A
Sbjct: 97 SRHAT 101
>gnl|CDD|235829 PRK06557, PRK06557, L-ribulose-5-phosphate 4-epimerase; Validated.
Length = 221
Score = 39.6 bits (93), Expect = 7e-04
Identities = 32/110 (29%), Positives = 49/110 (44%), Gaps = 19/110 (17%)
Query: 7 AKVEESHPEHPRNLIPELCKQFYHLGWVTGTGGGMTIKL--GDEIYIAPSGVQKERLTSK 64
+V + H E P+ G V T G ++ + D + I PSGV + LT +
Sbjct: 13 EEVCKLHLELPKY------------GLVVWTSGNVSARDPGTDLVVIKPSGVSYDDLTPE 60
Query: 65 DLFVQDMEGKDLQLPEDKTLKKSQCTPLFMCSYT-LRNAGAVIHTHSKAA 113
D+ V D++G + LK S T + Y + + G V+HTHS A
Sbjct: 61 DMVVVDLDGN----VVEGDLKPSSDTASHLYVYRHMPDVGGVVHTHSTYA 106
Score = 28.0 bits (63), Expect = 4.5
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 202 DSLERALVEFPSTS---AVLVRRHGVYVWGGD 230
+++ + +VE AVL++ HGV+ G D
Sbjct: 142 EAIGKGIVETLKGGRSPAVLMQNHGVFTIGKD 173
>gnl|CDD|102532 PRK06755, PRK06755, hypothetical protein; Validated.
Length = 209
Score = 39.2 bits (91), Expect = 7e-04
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 4/69 (5%)
Query: 184 EELVVPIIENTPQEKDLRDSLERALVEFPSTSAV-LVRRHGVYVWGGDWKSTKTQTECYD 242
E+ +PI+E+ EK D LE + F V LV +G+ VWG + K E +
Sbjct: 133 TEMTIPIVED---EKKFADLLENNVPNFIEGGGVVLVHNYGMIVWGKTPEEAKKWLEGIE 189
Query: 243 YLFELAVSM 251
YL V +
Sbjct: 190 YLMNYHVKL 198
>gnl|CDD|180717 PRK06833, PRK06833, L-fuculose phosphate aldolase; Provisional.
Length = 214
Score = 38.2 bits (89), Expect = 0.002
Identities = 28/108 (25%), Positives = 50/108 (46%), Gaps = 8/108 (7%)
Query: 15 EHPRNLIPELCKQFYHLGWVTGTGGGMTIKLGDEIYIA--PSGVQKERLTSKDLFVQDME 72
+ R I K+ G GTGG ++I ++ +A PSG+ + +D+ + D++
Sbjct: 4 QKEREEIVAYGKKLISSGLTKGTGGNISIFNREQGLMAITPSGIDYFEIKPEDIVIMDLD 63
Query: 73 GKDLQLPEDKTLKKSQCTPLFMCSYTLR-NAGAVIHTHSK-AAVLVTM 118
GK + + K S + + Y R + A++HTHS A L +
Sbjct: 64 GKVV----EGERKPSSELDMHLIFYRNREDINAIVHTHSPYATTLACL 107
>gnl|CDD|129843 TIGR00760, araD, L-ribulose-5-phosphate 4-epimerase. E. coli has
two genes, sgaE and sgbE (YiaS), that are very close
homologs of araD, the established L-ribulose-5-phosphate
4-epimerase of E. coli. SgbE, part of an operon for
L-xylulose metabolism, also has L-ribulose-5-phosphate
4-epimerase activity; L-xylulose-5-phosphate may be
converted into L-ribulose-5-phosphate by another product
of that operon. The homolog to this family from
Mycobacterium smegmatis is flanked by putative araB and
araA genes, consistent with it also being araD [Energy
metabolism, Sugars].
Length = 231
Score = 38.3 bits (89), Expect = 0.002
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 4/66 (6%)
Query: 49 IYIAPSGVQKERLTSKDLFVQDMEGKDLQLPEDKTLKKSQCTPLFMCSY-TLRNAGAVIH 107
+ I PSGV+ + +T+ D+ V D+E ++ + + K S TP + Y + G ++H
Sbjct: 39 VVIKPSGVEYDVMTADDMVVVDLETGNVV---EGSKKPSSDTPTHLALYRAFPSIGGIVH 95
Query: 108 THSKAA 113
THS+ A
Sbjct: 96 THSRHA 101
>gnl|CDD|181393 PRK08333, PRK08333, L-fuculose phosphate aldolase; Provisional.
Length = 184
Score = 36.0 bits (83), Expect = 0.009
Identities = 23/99 (23%), Positives = 47/99 (47%), Gaps = 7/99 (7%)
Query: 30 HLGWVTGT-GGGMTIKLGDEIYIAPSGVQKERLTSKDLFVQDMEGKDLQLPEDKTLKKSQ 88
H +T GG ++I++G+ ++I +G + LT + + V D+ G L +++ S
Sbjct: 16 HERGLTAAFGGNLSIRVGNLVFIKATGSVMDELTREQVAVIDLNGNQLS-----SVRPSS 70
Query: 89 CTPLFMCSYTLR-NAGAVIHTHSKAAVLVTMLYPGNVSI 126
L + Y R + A+ H H +++ + L + I
Sbjct: 71 EYRLHLAVYRNRPDVRAIAHLHPPYSIVASTLLEEELPI 109
>gnl|CDD|181527 PRK08660, PRK08660, L-fuculose phosphate aldolase; Provisional.
Length = 181
Score = 33.0 bits (76), Expect = 0.074
Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 5/88 (5%)
Query: 32 GWVTGTGGGMTIKLGDEIYIAPSGVQKERLTSKDLFVQDMEGKDLQLPEDKTLKKSQCTP 91
G V+ G ++++ GD + I +G + +T D+ ++ S TP
Sbjct: 16 GLVSSHFGNISVRTGDGLLITRTGSMLDEITEGDVIEVGIDDDG-----SVDPLASSETP 70
Query: 92 LFMCSYTLRNAGAVIHTHSKAAVLVTML 119
+ Y +A A++H H AV +++L
Sbjct: 71 VHRAIYRRTSAKAIVHAHPPYAVALSLL 98
>gnl|CDD|183459 PRK12347, sgbE, L-ribulose-5-phosphate 4-epimerase; Reviewed.
Length = 231
Score = 31.7 bits (72), Expect = 0.24
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 51 IAPSGVQKERLTSKDLFVQDME-GKDLQLPEDKTLKKSQCTPLFMCSY-TLRNAGAVIHT 108
I PSGV+ + +T+ D+ V ++ GK ++ + K S TP + Y G ++HT
Sbjct: 41 IKPSGVEYDVMTADDMVVVEIASGKVVE----GSKKPSSDTPTHLALYRRYPEIGGIVHT 96
Query: 109 HSKAAVL 115
HS+ A +
Sbjct: 97 HSRHATI 103
>gnl|CDD|239667 cd03696, selB_II, selB_II: this subfamily represents the domain
of elongation factor SelB, homologous to domain II of
EF-Tu. SelB may function by replacing EF-Tu. In
prokaryotes, the incorporation of selenocysteine as the
21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3' or 5' non-coding elements of mRNA have been found as
probable structures for directing selenocysteine
incorporation.
Length = 83
Score = 29.8 bits (68), Expect = 0.35
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 4/27 (14%)
Query: 34 VTGT--GGGMTIKLGDEIYIAPSGVQK 58
VTGT G ++K+GD++ I P G +
Sbjct: 18 VTGTVLSG--SVKVGDKVEILPLGEET 42
>gnl|CDD|225884 COG3347, COG3347, Uncharacterized conserved protein [Function
unknown].
Length = 404
Score = 30.0 bits (68), Expect = 1.2
Identities = 8/44 (18%), Positives = 17/44 (38%), Gaps = 6/44 (13%)
Query: 199 DLRDSLERALVEFPSTSAVLVRRHGVYVWGGDWKSTKTQTECYD 242
L ++ P +++ HG++ +G K E Y+
Sbjct: 168 PLAKAIAERFKANPDAEGLVLENHGLFTFGDTAK------EAYE 205
>gnl|CDD|143311 cd07687, IgC_TCR_delta, Immunoglobulin Constant domain.
IgC_TCR_delta: Constant domain of the delta chain of
delta/gamma T-cell antigen receptors (TCRs). TCRs
mediate antigen recognition by T lymphocytes, and are
composed of alpha and beta, or gamma and delta,
polypeptide chains with variable (V) and constant (C)
regions. The majority of T cells contain alpha-beta TCRs
but a small subset contain gamma-delta TCRs. Alpha-beta
TCRs recognize antigen as peptide fragments presented by
major histocompatibility complex (MHC) molecules.
Gamma-delta TCRs recognize intact protein antigens; they
recognize protein antigens directly and without antigen
processing, and MHC independently of the bound peptide.
Gamma-delta T cells can also be stimulated by
non-peptide antigens such as small phosphate- or
amine-containing compounds.
Length = 80
Score = 27.9 bits (62), Expect = 1.7
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 105 VIHTHSKAAVLVTMLYPGNVSIELVSS 131
V+ + A LV YP ++SI L SS
Sbjct: 3 VMKNGTNVACLVKEFYPKSISINLSSS 29
>gnl|CDD|106181 PRK13213, araD, L-ribulose-5-phosphate 4-epimerase; Reviewed.
Length = 231
Score = 29.3 bits (65), Expect = 1.8
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 49 IYIAPSGVQKERLTSKDLFVQDM-EGKDLQLPEDKTLKKSQCTPLFMCSY-TLRNAGAVI 106
+ I PSGV+ + ++ D+ V D+ GK ++ DK K S T + Y G ++
Sbjct: 39 VVIKPSGVEYDVMSVNDMVVVDLATGKVVE--GDK--KPSSDTDTHLVLYRAFAEIGGIV 94
Query: 107 HTHSKAAVL 115
HTHS+ A +
Sbjct: 95 HTHSRHATI 103
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2.
Elongation factor Tu consists of three structural
domains, this is the second domain. This domain adopts
a beta barrel structure. This the second domain is
involved in binding to charged tRNA. This domain is
also found in other proteins such as elongation factor
G and translation initiation factor IF-2. This domain
is structurally related to pfam03143, and in fact has
weak sequence matches to this domain.
Length = 70
Score = 27.2 bits (61), Expect = 2.3
Identities = 11/23 (47%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 42 TIKLGDEIYIAPSGV-QKERLTS 63
T+K GD++ I P+G +K R+TS
Sbjct: 12 TLKKGDKVVIGPNGTGKKGRVTS 34
>gnl|CDD|217571 pfam03458, UPF0126, UPF0126 domain. Domain always found as pair
in bacterial membrane proteins of unknown function.
This domain contains three transmembrane helices. The
conserved glycines are suggestive of an ion channel (C.
Yeats unpublished obs.).
Length = 81
Score = 27.1 bits (61), Expect = 2.6
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 10/34 (29%)
Query: 31 LGWVTGTGGGM----------TIKLGDEIYIAPS 54
LG VT GGG+ + DEIY +
Sbjct: 33 LGVVTAVGGGILRDVLLGEVPLVLRKDEIYATAA 66
>gnl|CDD|222210 pfam13539, Peptidase_M15_4, D-alanyl-D-alanine carboxypeptidase.
This family resembles VanY, pfam02557, which is part of
the peptidase M15 family.
Length = 67
Score = 26.5 bits (59), Expect = 3.2
Identities = 13/29 (44%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 220 RRHGVYVWGGDWKSTKTQTECYDYL-FEL 247
G WGGDW S K DY+ FEL
Sbjct: 46 ESVGFR-WGGDWSSRK------DYMHFEL 67
>gnl|CDD|197305 cd07026, Ribosomal_L20, Ribosomal protein L20. The ribosomal
protein family L20 contains members from eubacteria, as
well as their mitochondrial and plastid homologs. L20 is
an assembly protein, required for the first in-vitro
reconstitution step of the 50S ribosomal subunit, but
does not seem to be essential for ribosome activity. L20
has been shown to partially unfold in the absence of
RNA, in regions corresponding to the RNA-binding sites.
L20 represses the translation of its own mRNA via
specific binding to two distinct mRNA sites, in a manner
similar to the L20 interaction with 23S ribosomal RNA. .
Length = 106
Score = 27.4 bits (62), Expect = 3.6
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 156 WSNVFRIAYQEMIKGTWNSTLGRYNR 181
S +FR A Q ++K + R +
Sbjct: 23 RSRLFRTAKQAVMKALAYAYRDRKQK 48
>gnl|CDD|132444 TIGR03403, nifS_epsilon, cysteine desulfurase, NifS family, epsilon
proteobacteria type. Members of this family are the
NifS-like cysteine desulfurase of the epsilon division
of the Proteobacteria, similar to the NifS protein of
nitrogen-fixing bacteria. Like NifS, and unlike IscS,
this protein is found as part of a system of just two
proteins, a cysteine desulfurase and a scaffold, for
iron-sulfur cluster biosynthesis. This protein is called
NifS by Olsen, et al. (PMID:11123951), so we use this
designation.
Length = 382
Score = 28.7 bits (64), Expect = 3.7
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 198 KDLRDSLERALVEFPSTSAVLVRRHGV 224
+ LRD LE AL+E P V R H V
Sbjct: 265 RRLRDRLEDALLELPDVFVVGDREHRV 291
>gnl|CDD|215277 PLN02501, PLN02501, digalactosyldiacylglycerol synthase.
Length = 794
Score = 28.8 bits (64), Expect = 3.8
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 2 SSNEIAKVEESHPEHPRNLIPELCKQFYHLGWVTGTGGGMTIKLGDEIYIAPSGVQKERL 61
S + +AKV+E+ P+ L PE Q Y+L W T M D++ + +
Sbjct: 668 SEDFVAKVKEALANEPQPLTPE---QRYNLSWEAATQRFMEYSDLDKVLNNGDDAKLSKS 724
Query: 62 TSKDL 66
K +
Sbjct: 725 GGKSI 729
>gnl|CDD|168637 PRK06661, PRK06661, hypothetical protein; Provisional.
Length = 231
Score = 28.3 bits (63), Expect = 3.8
Identities = 25/104 (24%), Positives = 50/104 (48%), Gaps = 9/104 (8%)
Query: 47 DEIYIAPSGVQKERLTSKDLFVQDMEGKDLQLPEDKTLKKSQCTPLFMCSYTLRNAGAVI 106
D YI P G++ E +T+++L ++G+ L+ E+ K+ T + A+
Sbjct: 35 DFYYIYPFGLRFEEVTTENLLKVSLDGQILE-GEEYQYNKTGYFIHGSIYKTRPDISAIF 93
Query: 107 HTHSKAAVLVTMLYPGNVSIELVSSYLGNIFQLKFFVQFTYNWY 150
H H+ A++ V+ L G + I + + L F+ + +Y+ Y
Sbjct: 94 HYHTPASIAVSALKCGLLPI--------SQWALHFYDRISYHNY 129
>gnl|CDD|225184 COG2301, CitE, Citrate lyase beta subunit [Carbohydrate transport
and metabolism].
Length = 283
Score = 28.4 bits (64), Expect = 3.8
Identities = 15/30 (50%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 195 PQEKDL-RDSLERALVEFPSTSAVLVRRHG 223
P +KD RD+L RAL++ P T V+VR +G
Sbjct: 34 PADKDAARDNLRRALLDLPFTGEVVVRING 63
>gnl|CDD|240384 PTZ00367, PTZ00367, squalene epoxidase; Provisional.
Length = 567
Score = 28.3 bits (63), Expect = 5.4
Identities = 13/30 (43%), Positives = 15/30 (50%)
Query: 37 TGGGMTIKLGDEIYIAPSGVQKERLTSKDL 66
TGGGMT D I +A S + L S D
Sbjct: 353 TGGGMTCCFSDCIRLAKSLTGIKSLRSIDQ 382
>gnl|CDD|201846 pfam01538, HCV_NS2, Hepatitis C virus non-structural protein NS2.
The viral genome is translated into a single polyprotein
of about 3000 amino acids. Generation of the mature
non-structural proteins relies on the activity of viral
proteases. Cleavage at the NS2/NS3 junction is
accomplished by a metal-dependent autoprotease encoded
within NS2 and the N-terminus of NS3.
Length = 195
Score = 27.6 bits (62), Expect = 5.5
Identities = 12/38 (31%), Positives = 13/38 (34%)
Query: 146 TYNWYLVAYCWSNVFRIAYQEMIKGTWNSTLGRYNRYD 183
TY L W + IA QE W LG D
Sbjct: 24 TYKGLLAKLLWWLQYFIARQEARLHVWVPPLGVRGGRD 61
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 27.5 bits (61), Expect = 8.2
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 34 VTGTGGGMTIKLGDEIYIAPSGVQKERLTSKDLFVQDME 72
VTGT +K+GD + + P + R+ + QD+E
Sbjct: 194 VTGTAFSGEVKVGDNLRLLPIN-HEVRVKAIQAQNQDVE 231
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.417
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,346,778
Number of extensions: 1249889
Number of successful extensions: 1128
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1100
Number of HSP's successfully gapped: 48
Length of query: 262
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 167
Effective length of database: 6,723,972
Effective search space: 1122903324
Effective search space used: 1122903324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.1 bits)