RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10089
(559 letters)
>gnl|CDD|214473 smart00020, Tryp_SPc, Trypsin-like serine protease. Many of these
are synthesised as inactive precursor zymogens that are
cleaved during limited proteolysis to generate their
active forms. A few, however, are active as single chain
molecules, and others are inactive due to substitutions
of the catalytic triad residues.
Length = 229
Score = 212 bits (541), Expect = 3e-65
Identities = 84/246 (34%), Positives = 116/246 (47%), Gaps = 31/246 (12%)
Query: 301 GEYPWMMAILTNKINKDGSVTENVFQCGATLILPHVVMTAAHCVNNIPVTDIKVRGGEWD 360
G +PW +++ CG +LI P V+TAAHCV ++I+VR G D
Sbjct: 11 GSFPWQVSLQYGG---------GRHFCGGSLISPRWVLTAAHCVRGSDPSNIRVRLGSHD 61
Query: 361 TITNNRTDREPFPYQERTVSQIYIHENFEAKTVFNDIALIILDFPFPVKNHIGLACTPNS 420
Q VS++ IH N+ T NDIAL+ L P + +++ C P+S
Sbjct: 62 L-------SSGEEGQVIKVSKVIIHPNYNPSTYDNDIALLKLKEPVTLSDNVRPICLPSS 114
Query: 421 AEEY-DDQNCIVTGWGKDKFGVEGRYQSTLKKVEVKLVPRNVCQQQLRKTRLGGVFKLHD 479
C V+GWG+ G G TL++V V +V C++ G + D
Sbjct: 115 NYNVPAGTTCTVSGWGRTSEGA-GSLPDTLQEVNVPIVSNATCRR-----AYSGGGAITD 168
Query: 480 SFICASGGPN--QDACKGDGGGPLVCQLKNERDRFTQVGIVSWGIGCGS-DTPGVYVDVR 536
+ +CA GG +DAC+GD GGPLVC R+ VGIVSWG GC PGVY V
Sbjct: 169 NMLCA-GGLEGGKDACQGDSGGPLVCN----DGRWVLVGIVSWGSGCARPGKPGVYTRVS 223
Query: 537 KFKKWI 542
+ WI
Sbjct: 224 SYLDWI 229
Score = 141 bits (358), Expect = 7e-39
Identities = 69/229 (30%), Positives = 85/229 (37%), Gaps = 67/229 (29%)
Query: 34 ISGRNTYFGEFPWMLVLFYYKRNMEYFKCGASLIGPNIALTAAHCVQYDV--TYSVAAGE 91
+ G G FPW + L Y CG SLI P LTAAHCV+ V G
Sbjct: 3 VGGSEANIGSFPWQVSLQYGGG---RHFCGGSLISPRWVLTAAHCVRGSDPSNIRVRLGS 59
Query: 92 WFINGIVEEELEEEQRRDVLDVRIHPNYSTETLENNIALLKLSSNIDFDDYIHPICLPDW 151
++ EE Q V V IHPNY+ T +N+IALLKL + D + PICLP
Sbjct: 60 HDLS-----SGEEGQVIKVSKVIIHPNYNPSTYDNDIALLKLKEPVTLSDNVRPICLPSS 114
Query: 152 NVTY-DSENCVITGWGR------------------------------------------- 167
N C ++GWGR
Sbjct: 115 NYNVPAGTTCTVSGWGRTSEGAGSLPDTLQEVNVPIVSNATCRRAYSGGGAITDNMLCAG 174
Query: 168 ------DSADG--GGPLVCPSKEDPTTFFQVGIAAWSVVCT-PDMPGLY 207
D+ G GGPLVC + VGI +W C P PG+Y
Sbjct: 175 GLEGGKDACQGDSGGPLVCNDG----RWVLVGIVSWGSGCARPGKPGVY 219
Score = 83.1 bits (206), Expect = 5e-18
Identities = 32/84 (38%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 211 YSVAAGEWFINGIVEEELEEEQRRDVLDVRIHPNYSTETLENNIALLKLSSNIDFDDYIH 270
V G ++ EE Q V V IHPNY+ T +N+IALLKL + D +
Sbjct: 53 IRVRLGSHDLS-----SGEEGQVIKVSKVIIHPNYNPSTYDNDIALLKLKEPVTLSDNVR 107
Query: 271 PICLPDWNVTY-DSENCVITGWGR 293
PICLP N C ++GWGR
Sbjct: 108 PICLPSSNYNVPAGTTCTVSGWGR 131
>gnl|CDD|238113 cd00190, Tryp_SPc, Trypsin-like serine protease; Many of these are
synthesized as inactive precursor zymogens that are
cleaved during limited proteolysis to generate their
active forms. Alignment contains also inactive enzymes
that have substitutions of the catalytic triad residues.
Length = 232
Score = 210 bits (538), Expect = 9e-65
Identities = 79/245 (32%), Positives = 115/245 (46%), Gaps = 28/245 (11%)
Query: 301 GEYPWMMAILTNKINKDGSVTENVFQCGATLILPHVVMTAAHCVNNIPVTDIKVRGGEWD 360
G +PW +++ CG +LI P V+TAAHCV + ++ VR G
Sbjct: 10 GSFPWQVSLQYTG---------GRHFCGGSLISPRWVLTAAHCVYSSAPSNYTVRLGSH- 59
Query: 361 TITNNRTDREPFPYQERTVSQIYIHENFEAKTVFNDIALIILDFPFPVKNHIGLACTPNS 420
+ + E Q V ++ +H N+ T NDIAL+ L P + +++ C P+S
Sbjct: 60 ----DLSSNEG-GGQVIKVKKVIVHPNYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSS 114
Query: 421 AEE-YDDQNCIVTGWGKDKFGVEGRYQSTLKKVEVKLVPRNVCQQQLRKTRLGGVFKLHD 479
C V+GWG+ G G L++V V +V C++ + D
Sbjct: 115 GYNLPAGTTCTVSGWGRTSEG--GPLPDVLQEVNVPIVSNAECKRAYSYG-----GTITD 167
Query: 480 SFICASG-GPNQDACKGDGGGPLVCQLKNERDRFTQVGIVSWGIGCGS-DTPGVYVDVRK 537
+ +CA G +DAC+GD GGPLVC N+ R VGIVSWG GC + PGVY V
Sbjct: 168 NMLCAGGLEGGKDACQGDSGGPLVC---NDNGRGVLVGIVSWGSGCARPNYPGVYTRVSS 224
Query: 538 FKKWI 542
+ WI
Sbjct: 225 YLDWI 229
Score = 145 bits (368), Expect = 3e-40
Identities = 67/228 (29%), Positives = 84/228 (36%), Gaps = 64/228 (28%)
Query: 34 ISGRNTYFGEFPWMLVLFYYKRNMEYFKCGASLIGPNIALTAAHCVQYDV--TYSVAAGE 91
+ G G FPW + L Y CG SLI P LTAAHCV Y+V G
Sbjct: 2 VGGSEAKIGSFPWQVSLQYTGG---RHFCGGSLISPRWVLTAAHCVYSSAPSNYTVRLGS 58
Query: 92 WFINGIVEEELEEEQRRDVLDVRIHPNYSTETLENNIALLKLSSNIDFDDYIHPICLPDW 151
++ Q V V +HPNY+ T +N+IALLKL + D + PICLP
Sbjct: 59 HDLS----SNEGGGQVIKVKKVIVHPNYNPSTYDNDIALLKLKRPVTLSDNVRPICLPSS 114
Query: 152 NVT-YDSENCVITGWGR------------------------------------------- 167
C ++GWGR
Sbjct: 115 GYNLPAGTTCTVSGWGRTSEGGPLPDVLQEVNVPIVSNAECKRAYSYGGTITDNMLCAGG 174
Query: 168 -----DSADG--GGPLVCPSKEDPTTFFQVGIAAWSVVC-TPDMPGLY 207
D+ G GGPLVC D VGI +W C P+ PG+Y
Sbjct: 175 LEGGKDACQGDSGGPLVC---NDNGRGVLVGIVSWGSGCARPNYPGVY 219
Score = 83.5 bits (207), Expect = 3e-18
Identities = 29/84 (34%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 211 YSVAAGEWFINGIVEEELEEEQRRDVLDVRIHPNYSTETLENNIALLKLSSNIDFDDYIH 270
Y+V G ++ Q V V +HPNY+ T +N+IALLKL + D +
Sbjct: 52 YTVRLGSHDLS----SNEGGGQVIKVKKVIVHPNYNPSTYDNDIALLKLKRPVTLSDNVR 107
Query: 271 PICLPDWNVT-YDSENCVITGWGR 293
PICLP C ++GWGR
Sbjct: 108 PICLPSSGYNLPAGTTCTVSGWGR 131
>gnl|CDD|215708 pfam00089, Trypsin, Trypsin.
Length = 218
Score = 151 bits (383), Expect = 1e-42
Identities = 82/248 (33%), Positives = 116/248 (46%), Gaps = 37/248 (14%)
Query: 297 ETFFGEYPWMMAILTNKINKDGSVTENVFQCGATLILPHVVMTAAHCVNNIPVTDIKVRG 356
E G +PW +++ V+ CG +LI + V+TAAHCV+N ++V
Sbjct: 6 EAQPGSFPWQVSL---------QVSSGKHFCGGSLISENWVLTAAHCVSN--AKSVRVVL 54
Query: 357 GEWDTITNNRTDREPFPYQERTVSQIYIHENFEAKTVFNDIALIILDFPFPVKNHIGLAC 416
G I Q+ V ++ +H N+ T NDIAL+ L P + + + C
Sbjct: 55 GA-HNIVLREGG-----EQKFDVKKVIVHPNYNPDT-DNDIALLKLKSPVTLGDTVRPIC 107
Query: 417 TP-NSAEEYDDQNCIVTGWGKDKFGVEGRYQSTLKKVEVKLVPRNVCQQQLRKTRLGGVF 475
P S++ C V+GWG K TL++V V +V R C+ T
Sbjct: 108 LPTASSDLPVGTTCTVSGWGNTK---TLGLPDTLQEVTVPVVSRETCRSAYGGT------ 158
Query: 476 KLHDSFICASGGPNQDACKGDGGGPLVCQLKNERDRFTQVGIVSWGIGCGS-DTPGVYVD 534
+ D+ ICA G +DAC+GD GGPLVC E +GIVSWG GC S + PGVY
Sbjct: 159 -VTDNMICA-GAGGKDACQGDSGGPLVC-SDGE-----LIGIVSWGYGCASGNYPGVYTP 210
Query: 535 VRKFKKWI 542
V + WI
Sbjct: 211 VSSYLDWI 218
Score = 113 bits (285), Expect = 8e-29
Identities = 67/223 (30%), Positives = 87/223 (39%), Gaps = 65/223 (29%)
Query: 34 ISGRNTYFGEFPWMLVLFYYKRNMEYFKCGASLIGPNIALTAAHCVQYDVTYSVAAGEWF 93
+ G G FPW + L + ++F CG SLI N LTAAHCV + V G
Sbjct: 2 VGGDEAQPGSFPWQVSLQV--SSGKHF-CGGSLISENWVLTAAHCVSNAKSVRVVLGAHN 58
Query: 94 INGIVEEELEEEQRRDVLDVRIHPNYSTETLENNIALLKLSSNIDFDDYIHPICLPDWNV 153
I EQ+ DV V +HPNY+ +T N+IALLKL S + D + PICLP +
Sbjct: 59 IV----LREGGEQKFDVKKVIVHPNYNPDTD-NDIALLKLKSPVTLGDTVRPICLPTAS- 112
Query: 154 TYDSEN---CVITGWGRDSADG-------------------------------------- 172
D C ++GWG G
Sbjct: 113 -SDLPVGTTCTVSGWGNTKTLGLPDTLQEVTVPVVSRETCRSAYGGTVTDNMICAGAGGK 171
Query: 173 -------GGPLVCPSKEDPTTFFQVGIAAWSVVCT-PDMPGLY 207
GGPLVC E +GI +W C + PG+Y
Sbjct: 172 DACQGDSGGPLVCSDGE------LIGIVSWGYGCASGNYPGVY 208
Score = 62.5 bits (152), Expect = 4e-11
Identities = 29/69 (42%), Positives = 39/69 (56%), Gaps = 6/69 (8%)
Query: 231 EQRRDVLDVRIHPNYSTETLENNIALLKLSSNIDFDDYIHPICLPDWNVTYDSEN---CV 287
EQ+ DV V +HPNY+ +T N+IALLKL S + D + PICLP + D C
Sbjct: 66 EQKFDVKKVIVHPNYNPDTD-NDIALLKLKSPVTLGDTVRPICLPTAS--SDLPVGTTCT 122
Query: 288 ITGWGRDSA 296
++GWG
Sbjct: 123 VSGWGNTKT 131
>gnl|CDD|227927 COG5640, COG5640, Secreted trypsin-like serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 413
Score = 81.8 bits (202), Expect = 1e-16
Identities = 75/261 (28%), Positives = 107/261 (40%), Gaps = 43/261 (16%)
Query: 301 GEYPWMMAILTNKINKDGSVTENVFQCGATLILPHVVMTAAHCVN-NIPVTDIKVRGGEW 359
GEYP ++A L ++I+ S T CG + + V+TAAHC + + P++ R
Sbjct: 42 GEYPSLVA-LVDRISDYVSGT----FCGGSKLGGRYVLTAAHCADASSPISSDVNRVV-- 94
Query: 360 DTITNNRTDREPFPYQER-TVSQIYIHENFEAKTVFNDIALIILDFPFPVKNHIGLACTP 418
D ER V IY+HE + + NDIA++ L +
Sbjct: 95 -------VDLNDSSQAERGHVRTIYVHEFYSPGNLGNDIAVLELARAASLP-----RVKI 142
Query: 419 NSAEEYDDQNCIVTGWGKDKFGVEG--------RYQ---STLKKVEVKLVPRNVCQQQLR 467
S + D VT G G R + L +V V VP + C Q
Sbjct: 143 TSFDASDTFLNSVTTVSPMTNGTFGVTTPSDVPRSSPKGTILHEVAVLFVPLSTCAQYKG 202
Query: 468 KTRLGGVFKLHDSF--ICASGGPNQDACKGDGGGPLVCQLKNERDRFTQVGIVSWGIG-C 524
CA G P +DAC+GD GGP+ + + R Q G+VSWG G C
Sbjct: 203 CANAS---DGATGLTGFCA-GRPPKDACQGDSGGPIFHKGEEGR---VQRGVVSWGDGGC 255
Query: 525 G-SDTPGVYVDVRKFKKWILD 544
G + PGVY +V ++ WI
Sbjct: 256 GGTLIPGVYTNVSNYQDWIAA 276
Score = 48.7 bits (116), Expect = 5e-06
Identities = 34/118 (28%), Positives = 50/118 (42%), Gaps = 12/118 (10%)
Query: 20 TSAENTEEYDYIEPISGRNTYFGEFPWMLVLFYYKRNMEYFK---CGASLIGPNIALTAA 76
+ E I I G N GE+P ++ L R +Y CG S +G LTAA
Sbjct: 22 AAQTADEVSSRI--IGGSNANAGEYPSLVALV--DRISDYVSGTFCGGSKLGGRYVLTAA 77
Query: 77 HCVQYDVTYSVAAGEWFINGIVE-EELEEEQRRDVLDVRIHPNYSTETLENNIALLKL 133
HC S +V+ + + +R V + +H YS L N+IA+L+L
Sbjct: 78 HCADASSPISSD----VNRVVVDLNDSSQAERGHVRTIYVHEFYSPGNLGNDIAVLEL 131
>gnl|CDD|226119 COG3591, COG3591, V8-like Glu-specific endopeptidase [Amino acid
transport and metabolism].
Length = 251
Score = 33.9 bits (78), Expect = 0.17
Identities = 26/129 (20%), Positives = 48/129 (37%), Gaps = 10/129 (7%)
Query: 325 FQCGATLILPHVVMTAAHCVNNIPVTDIKVRGGEWDTITNNRTD-REPFPYQERTVSQIY 383
ATLI P+ V+TA HC+ + GE D + P+ T +I
Sbjct: 64 LCTAATLIGPNTVLTAGHCIYSPDY-------GEDDIAAAPPGVNSDGGPFYGITKIEIR 116
Query: 384 IHENF--EAKTVFNDIALIILDFPFPVKNHIGLACTPNSAEEYDDQNCIVTGWGKDKFGV 441
++ + D+ L+ + + + ++E + V G+ DK +
Sbjct: 117 VYPGELYKEDGASYDVGEAALESGINIGDVVNYLKRNTASEAKANDRITVIGYPGDKPNI 176
Query: 442 EGRYQSTLK 450
++ST K
Sbjct: 177 GTMWESTGK 185
Score = 33.1 bits (76), Expect = 0.30
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 60 FKCGASLIGPNIALTAAHCV 79
A+LIGPN LTA HC+
Sbjct: 64 LCTAATLIGPNTVLTAGHCI 83
>gnl|CDD|216715 pfam01808, AICARFT_IMPCHas, AICARFT/IMPCHase bienzyme. This is a
family of bifunctional enzymes catalyzing the last two
steps in de novo purine biosynthesis. The bifunctional
enzyme is found in both prokaryotes and eukaryotes. The
second last step is catalyzed by
5-aminoimidazole-4-carboxamide ribonucleotide
formyltransferase EC:2.1.2.3 (AICARFT), this enzyme
catalyzes the formylation of AICAR with
10-formyl-tetrahydrofolate to yield FAICAR and
tetrahydrofolate. This is catalyzed by a pair of
C-terminal deaminase fold domains in the protein, where
the active site is formed by the dimeric interface of
two monomeric units. The last step is catalyzed by the
N-terminal IMP (Inosine monophosphate) cyclohydrolase
domain EC:3.5.4.10 (IMPCHase), cyclizing FAICAR
(5-formylaminoimidazole-4-carboxamide ribonucleotide) to
IMP.
Length = 315
Score = 32.8 bits (75), Expect = 0.48
Identities = 21/64 (32%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 62 CGASLIGPNIALTAAHCVQYDVTYSVAAGEWFINGIVEEELEEEQRRDVLDVRIHPNYST 121
CG + +GP+IA A + D S G +N V+ E +E + +V I P Y
Sbjct: 147 CGVA-VGPSIAEAYARAREADPM-SAFGGIIALNDEVDVETAKEISEEFSEVIIAPGYEP 204
Query: 122 ETLE 125
E LE
Sbjct: 205 EALE 208
Score = 28.9 bits (65), Expect = 7.5
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 221 NGIVEEELEEEQRRDVLDVRIHPNYSTETLE 251
N V+ E +E + +V I P Y E LE
Sbjct: 178 NDEVDVETAKEISEEFSEVIIAPGYEPEALE 208
>gnl|CDD|225802 COG3263, COG3263, NhaP-type Na+/H+ and K+/H+ antiporters with a
unique C-terminal domain [Inorganic ion transport and
metabolism].
Length = 574
Score = 30.8 bits (70), Expect = 2.4
Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 4/58 (6%)
Query: 83 VTYSVAAGEWFINGIVEEELEEEQRRDVLDVR----IHPNYSTETLENNIALLKLSSN 136
Y +A +W + + + R R IHP ST E ++ + S
Sbjct: 415 FVYELAKDKWCVGAALRNLRMPKWTRIAAVFRDGQLIHPQGSTRLREGDVLCVIGSER 472
Score = 30.8 bits (70), Expect = 2.4
Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 4/58 (6%)
Query: 209 VTYSVAAGEWFINGIVEEELEEEQRRDVLDVR----IHPNYSTETLENNIALLKLSSN 262
Y +A +W + + + R R IHP ST E ++ + S
Sbjct: 415 FVYELAKDKWCVGAALRNLRMPKWTRIAAVFRDGQLIHPQGSTRLREGDVLCVIGSER 472
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 30.5 bits (69), Expect = 3.1
Identities = 26/151 (17%), Positives = 48/151 (31%), Gaps = 16/151 (10%)
Query: 189 QVGIAAWSVVCTPDMPGLYDVTYS---VAAGEWFINGIVEEELEEEQRRDVLDVRIHPNY 245
A ++ PD+ L + S G+ + EE E+ + L R P
Sbjct: 13 LDPDTADPLLGIPDLMALRSLQASDLGTRKGKPALEFKAEEA-EKLAPEEGLKTRQ-PKI 70
Query: 246 STETLENNIALLKLSSNIDFDDYIHPICLPDWNVTYDSENCVITGWGRDSAETFFGEYP- 304
T L A + S+ F + + L + N W ++ G
Sbjct: 71 RTFLL----ADARRST---FGEICQVLLL-NLNEILLHAKVFKELWLGETWLRLLGAQTT 122
Query: 305 --WMMAILTNKINKDGSVTENVFQCGATLIL 333
+L ++ + ++ + Q G L L
Sbjct: 123 RIDDDPLLLQQLRCEWQESKILAQAGTLLEL 153
>gnl|CDD|232936 TIGR00355, purH, phosphoribosylaminoimidazolecarboxamide
formyltransferase/IMP cyclohydrolase. PurH is
bifunctional: IMP cyclohydrolase (EC 3.5.4.10);
phosphoribosylaminoimidazolecarboxamide
formyltransferase (EC 2.1.2.3) Involved in purine
ribonucleotide biosynthesis. The IMP cyclohydrolase
activity is in the N-terminal region [Purines,
pyrimidines, nucleosides, and nucleotides, Purine
ribonucleotide biosynthesis].
Length = 511
Score = 29.4 bits (66), Expect = 5.9
Identities = 22/78 (28%), Positives = 31/78 (39%), Gaps = 9/78 (11%)
Query: 62 CGASLIGPNIALTAAHCVQYDVTYSVAAGEWF-INGIVEEELEEEQRRDVLDVRIHPNYS 120
CG +L G I D T + G +N ++ + R L+V I P YS
Sbjct: 275 CGVAL-GKTILDAYDRAFGADPTSAF--GGIIALNRELDVPTAKAIVRQFLEVIIAPGYS 331
Query: 121 TETLE-----NNIALLKL 133
E LE N+ +L L
Sbjct: 332 AEALEILAKKKNLRVLIL 349
>gnl|CDD|224840 COG1929, COG1929, Glycerate kinase [Carbohydrate transport and
metabolism].
Length = 378
Score = 29.1 bits (66), Expect = 6.4
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 8/50 (16%)
Query: 287 VITGWGRDSAETFFGEYPWMMAILTNKINKD-----GSVTEN---VFQCG 328
VITG GR +++ G+ P +A L K GS+ E+ V Q G
Sbjct: 288 VITGEGRIDSQSLHGKTPIGVAKLAKKYGVPVIAIAGSLGEDYEVVHQEG 337
>gnl|CDD|223457 COG0380, OtsA, Trehalose-6-phosphate synthase [Carbohydrate
transport and metabolism].
Length = 486
Score = 29.2 bits (66), Expect = 6.5
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 19 HTSAENTEEYDY----IEPISGR-NTYFGEFPWMLVLFYYK 54
S E+ EEY IE + GR N FG W V + ++
Sbjct: 325 PPSREDVEEYQALRLQIEELVGRINGEFGSLSWTPVHYLHR 365
>gnl|CDD|240650 cd12173, PGDH_4, Phosphoglycerate dehydrogenases, NAD-binding and
catalytic domains. Phosphoglycerate dehydrogenases
(PGDHs) catalyze the initial step in the biosynthesis of
L-serine from D-3-phosphoglycerate. PGDHs come in 3
distinct structural forms, with this first group being
related to 2-hydroxy acid dehydrogenases, sharing
structural similarity to formate and glycerate
dehydrogenases. PGDH in E. coli and Mycobacterium
tuberculosis form tetramers, with subunits containing a
Rossmann-fold NAD binding domain. Formate/glycerate and
related dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as formate
dehydrogenase, glycerate dehydrogenase, L-alanine
dehydrogenase, and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence.
Length = 304
Score = 28.9 bits (66), Expect = 6.8
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 335 HVVMTAAHCVNNIPVTDIKVRGGEWD 360
H + NIP D +R G+WD
Sbjct: 102 HTIALMLALARNIPQADASLRAGKWD 127
>gnl|CDD|139075 PRK12568, PRK12568, glycogen branching enzyme; Provisional.
Length = 730
Score = 28.8 bits (64), Expect = 9.1
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 150 DWNVTYDSENCVITGWGRDSADGGGPLVCPSKEDPTTF--FQVGI---AAWSVVCTPD 202
DW+V D+ N V+ D GG PL+ S P ++VG+ W + D
Sbjct: 628 DWSVADDARNSVLAFIRHDPDGGGVPLLAVSNLTPQPHHDYRVGVPRAGGWREILNTD 685
>gnl|CDD|235968 PRK07209, PRK07209, ribonucleotide-diphosphate reductase subunit
beta; Validated.
Length = 369
Score = 28.8 bits (65), Expect = 9.3
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 6/34 (17%)
Query: 54 KRNMEYFKCGASLIGPNIAL------TAAHCVQY 81
KRN+ +F SL+ NI L T C QY
Sbjct: 100 KRNLGFFSTADSLVANNIVLAIYRHITNPECRQY 133
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 0.138 0.438
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,941,350
Number of extensions: 2823727
Number of successful extensions: 2173
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2130
Number of HSP's successfully gapped: 29
Length of query: 559
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 457
Effective length of database: 6,413,494
Effective search space: 2930966758
Effective search space used: 2930966758
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 (21.7 bits)
S2: 62 (27.6 bits)