RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13453
(764 letters)
>gnl|CDD|215836 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase
conserved domain.
Length = 373
Score = 375 bits (964), Expect = e-124
Identities = 149/281 (53%), Positives = 195/281 (69%), Gaps = 7/281 (2%)
Query: 484 PGYLASLVPGEMPEEGEDWRHIMRDMNTVIMPGITHWQSPQFNAYFPTGSSYPSIVGDML 543
PGYL L+P P E I+ D+ IMPG+T W SP F+AYFP G+SYPS++GDML
Sbjct: 1 PGYLRPLLPEAAPIIPEPLLDILGDIRKNIMPGVTTWHSPNFHAYFPAGNSYPSLLGDML 60
Query: 544 SGAFGLIGFSWLSSPACTELEVLVMNWLGKALGLPEEFLNCSPGPGGGIIQSTASEATLV 603
S A GF+W SSPACTELE +VM+WL K LGLP+EFL G GGG++Q +SE+ L+
Sbjct: 61 SDAINCNGFTWESSPACTELENVVMDWLAKMLGLPKEFLGS--GEGGGVLQGGSSESNLL 118
Query: 604 SILVAKRKMINHWQSKNPSLTENDIRNKLVAYTSDQSNSSVEKSAIIGDVPVRQLRSDDN 663
++L A+ K I ++ KLVAYTSDQ++SS+EK+A+I V +R++ +D+N
Sbjct: 119 ALLAARTKWIRRMKAAGKPSLG-----KLVAYTSDQAHSSIEKAALIAGVELREIPTDEN 173
Query: 664 GVLRGDALLTAVKEDLAKGLIPCCLIATLGTTGTCAFDNLEELGPICQEYNIWLHVDAAY 723
G +RG L A++ED GLIP + ATLGTTG+ AFD L+ELG IC +Y++WLHVDAAY
Sbjct: 174 GKMRGMDLEKAIEEDKENGLIPFFVCATLGTTGSGAFDPLQELGDICNKYDLWLHVDAAY 233
Query: 724 AGSALLLPEYAHLKRGLEYVDSFDFNTHKWLLVNFDCSAMW 764
AGSA + PE+ H G+E DSF FN HKW+LV DCSA+W
Sbjct: 234 AGSAFICPEFRHWLFGIERADSFSFNPHKWMLVLLDCSALW 274
Score = 108 bits (272), Expect = 2e-25
Identities = 41/69 (59%), Positives = 50/69 (72%)
Query: 126 FQHWQIPLGRRFRALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEQDDRFELVCPPS 185
+ WQIPL RRFR LKLW LRSYG++GLQ +R+H+ LAK F LV +D RFE+
Sbjct: 305 YGDWQIPLSRRFRILKLWFVLRSYGVEGLQNQIRRHVELAKYFEALVRKDSRFEICAERG 364
Query: 186 MGLVCFRLK 194
+GLVCFRLK
Sbjct: 365 LGLVCFRLK 373
>gnl|CDD|215475 PLN02880, PLN02880, tyrosine decarboxylase.
Length = 490
Score = 322 bits (827), Expect = e-102
Identities = 148/328 (45%), Positives = 203/328 (61%), Gaps = 15/328 (4%)
Query: 442 TKASPVTPPPNEEFREFGKAAIDFIADYVDNIRERPVLPSVEPGYLASLVPGEMPEEGED 501
+ P E+ RE G +DFIADY +I PVL V+PGYL L+P P + E
Sbjct: 2 GGEEWLRPMDAEQLRECGHRMVDFIADYYKSIENFPVLSQVQPGYLRELLPDSAPNQPET 61
Query: 502 WRHIMRDMNTVIMPGITHWQSPQFNAYFPTGSSYPSIVGDMLSGAFGLIGFSWLSSPACT 561
++ D+ I+PG+THWQSP + AY+P+ SS +G+MLS ++GFSW++SPA T
Sbjct: 62 LDQVLDDVQAKILPGVTHWQSPNYFAYYPSNSSVAGFLGEMLSAGLNIVGFSWITSPAAT 121
Query: 562 ELEVLVMNWLGKALGLPEEFLNCSPGPGGGIIQSTASEATLVSILVAKRKMINHWQSKNP 621
ELE++V++WL K L LPE+FL S G GGG+IQ TASEA LV +L A+ +++
Sbjct: 122 ELEMIVLDWLAKLLNLPEQFL--STGNGGGVIQGTASEAVLVVLLAARDRVLR------- 172
Query: 622 SLTENDIRNKLVAYTSDQSNSSVEKSAIIGDV---PVRQLRSDD--NGVLRGDALLTAVK 676
+ +N + KLV Y SDQ++S+++K+ I + R L++D N L + L A+
Sbjct: 173 KVGKNALE-KLVVYASDQTHSALQKACQIAGIHPENCRLLKTDSSTNYALAPELLSEAIS 231
Query: 677 EDLAKGLIPCCLIATLGTTGTCAFDNLEELGPICQEYNIWLHVDAAYAGSALLLPEYAHL 736
DL+ GLIP L AT+GTT + A D L ELG I + +W HVDAAYAGSA + PEY H
Sbjct: 232 TDLSSGLIPFFLCATVGTTSSTAVDPLLELGKIAKSNGMWFHVDAAYAGSACICPEYRHY 291
Query: 737 KRGLEYVDSFDFNTHKWLLVNFDCSAMW 764
G+E DSF+ N HKW L NFDCS +W
Sbjct: 292 IDGVEEADSFNMNAHKWFLTNFDCSLLW 319
Score = 125 bits (316), Expect = 2e-30
Identities = 62/146 (42%), Positives = 84/146 (57%), Gaps = 9/146 (6%)
Query: 126 FQHWQIPLGRRFRALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEQDDRFELVCPPS 185
++ WQIPLGRRFR+LKLWM LR YG++ LQ+Y+R HI LAK+F LV QD RFE+V P
Sbjct: 350 YKDWQIPLGRRFRSLKLWMVLRLYGVENLQSYIRNHIKLAKEFEQLVAQDSRFEVVTPRI 409
Query: 186 MGLVCFRLKVRFWDKLDNLFGTISFGDNDLNKAVYDRIIARKVIYIVKGSFQDRLFMRFA 245
LVCFRL V + DN N LN + D + + I+I + +RFA
Sbjct: 410 FSLVCFRL-VPPKNNEDN--------GNKLNHDLLDAVNSSGKIFISHTVLSGKYVLRFA 460
Query: 246 ICSSQTEESDVQLGWNEIRTATEEVL 271
+ + TEE V W ++ ++L
Sbjct: 461 VGAPLTEERHVTAAWKVLQDEASKLL 486
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 279 bits (714), Expect = 5e-85
Identities = 142/331 (42%), Positives = 202/331 (61%), Gaps = 19/331 (5%)
Query: 443 KASPVTPPPNEEFREFGKAAIDFIADYVDNIRERP----VLPSVEPGYLASLVPGEMPEE 498
K + P +E RE G +DFIADY N+++ P VL V+PGYL ++P PE
Sbjct: 47 KVVKMKPMDSELLREQGHIMVDFIADYYKNLQDSPQDFPVLSQVQPGYLRDMLPDSAPER 106
Query: 499 GEDWRHIMRDMNTVIMPGITHWQSPQFNAYFPTGSSYPSIVGDMLSGAFGLIGFSWLSSP 558
E + ++ D++ IMPGITHWQSP + AY+ + +S +G+ML+ ++GF+WL+SP
Sbjct: 107 PESLKELLDDVSKKIMPGITHWQSPSYFAYYASSTSVAGFLGEMLNAGLSVVGFTWLTSP 166
Query: 559 ACTELEVLVMNWLGKALGLPEEFLNCSPGPGGGIIQSTASEATLVSILVAKRKMINHWQS 618
A TELE++V++WL K L LP+ FL S G GGG+IQ T EA LV +L A+ +++
Sbjct: 167 AATELEIIVLDWLAKLLQLPDHFL--STGNGGGVIQGTGCEAVLVVVLAARDRILKK--- 221
Query: 619 KNPSLTENDIRNKLVAYTSDQSNSSVEKSAIIGDV---PVRQLRSDD--NGVLRGDALLT 673
+ +LV Y SDQ++SS K+ +IG + +R L++D N + ++L
Sbjct: 222 -----VGKTLLPQLVVYGSDQTHSSFRKACLIGGIHEENIRLLKTDSSTNYGMPPESLEE 276
Query: 674 AVKEDLAKGLIPCCLIATLGTTGTCAFDNLEELGPICQEYNIWLHVDAAYAGSALLLPEY 733
A+ DLAKG IP + AT+GTT + A D L LG I ++Y IWLHVDAAYAG+A + PEY
Sbjct: 277 AISHDLAKGFIPFFICATVGTTSSAAVDPLVPLGNIAKKYGIWLHVDAAYAGNACICPEY 336
Query: 734 AHLKRGLEYVDSFDFNTHKWLLVNFDCSAMW 764
G+E DSF+ N HKWL N CS +W
Sbjct: 337 RKFIDGIENADSFNMNAHKWLFANQTCSPLW 367
Score = 97.1 bits (241), Expect = 5e-21
Identities = 51/139 (36%), Positives = 74/139 (53%), Gaps = 9/139 (6%)
Query: 126 FQHWQIPLGRRFRALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEQDDRFELVCPPS 185
++ WQI L RRFR+LKLWM LR YG + L+ ++R H++LAK F D V QD FE+V
Sbjct: 398 YKDWQISLSRRFRSLKLWMVLRLYGSENLRNFIRDHVNLAKHFEDYVAQDPSFEVVTTRY 457
Query: 186 MGLVCFRLKVRFWDKLDNLFGTISFGDNDLNKAVYDRIIARKVIYIVKGSFQDRLFMRFA 245
LVCFRL D+ N+ N+ + + + I+I + + +RFA
Sbjct: 458 FSLVCFRLAPVDGDEDQC---------NERNRELLAAVNSTGKIFISHTALSGKFVLRFA 508
Query: 246 ICSSQTEESDVQLGWNEIR 264
+ + TEE V W I+
Sbjct: 509 VGAPLTEEKHVTEAWQIIQ 527
>gnl|CDD|99743 cd06450, DOPA_deC_like, DOPA decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD correspond to DOPA/tyrosine decarboxylase
(DDC), histidine decarboxylase (HDC), and glutamate
decarboxylase (GDC). DDC is active as a dimer and
catalyzes the decarboxylation of tyrosine. GDC catalyzes
the decarboxylation of glutamate and HDC catalyzes the
decarboxylation of histidine.
Length = 345
Score = 266 bits (683), Expect = 1e-82
Identities = 95/238 (39%), Positives = 135/238 (56%), Gaps = 12/238 (5%)
Query: 527 AYFPTGSSYPSIVGDMLSGAFGLIGFSWLSSPACTELEVLVMNWLGKALGLPEEFLNCSP 586
A F T P+++ +ML+ A I F+W SPA TE+E V+NWL K GLP
Sbjct: 3 AGFVTTMDPPALLLEMLTSAKNAIDFTWDESPAATEMEAEVVNWLAKLFGLP-------S 55
Query: 587 GPGGGIIQSTASEATLVSILVAKRKMINHWQSKNPSLTENDIRNKLVAYTSDQSNSSVEK 646
G+ S SE+ L+++L A+ + ++ +KLV SDQ++ SVEK
Sbjct: 56 EDADGVFTSGGSESNLLALLAARDRARKRLKAGGG-----RGIDKLVIVCSDQAHVSVEK 110
Query: 647 SAIIGDVPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLIATLGTTGTCAFDNLEEL 706
+A DV VR + D++G + +AL A+ ED A+GL P ++AT GTT T A D LEE+
Sbjct: 111 AAAYLDVKVRLVPVDEDGRMDPEALEAAIDEDKAEGLNPIMVVATAGTTDTGAIDPLEEI 170
Query: 707 GPICQEYNIWLHVDAAYAGSALLLPEYAHLKRGLEYVDSFDFNTHKWLLVNFDCSAMW 764
+ ++Y++WLHVDAAY G L PE HL G+E VDS + HK+ LV CSA+
Sbjct: 171 ADLAEKYDLWLHVDAAYGGFLLPFPEPRHLDFGIERVDSISVDPHKYGLVPLGCSAVL 228
Score = 104 bits (263), Expect = 2e-24
Identities = 40/130 (30%), Positives = 61/130 (46%), Gaps = 13/130 (10%)
Query: 137 FRALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEQDDRFELVCPPSMGLVCFRLKVR 196
RALKLW TLR +G G ++ + + LAK A+L+ D FEL+ P++ LVCFRLK
Sbjct: 229 VRALKLWATLRRFGRDGYGEHIDRIVDLAKYLAELIRADPGFELLGEPNLSLVCFRLKP- 287
Query: 197 FWDKLDNLFGTISFGDNDLNKAVYDRIIARKVIYIVKGSFQDRLFMRFAICSSQTEESDV 256
S ++LN + DR+ R ++ + +RF + + T D
Sbjct: 288 ------------SVKLDELNYDLSDRLNERGGWHVPATTLGGPNVLRFVVTNPLTTRDDA 335
Query: 257 QLGWNEIRTA 266
+I A
Sbjct: 336 DALLEDIERA 345
>gnl|CDD|223154 COG0076, GadB, Glutamate decarboxylase and related PLP-dependent
proteins [Amino acid transport and metabolism].
Length = 460
Score = 182 bits (465), Expect = 2e-50
Identities = 86/305 (28%), Positives = 132/305 (43%), Gaps = 24/305 (7%)
Query: 463 IDFIADYVDNIRERPVLPSVEPGYLASLVPGEMPEEGEDWRHIMRDMN-TVIMPGITHWQ 521
ID + D +R S+ P + A PE+GE ++ ++ +I +
Sbjct: 1 IDGLIDKDMLNSKRYSGDSLSPLFGALSDSRMAPEKGEPLEEVLDELAELLIKDELYLDG 60
Query: 522 SPQFNAYFPTGSSYPSIVGDMLSGAFGLIGFSWLSSPACTELEVLVMNWLGKALGLPEEF 581
P+ N + P + ++L A SPA ELE V+N L LG PEE
Sbjct: 61 HPRANLAGFCPTRVPPVAAELLVSALNKNLGDPDESPAAAELEERVVNMLSDLLGAPEEA 120
Query: 582 LNCSPGPGGGIIQSTASEATLVSILVAKRKMINHW--QSKNPSLTENDIRNKLVAYTSDQ 639
G S +EA L+++L A+ W ++ S N S+
Sbjct: 121 S--------GTFTSGGTEANLLALLAAR----ERWRKRALAESGKPGGKPN---IVCSET 165
Query: 640 SNSSVEKSAIIGDVPVRQLRSD-DNGVLRGDALLTAVKEDLAKGLIPCCLIATLGTTGTC 698
++ S EK+A + +R++ + + + DAL A+ E+ G ++ T GTT T
Sbjct: 166 AHFSFEKAARYLGLGLRRVPTVPTDYRIDVDALEEAIDENTIGG----VVVGTAGTTDTG 221
Query: 699 AFDNLEELGPICQEYNIWLHVDAAYAGSALLLPEYAHLK-RGLEYVDSFDFNTHKWLLVN 757
+ D++EEL I +EY IWLHVDAA+ G L E GLE VDS + HK+ L
Sbjct: 222 SIDDIEELADIAEEYGIWLHVDAAFGGFLLPFLEPDGRWDFGLEGVDSITVDGHKYGLAP 281
Query: 758 FDCSA 762
C
Sbjct: 282 IGCGV 286
Score = 66.6 bits (163), Expect = 2e-11
Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 126 FQHWQIPLGRRFRALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEQDDRFELVCPPS 185
F GR+ AL L+ LR G +G + L + + LA+ A+ +E+ FELV P
Sbjct: 314 FTILGSRPGRQ--ALALYANLRRLGREGYRKLLDRTLELARYLAEELEKLGDFELVNEPE 371
Query: 186 MGLVCFRLK 194
+ +V FRLK
Sbjct: 372 LPIVAFRLK 380
>gnl|CDD|163511 TIGR03799, NOD_PanD_pyr, putative pyridoxal-dependent aspartate
1-decarboxylase. This enzyme is proposed here to be a
form of aspartate 1-decarboxylase, pyridoxal-dependent,
that represents a non-orthologous displacement to the
more widely distributed pyruvoyl-dependent form
(TIGR00223). Aspartate 1-decarboxylase makes
beta-alanine, used usually in pathothenate biosynthesis,
by decarboxylation from asparatate. A number of species
with the PanB and PanC enzymes, however, lack PanD. This
protein family occurs in a number of Proteobacteria that
lack PanD. This enzyme family appears to be a
pyridoxal-dependent enzyme (see pfam00282). The family
was identified by Partial Phylogenetic Profiling;
members in Geobacter sulfurreducens, G. metallireducens,
and Pseudoalteromonas atlantica are clustered with the
genes for PanB and PanC. We suggest the gene symbol panP
(panthothenate biosynthesis enzyme, Pyridoxal-dependent)
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pantothenate and coenzyme A].
Length = 522
Score = 75.5 bits (186), Expect = 4e-14
Identities = 43/130 (33%), Positives = 65/130 (50%), Gaps = 3/130 (2%)
Query: 630 NKLVAYTSDQSNSSVEKSAI---IGDVPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPC 686
+ L S++ + S+ K+A IG + +++D N + DAL E + + P
Sbjct: 208 DGLAILVSERGHYSLGKAADVLGIGRDNLIAIKTDANNRIDVDALRDKCAELAEQNIKPL 267
Query: 687 CLIATLGTTGTCAFDNLEELGPICQEYNIWLHVDAAYAGSALLLPEYAHLKRGLEYVDSF 746
++ GTT T D L+E+ I QE HVDAA+ G+ LL Y HL +G+E DS
Sbjct: 268 AIVGVAGTTETGNIDPLDEMADIAQELGCHFHVDAAWGGATLLSNTYRHLLKGIERADSV 327
Query: 747 DFNTHKWLLV 756
+ HK L V
Sbjct: 328 TIDAHKQLYV 337
Score = 38.1 bits (89), Expect = 0.017
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 16/82 (19%)
Query: 139 ALKLWMTLRSYGLKGLQAYLRKHISLAKKFADLVEQDDRFELVCPPSMGLVCFR------ 192
A+ ++ L G KG + + + I AK FADL++Q FELV P + L+ +R
Sbjct: 383 AMLVYAGLHIIGRKGYELLIDQSIEKAKYFADLIQQQPDFELVTEPELCLLTYRYVPEEV 442
Query: 193 ----------LKVRFWDKLDNL 204
+ + + LD L
Sbjct: 443 QQALAKADEEQREKINELLDRL 464
>gnl|CDD|99742 cd01494, AAT_I, Aspartate aminotransferase (AAT) superfamily (fold
type I) of pyridoxal phosphate (PLP)-dependent enzymes.
PLP combines with an alpha-amino acid to form a compound
called a Schiff base or aldimine intermediate, which
depending on the reaction, is the substrate in four
kinds of reactions (1) transamination (movement of amino
groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
Structure and sequence analysis has revealed that the
PLP dependent enzymes can be classified into four major
groups of different evolutionary origin: aspartate
aminotransferase superfamily (fold type I), tryptophan
synthase beta superfamily (fold type II), alanine
racemase superfamily (fold type III), and D-amino acid
superfamily (fold type IV) and Glycogen phophorylase
family (fold type V).
Length = 170
Score = 64.7 bits (158), Expect = 4e-12
Identities = 36/180 (20%), Positives = 53/180 (29%), Gaps = 27/180 (15%)
Query: 586 PGPGGGIIQSTASEATLVSILVAKRKMINHWQSKNPSLTENDIRNKLVAYTSDQSNSSVE 645
PG + + + A ++L + S
Sbjct: 15 PGNDKAVFVPSGTGANEAALLALLGP-------------------GDEVIVDANGHGSRY 55
Query: 646 KSAI-IGDVPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLIATLGTTGTCAFDNLE 704
A + + DD G L A+ E+L ++ T TT L+
Sbjct: 56 WVAAELAGAKPVPVPVDDAG---YGGLDVAILEELKAKPNVALIVITPNTTSGGVLVPLK 112
Query: 705 ELGPICQEYNIWLHVDAAYAGSALLLPEYAHLKRGLEYVDSFDFNTHKWLLVNFDCSAMW 764
E+ I +EY I L VDAA AG A P D F+ HK L +
Sbjct: 113 EIRKIAKEYGILLLVDAASAGGASPAPGV---LIPEGGADVVTFSLHKNLGGE-GGGVVI 168
>gnl|CDD|234361 TIGR03812, tyr_de_CO2_Arch, tyrosine decarboxylase MnfA. Members
of this protein family are the archaeal form, MnfA, of
tyrosine decarboxylase, and are involved in methanofuran
biosynthesis. Members show clear homology to the
Enterococcus form, Tdc, that is involved in tyrosine
decarboxylation for resistance to acidic conditions
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 373
Score = 65.4 bits (160), Expect = 3e-11
Identities = 50/191 (26%), Positives = 81/191 (42%), Gaps = 34/191 (17%)
Query: 558 PACTELEVLVMNWLGKALGLPEEFLNCSPGPGGGIIQSTASEATLVSILVAKRKMINHWQ 617
P ++E V+ LG L LP+ G I S +EA + A R N +
Sbjct: 55 PGTKKIEEEVVGSLGNLLHLPD---------AYGYIVSGGTEANIQ----AVRAAKNLAR 101
Query: 618 SKNPSLTENDIRNKLVAYTSDQSNSSVEKSAIIGDVPVRQLRSDDNGVLRGDALLTAVKE 677
+ ++ S ++ S EK+A + + +R D++ D + V++
Sbjct: 102 EEKR-------TPNIIVPES--AHFSFEKAAEMLGLELRYAPLDED--YTVD--VKDVED 148
Query: 678 DLAKGLIPCCLIATLGTTGTCAFDNLEELGPICQEYNIWLHVDAAYAGSALLLPEYAHLK 737
+ I ++ GTT D++EEL I E I+LHVDAA+ G ++P LK
Sbjct: 149 LIDDNTI--GIVGIAGTTELGQIDDIEELSKIALENGIYLHVDAAFGG--FVIP---FLK 201
Query: 738 RGLEYVDSFDF 748
+G FDF
Sbjct: 202 KGYNPPP-FDF 211
>gnl|CDD|237409 PRK13520, PRK13520, L-tyrosine decarboxylase; Provisional.
Length = 371
Score = 58.4 bits (142), Expect = 7e-09
Identities = 53/196 (27%), Positives = 86/196 (43%), Gaps = 31/196 (15%)
Query: 558 PACTELEVLVMNWLGKALGLPEEFLNCSPGPGGGIIQSTASEATLVSILVAKRKMINHWQ 617
P +LE + LG+ L LP+ G I S +EA + ++ R N +
Sbjct: 55 PGTAKLEEEAVEMLGELLHLPD---------AYGYITSGGTEANIQAV----RAARNLAK 101
Query: 618 SKNPSLTENDIRNKLVAYTSDQSNSSVEKSAIIGDVPVRQLRSDDNGVLRGDALLTAVKE 677
++ P +V S ++ S +K+A + V +R+ DD+ R D + AV++
Sbjct: 102 AEKP---------NIVVPES--AHFSFDKAADMLGVELRRAPLDDD--YRVD--VKAVED 146
Query: 678 DLAKGLIPCCLIATLGTTGTCAFDNLEELGPICQEYNIWLHVDAAYAGSAL-LLPEYAHL 736
+ I ++ GTT D + EL I E I+LHVDAA+ G + L + +
Sbjct: 147 LIDDNTI--GIVGIAGTTELGQVDPIPELSKIALENGIFLHVDAAFGGFVIPFLDDPPNF 204
Query: 737 KRGLEYVDSFDFNTHK 752
L VDS + HK
Sbjct: 205 DFSLPGVDSITIDPHK 220
>gnl|CDD|235068 PRK02769, PRK02769, histidine decarboxylase; Provisional.
Length = 380
Score = 57.0 bits (138), Expect = 2e-08
Identities = 36/125 (28%), Positives = 62/125 (49%), Gaps = 6/125 (4%)
Query: 633 VAYTSDQSNSSVEKSAIIGDVPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLIATL 692
Y S ++ SV K A + + R + S NG + D L++ +KE+ + I + A +
Sbjct: 112 TLYYSKDTHYSVSKIARLLRIKSRVITSLPNGEIDYDDLISKIKENKNQPPI---IFANI 168
Query: 693 GTTGTCAFDNLEELGPICQEYNI---WLHVDAAYAGSALLLPEYAHLKRGLEYVDSFDFN 749
GTT T A DN++E+ I ++ I ++H DAA +G L + +DS +
Sbjct: 169 GTTMTGAIDNIKEIQEILKKIGIDDYYIHADAALSGMILPFVNNPPPFSFADGIDSIAIS 228
Query: 750 THKWL 754
HK++
Sbjct: 229 GHKFI 233
>gnl|CDD|216367 pfam01212, Beta_elim_lyase, Beta-eliminating lyase.
Length = 288
Score = 43.0 bits (102), Expect = 3e-04
Identities = 29/119 (24%), Positives = 43/119 (36%), Gaps = 14/119 (11%)
Query: 648 AIIGDVPVRQLRSDDNGVLRGDALLTAVKEDLAK-----GLIPCCLIATLGTTGTC-AFD 701
A +G L + G L + L A++ GLI G + +
Sbjct: 91 AELGGAQPVPLPGAEAGKLDLEDLEAAIRPVGDIHFPPTGLI-SLENTHNSAGGQVVSLE 149
Query: 702 NLEELGPICQEYNIWLHVDAA---YAGSALLLPEYAHLKRGLEYVDSFDFNTHKWLLVN 757
L E+ I +E+ I LH+D A A AL + +K Y DS + K L
Sbjct: 150 ELREIRAIAREHGIPLHLDGARLANAAVALGVI----VKEITSYADSVSMSLSKGLGAP 204
>gnl|CDD|211833 TIGR03531, selenium_SpcS, O-phosphoseryl-tRNA(Sec) selenium
transferase. In the archaea and eukaryotes, the
conversion of the mischarged serine to selenocysteine
(Sec) on its tRNA is accomplished in two steps. This
enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase,
acts second, after a phosphophorylation step catalyzed
by a homolog of the bacterial SelA protein [Protein
synthesis, tRNA aminoacylation].
Length = 444
Score = 43.5 bits (103), Expect = 3e-04
Identities = 30/105 (28%), Positives = 49/105 (46%), Gaps = 21/105 (20%)
Query: 665 VLRGDALLTAVK------EDLAKGLIPCCLIATLGTTGTC----AFDNLEELGPICQEYN 714
VL GD L T V+ E++ I C L +T +C + D++EE+ IC Y+
Sbjct: 181 VLDGDELTTDVEDIERAIEEIGPDNILCVL-----STTSCFAPRSPDDIEEIAKICANYD 235
Query: 715 IWLHVDAAYAGSALLLPEYAH-LKRGLEY--VDSFDFNTHKWLLV 756
I V+ AY L +Y + + ++ VD+ +T K +V
Sbjct: 236 IPHIVNNAY---GLQSNKYMELINKAIKVGRVDAVVSSTDKNFMV 277
>gnl|CDD|224029 COG1104, NifS, Cysteine sulfinate desulfinase/cysteine desulfurase
and related enzymes [Amino acid transport and
metabolism].
Length = 386
Score = 41.8 bits (99), Expect = 0.001
Identities = 31/117 (26%), Positives = 51/117 (43%), Gaps = 26/117 (22%)
Query: 624 TEND---IRNKLVAYTSDQSN-----SSVEKSAIIGDVPVRQLRS----------DDNGV 665
TE++ I+ +AY + Q S++E A++ R L D NG+
Sbjct: 71 TESNNLAIKGAALAYRNAQKGKHIITSAIEHPAVLN--TCRYLERQGFEVTYLPVDSNGL 128
Query: 666 LRGDALLTAVKEDLAKGLIPCCLIATLGTTGTCAFDNLEELGPICQEYNIWLHVDAA 722
+ + L A++ D L+ ++ TGT + E+G IC+E I HVDA
Sbjct: 129 VDLEQLEEALRPDTI--LV--SIMHANNETGTIQ--PIAEIGEICKERGILFHVDAV 179
>gnl|CDD|223594 COG0520, csdA, Selenocysteine lyase/Cysteine desulfurase
[Posttranslational modification, protein turnover,
chaperones].
Length = 405
Score = 40.4 bits (95), Expect = 0.003
Identities = 30/101 (29%), Positives = 45/101 (44%), Gaps = 12/101 (11%)
Query: 655 VRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLIATLGTTGTCAFDNLEELGPICQEYN 714
VR + DD+G+L DAL + K L+ L TGT ++E+ + E+
Sbjct: 139 VRVIPLDDDGLLDLDALEKLITPK-TK-LV--ALSHVSNVTGTVN--PVKEIAELAHEHG 192
Query: 715 IWLHVDAAYAGSALLLPEYAHLKRGLEYVDSFDFNTHKWLL 755
+ VDAA A L + ++ D F+ HKWLL
Sbjct: 193 ALVLVDAAQAAGHLPID----VQE--LGCDFLAFSGHKWLL 227
>gnl|CDD|224919 COG2008, GLY1, Threonine aldolase [Amino acid transport and
metabolism].
Length = 342
Score = 38.8 bits (91), Expect = 0.008
Identities = 26/96 (27%), Positives = 38/96 (39%), Gaps = 18/96 (18%)
Query: 663 NGVLRGDALLTAVKEDLA----KGLIPCCLIATLGTTGTC-AFDNLEELGPICQEYNIWL 717
+G L + + A++ D L L T GT D LE + +C+E+ + L
Sbjct: 109 DGKLTPEDVEAAIRPDDIHHAPTPLA--VLENTATEGGTVYPLDELEAISAVCKEHGLPL 166
Query: 718 HVDAAYAGSAL-----LLPEYAHLKRGLEYVDSFDF 748
H+D A +AL L YVDS F
Sbjct: 167 HMDGARLANALVALGVALKTIK------SYVDSVSF 196
>gnl|CDD|218796 pfam05889, SLA_LP_auto_ag, Soluble liver antigen/liver pancreas
antigen (SLA/LP autoantigen). This family consists of
several eukaryotic and archaeal proteins which are
related to the human soluble liver antigen/liver
pancreas antigen (SLA/LP autoantigen). Autoantibodies
are a hallmark of autoimmune hepatitis, but most are not
disease specific. Autoantibodies to soluble liver
antigen (SLA) and to liver and pancreas antigen (LP)
have been described as disease specific, occurring in
about 30% of all patients with autoimmune hepatitis. The
function of SLA/LP is unknown, however, it has been
suggested that the protein may function as a serine
hydroxymethyltransferase and may be an important enzyme
in the thus far poorly understood selenocysteine
pathway. The archaeal sequences Methanopyrus kandleri
spcS and MK0229 are annotated as being pyridoxal
phosphate-dependent enzymes.
Length = 386
Score = 37.2 bits (86), Expect = 0.028
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 665 VLRGDALLTAVK--EDLAKGLIPCCLIATLGTTGTCAF----DNLEELGPICQEYNIWLH 718
VL GD L+T V E + + ++A L TT +C D ++E+ IC EY++
Sbjct: 131 VLEGDYLITDVNDVETIIEEKGEEVILAVLSTT-SCFAPRSPDRVKEIAKICAEYDVPHL 189
Query: 719 VDAAYA 724
V+ AY
Sbjct: 190 VNGAYG 195
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 36.9 bits (86), Expect = 0.032
Identities = 28/97 (28%), Positives = 41/97 (42%), Gaps = 6/97 (6%)
Query: 633 VAYTSDQSNSSVEKSAIIGDVPVRQ--LRSDDNGVLRGDALLTAVKEDLA--KGLIPCCL 688
+ S + + V + L S ++ L DAL A+KE K ++
Sbjct: 92 AILVPAPTYPSYIRIFRLAGGEVVRYPLYSSNDFHLDFDALEAALKEATEGNKVVLHTSP 151
Query: 689 IATLGTTGTCAFDNLEELGPICQEYNIWLHVDAAYAG 725
GT T LE+L + +E+NI L VD AYAG
Sbjct: 152 HNPTGTVATLEE--LEKLLDLAKEHNILLLVDEAYAG 186
>gnl|CDD|215829 pfam00266, Aminotran_5, Aminotransferase class-V. This domain is
found in amino transferases, and other enzymes including
cysteine desulphurase EC:4.4.1.-.
Length = 370
Score = 34.5 bits (80), Expect = 0.17
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 655 VRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLIATLGTTGTCAFDNLEELGPICQEYN 714
VR + D NG+L DAL + L+ ++ + TGT +EE+G + EY
Sbjct: 116 VRVIPVDPNGLLDLDALEKLLTPRTK--LVAITHVSNV--TGTVNP--VEEIGKLAHEYG 169
Query: 715 IWLHVDAA 722
+ VDAA
Sbjct: 170 ALVVVDAA 177
>gnl|CDD|130848 TIGR01788, Glu-decarb-GAD, glutamate decarboxylase. This model
represents the pyridoxal phosphate-dependent glutamate
(alpha) decarboxylase found in bacteria (low and hi-GC
gram positive, proteobacteria and cyanobacteria),
plants, fungi and at least one archaon (Methanosarcina).
The product of the enzyme is gamma-aminobutyrate (GABA).
Length = 431
Score = 34.7 bits (80), Expect = 0.18
Identities = 57/213 (26%), Positives = 90/213 (42%), Gaps = 37/213 (17%)
Query: 558 PACTELEVLVMNWLGKALGLP---EEFLNCSPGPGGGIIQSTASEATLVSILVAKRKMIN 614
P E+E +N L P E + S I S SEA ++ L K +
Sbjct: 76 PQTAEIENRCVNMLADLWHAPAKDAEAVGTS------TIGS--SEAIMLGGLAMKWR--- 124
Query: 615 HWQSKNPSLTENDIRNKLVAYTSDQSNSSV--EKSAIIGDVPVRQLRSD-DNGVLRGDAL 671
W+ + + + + LV SN V EK A DV +R++ D V+ + +
Sbjct: 125 -WRKRMEAAGKPTDKPNLVM----GSNVQVCWEKFARYFDVELREVPMDPGRYVIDPEQV 179
Query: 672 LTAVKEDLAKGLIPCCLIATLGTTGTCAFDNLEELGPICQEYN------IWLHVDAAYAG 725
+ AV E+ ++ LGTT T +++++ L EYN I +HVDAA G
Sbjct: 180 VEAVDEN------TIGVVCILGTTYTGEYEDVKALNDALDEYNAKTGWDIPIHVDAASGG 233
Query: 726 --SALLLPEYAHLKRGLEYVDSFDFNTHKWLLV 756
+ + P+ R L V S + + HK+ LV
Sbjct: 234 FIAPFVYPDLEWDFR-LPRVKSINVSGHKYGLV 265
Score = 30.8 bits (70), Expect = 2.9
Identities = 11/48 (22%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 148 SYGLKGLQAYLRKHISLAKKFADLVEQDDRFELVCP-PSMGLVCFRLK 194
G +G + ++ + +A+ A+ + + FE++ + LV F+LK
Sbjct: 318 RLGREGYRKIMQNSLDVARYLAEEIAKLGPFEIISDGSGIPLVAFKLK 365
>gnl|CDD|131032 TIGR01977, am_tr_V_EF2568, cysteine desulfurase family protein.
This model describes a subfamily of probable pyridoxal
phosphate-dependent enzymes in the aminotransferase
class V family. Related families contain members active
as cysteine desulfurases, selenocysteine lyases, or
both. The members of this family form a distinct clade
and all are shorter at the N-terminus. The function of
this subfamily is unknown [Unknown function, Enzymes of
unknown specificity].
Length = 376
Score = 33.9 bits (78), Expect = 0.29
Identities = 23/99 (23%), Positives = 45/99 (45%), Gaps = 14/99 (14%)
Query: 658 LRSDDNGVLRGDALLTAVKEDLAKGLIPCCLIATLGTTGTCAFDNLEELGPICQEYNIWL 717
++ D+ G++ + + A+K + ++ + + T +EE+G + QE I+
Sbjct: 117 VKCDNEGLISPERIKRAIKTN------TKLIVVSHASNVTGTILPIEEIGELAQENGIFF 170
Query: 718 HVDAA-YAGSALLLPEYAHLKRGLEYVDSFDFNTHKWLL 755
+DAA AG ++P + +D F HK LL
Sbjct: 171 ILDAAQTAG---VIP----IDMTELAIDMLAFTGHKGLL 202
>gnl|CDD|99737 cd00613, GDC-P, Glycine cleavage system P-protein, alpha- and
beta-subunits. This family consists of Glycine cleavage
system P-proteins EC:1.4.4.2 from bacterial, mammalian
and plant sources. The P protein is part of the glycine
decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also
annotated as glycine cleavage system or glycine
synthase. GDC consists of four proteins P, H, L and T.
The reaction catalysed by this protein is: Glycine +
lipoylprotein <=> S-aminomethyldihydrolipoylprotein +
CO2. Alpha-beta-type dimers associate to form an
alpha(2)beta(2) tetramer, where the alpha- and
beta-subunits are structurally similar and appear to
have arisen by gene duplication and subsequent
divergence with a loss of one active site. The members
of this CD are widely dispersed among all three forms of
cellular life.
Length = 398
Score = 32.6 bits (75), Expect = 0.89
Identities = 32/155 (20%), Positives = 58/155 (37%), Gaps = 31/155 (20%)
Query: 570 WLGKALGLPEEFLNCSPGPGGGIIQSTASEATLVSILVAKRKMINHWQSKNPSLTENDIR 629
L + G+ N S A+EA ++ + A K R
Sbjct: 72 MLCELTGMD--VANASLQDEAT----AAAEAAGLAAIRAYHK-----------------R 108
Query: 630 NK-LVAYTSDQSNSSVEKSAIIG-DVPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCC 687
NK LV ++ +N +V ++ + V ++ SD+ G + +AL V E++A
Sbjct: 109 NKVLVPDSAHPTNPAVARTRGEPLGIEVVEVPSDEGGTVDLEALKEEVSEEVA------A 162
Query: 688 LIATLGTTGTCAFDNLEELGPICQEYNIWLHVDAA 722
L+ T D ++E+ I ++VD
Sbjct: 163 LMVQYPNTLGVFEDLIKEIADIAHSAGALVYVDGD 197
>gnl|CDD|216133 pfam00815, Histidinol_dh, Histidinol dehydrogenase.
Length = 413
Score = 32.3 bits (74), Expect = 0.92
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 4/25 (16%)
Query: 283 MGGAQAIA----GTESSGPADQVLG 303
GGAQAIA GTE+ D++ G
Sbjct: 172 AGGAQAIAAMAYGTETVPKVDKIFG 196
>gnl|CDD|99748 cd06502, TA_like, Low-specificity threonine aldolase (TA). This
family belongs to pyridoxal phosphate (PLP)-dependent
aspartate aminotransferase superfamily (fold I). TA
catalyzes the conversion of L-threonine or
L-allo-threonine to glycine and acetaldehyde in a
secondary glycine biosynthetic pathway.
Length = 338
Score = 32.3 bits (74), Expect = 0.97
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 11/53 (20%)
Query: 701 DNLEELGPICQEYNIWLHVDA-----AYAGSALLLPEYAHLKRGLEYVDSFDF 748
D L+ + + +E + LH+D A A + L Y VDS F
Sbjct: 146 DELKAISALAKENGLPLHLDGARLANAAAALGVALKTYK------SGVDSVSF 192
>gnl|CDD|237103 PRK12447, PRK12447, histidinol dehydrogenase; Reviewed.
Length = 426
Score = 32.2 bits (74), Expect = 1.0
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 4/26 (15%)
Query: 282 VMGGAQAIA----GTESSGPADQVLG 303
V+GG QA+A GTE+ P D ++G
Sbjct: 178 VLGGVQAVAAMAYGTETIKPVDMLVG 203
>gnl|CDD|232808 TIGR00069, hisD, histidinol dehydrogenase. This model describes a
polypeptide sequence catalyzing the final step in
histidine biosynthesis, found sometimes as an
independent protein and sometimes as a part of a
multifunctional protein [Amino acid biosynthesis,
Histidine family].
Length = 393
Score = 32.1 bits (74), Expect = 1.1
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 4/25 (16%)
Query: 283 MGGAQAIA----GTESSGPADQVLG 303
+GGAQAIA GTE+ D+++G
Sbjct: 153 VGGAQAIAALAYGTETVPKVDKIVG 177
>gnl|CDD|234614 PRK00074, guaA, GMP synthase; Reviewed.
Length = 511
Score = 31.9 bits (74), Expect = 1.2
Identities = 13/24 (54%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 571 LGKALGLPEEFLNCS--PGPGGGI 592
LG LGLPEE + PGPG I
Sbjct: 373 LGLELGLPEEIVYRHPFPGPGLAI 396
>gnl|CDD|151388 pfam10941, DUF2620, Protein of unknown function DUF2620. This is a
bacterial family of proteins with unknown function.
Length = 117
Score = 30.4 bits (69), Expect = 1.3
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 441 LTKASPVTPPPNEEFREF---GKAAIDFIADYVDNI 473
T A P PP EE + GK A F D+V++
Sbjct: 73 ATIAMPGKPPKEEEIEKAVDEGKKAFGFTIDHVEHA 108
>gnl|CDD|181320 PRK08247, PRK08247, cystathionine gamma-synthase; Reviewed.
Length = 366
Score = 32.0 bits (73), Expect = 1.4
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 143 WMTLRSYGLKGLQAYLRKHISLAKKFADLVEQDDRFELVCPPSM-GLVCFRLKVRFW 198
W+ +R G+K L +R+H AK A + + V P G++ FRL+ W
Sbjct: 238 WLLIR--GMKTLALRMRQHEENAKAIAAFLNEQPGVTDVLYPGRGGMLSFRLQDEEW 292
>gnl|CDD|99747 cd06454, KBL_like, KBL_like; this family belongs to the pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The major groups in this CD
corresponds to serine palmitoyltransferase (SPT),
5-aminolevulinate synthase (ALAS),
8-amino-7-oxononanoate synthase (AONS), and
2-amino-3-ketobutyrate CoA ligase (KBL). SPT is
responsible for the condensation of L-serine with
palmitoyl-CoA to produce 3-ketodihydrospingosine, the
reaction of the first step in sphingolipid biosynthesis.
ALAS is involved in heme biosynthesis; it catalyzes the
synthesis of 5-aminolevulinic acid from glycine and
succinyl-coenzyme A. AONS catalyses the decarboxylative
condensation of l-alanine and pimeloyl-CoA in the first
committed step of biotin biosynthesis. KBL catalyzes the
second reaction step of the metabolic degradation
pathway for threonine converting 2-amino-3-ketobutyrate,
to glycine and acetyl-CoA. The members of this CD are
widely found in all three forms of life.
Length = 349
Score = 31.4 bits (72), Expect = 1.7
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 688 LIATLG---TTGTCAFDNLEELGPICQEYNIWLHVDAAYA 724
LI T G G A L EL + ++Y L VD A++
Sbjct: 135 LIVTEGVYSMDGDIA--PLPELVDLAKKYGAILFVDEAHS 172
>gnl|CDD|233169 TIGR00884, guaA_Cterm, GMP synthase (glutamine-hydrolyzing),
C-terminal domain or B subunit. This protein of purine
de novo biosynthesis is well-conserved. However, it
appears to split into two separate polypeptide chains in
most of the Archaea. This C-terminal region would be the
larger subunit [Purines, pyrimidines, nucleosides, and
nucleotides, Purine ribonucleotide biosynthesis].
Length = 311
Score = 31.2 bits (71), Expect = 1.8
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 571 LGKALGLPEEFLNCSPGPGGGI 592
LGK LGLPEE + P PG G+
Sbjct: 173 LGKELGLPEEIVWRHPFPGPGL 194
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate
dehydrogenase. Shikimate dehydrogenase (DH) is an amino
acid DH family member. Shikimate pathway links
metabolism of carbohydrates to de novo biosynthesis of
aromatic amino acids, quinones and folate. It is
essential in plants, bacteria, and fungi but absent in
mammals, thus making enzymes involved in this pathway
ideal targets for broad spectrum antibiotics and
herbicides. Shikimate DH catalyzes the reduction of
3-hydroshikimate to shikimate using the cofactor NADH.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 30.3 bits (69), Expect = 1.9
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 2/57 (3%)
Query: 411 EVPGNKSFRGHSENLITLIIASDLIINSIPL-TKASPVTPPPNEEFREFGKAAIDFI 466
E G +L L+ +DLIIN+ P+ K P P + G D +
Sbjct: 61 ERFGELGIAIAYLDLEELLAEADLIINTTPVGMKPGDELPLPPSLLKP-GGVVYDVV 116
>gnl|CDD|132443 TIGR03402, FeS_nifS, cysteine desulfurase NifS. Members of this
protein family are NifS, one of several related families
of cysteine desulfurase involved in iron-sulfur (FeS)
cluster biosynthesis. NifS is part of the NIF system,
usually associated with other nif genes involved in
nitrogenase expression and nitrogen fixation. The
protein family is given a fairly broad interpretation
here. It includes a clade nearly always found in
extended nitrogen fixation genomic regions, plus a
second clade more closely related to the first than to
IscS and also part of NifS-like/NifU-like systems. This
model does not extend to a more distantly clade found in
the epsilon proteobacteria such as Helicobacter pylori,
also named NifS in the literature, built instead in
TIGR03403.
Length = 379
Score = 31.0 bits (71), Expect = 2.7
Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 20/94 (21%)
Query: 642 SSVEKSAIIG--------DVPVRQLRSDDNGVLRGDALLTAVKEDLAKGLIPCCLIATL- 692
++VE A++ V L D+ G L + L A+ +D A L++ +
Sbjct: 92 TAVEHPAVLSLCQHLEKQGYKVTYLPVDEEGRLDLEELRAAITDDTA-------LVSVMW 144
Query: 693 --GTTGTCAFDNLEELGPICQEYNIWLHVDAAYA 724
TGT +EE+G I +E H DA A
Sbjct: 145 ANNETGTIF--PIEEIGEIAKERGALFHTDAVQA 176
>gnl|CDD|223593 COG0519, GuaA, GMP synthase, PP-ATPase domain/subunit [Nucleotide
transport and metabolism].
Length = 315
Score = 30.6 bits (70), Expect = 2.8
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 571 LGKALGLPEEFLNCSPGPGGGI 592
LG+ LGLPEE + P PG G+
Sbjct: 177 LGRELGLPEEIVYRHPFPGPGL 198
>gnl|CDD|119329 cd06572, Histidinol_dh, Histidinol dehydrogenase, HisD, E.C
1.1.1.23. Histidinol dehydrogenase catalyzes the last
two steps in the L-histidine biosynthesis pathway, which
is conserved in bacteria, archaea, fungi, and plants.
These last two steps are (i) the NAD-dependent oxidation
of L-histidinol to L-histidinaldehyde, and (ii) the
NAD-dependent oxidation of L-histidinaldehyde to
L-histidine. In most fungi and in the unicellular
choanoflagellate Monosiga bevicollis, the HisD domain is
fused with units that catalyze the second and third
biosynthesis steps in this same pathway.
Length = 390
Score = 30.9 bits (71), Expect = 3.0
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 4/25 (16%)
Query: 283 MGGAQAIA----GTESSGPADQVLG 303
+GGAQAIA GTE+ D+++G
Sbjct: 157 VGGAQAIAALAYGTETIPKVDKIVG 181
>gnl|CDD|234853 PRK00877, hisD, bifunctional histidinal dehydrogenase/ histidinol
dehydrogenase; Reviewed.
Length = 425
Score = 30.8 bits (71), Expect = 3.0
Identities = 13/25 (52%), Positives = 17/25 (68%), Gaps = 4/25 (16%)
Query: 283 MGGAQAIA----GTESSGPADQVLG 303
+GGAQAIA GTES D+++G
Sbjct: 184 VGGAQAIAALAYGTESIPKVDKIVG 208
>gnl|CDD|223219 COG0141, HisD, Histidinol dehydrogenase [Amino acid transport and
metabolism].
Length = 425
Score = 30.6 bits (70), Expect = 3.0
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 4/25 (16%)
Query: 283 MGGAQAIA----GTESSGPADQVLG 303
+GGAQAIA GTE+ D+++G
Sbjct: 180 VGGAQAIAALAYGTETVPKVDKIVG 204
>gnl|CDD|184450 PRK14012, PRK14012, cysteine desulfurase; Provisional.
Length = 404
Score = 30.3 bits (69), Expect = 4.1
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 703 LEELGPICQEYNIWLHVDAA 722
+ +G IC+E I HVDAA
Sbjct: 163 IAAIGEICRERGIIFHVDAA 182
>gnl|CDD|240010 cd04639, CBS_pair_26, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 111
Score = 28.8 bits (65), Expect = 4.2
Identities = 23/77 (29%), Positives = 32/77 (41%), Gaps = 12/77 (15%)
Query: 298 ADQVLGEIQ---PVARAES--LGPV--DELMGDVQAIAGGKNSGPVETVLNSDTPQEVRS 350
AD +L Q PV + +G + D+L+ +A+A G PV V+ D P S
Sbjct: 16 ADALLATTQHEFPVVDGDGHLVGLLTRDDLI---RALAEGGPDAPVRGVMRRDFPTV--S 70
Query: 351 EDTPLGGVLGEESSGGC 367
L VL GG
Sbjct: 71 PSATLDAVLRLMQQGGA 87
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 29.9 bits (68), Expect = 5.2
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 12/58 (20%)
Query: 677 EDLAKGLIPCC-------LIATLG---TTGTCAFDNLEELGPICQEYNIWLHVDAAYA 724
+ L L LI T G G A L EL + ++Y L+VD A+A
Sbjct: 156 DHLEALLEEARENGARRKLIVTEGVFSMDGDIA--PLPELVELAEKYGALLYVDEAHA 211
>gnl|CDD|238955 cd01997, GMP_synthase_C, The C-terminal domain of GMP synthetase.
It contains two subdomains; the ATP pyrophosphatase
domain which closes to the N-termial and the
dimerization domain at C-terminal end. The ATP-PPase is
a twisted, five-stranded parallel beta-sheet sandwiched
between helical layers. It has a signature
nucleotide-binding motif, or P-loop, at the end of the
first-beta strand.The dimerization domain formed by the
C-terminal 115 amino acid for prokaryotic proteins. It
is adjacent to teh ATP-binding site of the ATP-PPase
subdomain. The largest difference between the primary
sequence of prokaryotic and eukaryotic GMP synthetase
map to the dimerization domain.Eukaryotic GMP synthetase
has several large insertions relative to prokaryotes.
Length = 295
Score = 29.4 bits (67), Expect = 6.0
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 571 LGKALGLPEEFLNCSPGPGGGI 592
LG+ LGLPEE + P PG G+
Sbjct: 158 LGRELGLPEEIVERHPFPGPGL 179
>gnl|CDD|221376 pfam12009, Telomerase_RBD, Telomerase ribonucleoprotein complex -
RNA binding domain. Telomeres in most organisms are
comprised of tandem simple sequence repeats. The total
length of telomeric repeat sequence at each chromosome
end is determined in a balance of sequence loss and
sequence addition. One major influence on telomere
length is the enzyme telomerase. It is a reverse
transcriptase that adds these simple sequence repeats to
chromosome ends by copying a template sequence within
the RNA component of the enzyme. The RNA binding domain
of telomerase - TRBD - is made up of twelve alpha
helices and two short beta sheets. How telomerase and
associated regulatory factors physically interact and
function with each other to maintain appropriate
telomere length is poorly understood. It is known
however that TRBD is involved in formation of the
holoenzyme (which performs the telomere extension) in
addition to recognition and binding of RNA.
Length = 136
Score = 28.7 bits (65), Expect = 6.4
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 100 LRRVYSSCLVPRGQKSLRTTVL---FHFLFQHWQIPLGRRF 137
L SS + + R +L ++LF+ IPL R F
Sbjct: 62 LGGSKSSKSLSKSDFRKRRQLLLRFLYWLFEDIVIPLIRSF 102
>gnl|CDD|223513 COG0436, COG0436, Aspartate/tyrosine/aromatic aminotransferase
[Amino acid transport and metabolism].
Length = 393
Score = 29.6 bits (67), Expect = 7.1
Identities = 7/32 (21%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 695 TGTCA-FDNLEELGPICQEYNIWLHVDAAYAG 725
TG + L+ + + +E++I + D Y
Sbjct: 176 TGAVYSKEELKAIVELAREHDIIIISDEIYEE 207
>gnl|CDD|163191 TIGR03235, DNA_S_dndA, cysteine desulfurase DndA. This model
describes DndA, a protein related to IscS and part of a
larger family of cysteine desulfurases. It is encoded,
typically, divergently from a conserved, sparsely
distributed operon for sulfur modification of DNA. This
modification system is designated dnd, after the
phenotype of DNA degradation during electrophoresis. The
system is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndB is described
as a putative ATPase [DNA metabolism,
Restriction/modification].
Length = 353
Score = 29.4 bits (66), Expect = 7.4
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 18/91 (19%)
Query: 642 SSVEKSAIIGDVPVRQLRS----------DDNGVLRGDALLTAVKEDLAKGLIPCCLIAT 691
S++E A++ P+R L D++G + D L A++ D L+ ++
Sbjct: 94 SAIEHPAVLE--PIRALERNGFTVTYLPVDESGRIDVDELADAIRPDTL--LVS--IMHV 147
Query: 692 LGTTGTCAFDNLEELGPICQEYNIWLHVDAA 722
TG+ + E+ + + + + HVDAA
Sbjct: 148 NNETGS--IQPIREIAEVLEAHEAFFHVDAA 176
>gnl|CDD|237843 PRK14869, PRK14869, putative manganese-dependent inorganic
pyrophosphatase; Provisional.
Length = 546
Score = 29.4 bits (67), Expect = 7.5
Identities = 19/53 (35%), Positives = 24/53 (45%), Gaps = 15/53 (28%)
Query: 536 PSIVGDMLSGAFGLIGFSWLS------SPACTELEVLVMNWLGKALGL-PEEF 581
P I G +L+ I LS SP TEL+ WL + G+ PEEF
Sbjct: 372 PEIAGLLLAA----I----LSDTLLFKSPTTTELDREAAEWLAEIAGIDPEEF 416
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 29.1 bits (66), Expect = 8.0
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 6/37 (16%)
Query: 461 AAIDFIADYVDNIRERPVLPSVEPGYLASLV--PGEM 495
A++D + D I+E + S++ Y+ LV PG+M
Sbjct: 76 ASVDLLLTKADEIKEE--IESLDADYV--LVDTPGQM 108
>gnl|CDD|223953 COG1022, FAA1, Long-chain acyl-CoA synthetases (AMP-forming) [Lipid
metabolism].
Length = 613
Score = 29.6 bits (67), Expect = 8.0
Identities = 36/158 (22%), Positives = 55/158 (34%), Gaps = 28/158 (17%)
Query: 593 IQSTASEATLVSILV-AKRKMI-----NHWQSKNPSLTENDIRNKLVAYTSDQSNSSVE- 645
I ST++ L IL ++ K+I P L + L+ D +VE
Sbjct: 100 IYSTSTPEQLAYILNESESKVIFVENQELLDLVLPVLEDCPKVVDLIV-IIDLVREAVEA 158
Query: 646 KSAIIGDVPVRQLRSDDNGVLRGDALLTAVK-EDLAKGLIPCCLIATLGTTGT-----CA 699
K+ ++ P + + + K +DL +I T GTTGT
Sbjct: 159 KALVLEVFPDEGISLFLIDSAGLEGRIAPPKPDDL------ATIIYTSGTTGTPKGVMLT 212
Query: 700 FDNLEELGPICQEYNIWLHVDAAYAGSALL--LPEYAH 735
NL + Q I + G +L LP AH
Sbjct: 213 HRNL-----LAQVAGIDEVLPPIGPGDRVLSFLP-LAH 244
>gnl|CDD|129937 TIGR00858, bioF, 8-amino-7-oxononanoate synthase.
7-keto-8-aminopelargonic acid synthetase is an alternate
name. This model represents 8-amino-7-oxononanoate
synthase, the BioF protein of biotin biosynthesis. This
model is based on a careful phylogenetic analysis to
separate members of this family from
2-amino-3-ketobutyrate and other related pyridoxal
phosphate-dependent enzymes. In several species,
including Staphylococcus and Coxiella, a candidate
8-amino-7-oxononanoate synthase is confirmed by location
in the midst of a biotin biosynthesis operon but scores
below the trusted cutoff of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 360
Score = 29.2 bits (66), Expect = 8.5
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 5/45 (11%)
Query: 687 CLIATLGT---TGTCAFDNLEELGPICQEYNIWLHVDAAYAGSAL 728
LI T G G A L +L + + Y WL VD A+ L
Sbjct: 148 KLIVTDGVFSMDGDIA--PLPQLVALAERYGAWLMVDDAHGTGVL 190
>gnl|CDD|99734 cd00609, AAT_like, Aspartate aminotransferase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). Pyridoxal
phosphate combines with an alpha-amino acid to form a
compound called a Schiff base or aldimine intermediate,
which depending on the reaction, is the substrate in
four kinds of reactions (1) transamination (movement of
amino groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
The major groups in this CD corresponds to Aspartate
aminotransferase a, b and c, Tyrosine, Alanine,
Aromatic-amino-acid, Glutamine phenylpyruvate,
1-Aminocyclopropane-1-carboxylate synthase,
Histidinol-phosphate, gene products of malY and cobC,
Valine-pyruvate aminotransferase and Rhizopine
catabolism regulatory protein.
Length = 350
Score = 29.2 bits (66), Expect = 9.0
Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 16/72 (22%)
Query: 661 DDNGVLRGDALLTAVKEDLAKGLI------PCCLIATLGTTGTCA-FDNLEELGPICQEY 713
++ G L LL A K K L P TG + LEEL + +++
Sbjct: 114 EEGGFLLDLELLEAAKTPKTKLLYLNNPNNP---------TGAVLSEEELEELAELAKKH 164
Query: 714 NIWLHVDAAYAG 725
I + D AYA
Sbjct: 165 GILIISDEAYAE 176
>gnl|CDD|224499 COG1583, COG1583, CRISPR system related protein, RAMP superfamily
[Defense mechanisms].
Length = 240
Score = 28.9 bits (65), Expect = 9.6
Identities = 8/51 (15%), Positives = 15/51 (29%), Gaps = 4/51 (7%)
Query: 190 CFRLKVRFWDKLDNLFGTISF----GDNDLNKAVYDRIIARKVIYIVKGSF 236
F + F F D + +A Y+ ++ I + F
Sbjct: 55 VFFISRIFPPNGIEKGSDAYFYISSPDPEFIRAFYEGLLKLPEIRLGNVKF 105
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 0.137 0.417
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 39,608,555
Number of extensions: 3944939
Number of successful extensions: 3287
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3259
Number of HSP's successfully gapped: 64
Length of query: 764
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 660
Effective length of database: 6,324,786
Effective search space: 4174358760
Effective search space used: 4174358760
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: 63 (27.9 bits)