Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_090216616.1 CV091_RS05315 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::Phaeo:GFF1160
(1158 letters)
>NCBI__GCF_002796795.1:WP_090216616.1
Length = 1135
Score = 1711 bits (4432), Expect = 0.0
Identities = 869/1136 (76%), Positives = 967/1136 (85%), Gaps = 8/1136 (0%)
Query: 24 LRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISANAAALVRDIRGHSSPGLMEVFLAE 83
LR RID TY D Q RD+L A A L A DR I AA LVRDIRGHS+PGLMEVFLAE
Sbjct: 7 LRDRIDLQTYADPEQKRDELIATAALSAEDRKAICGQAAGLVRDIRGHSAPGLMEVFLAE 66
Query: 84 YGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAPSEWGKHLGKSTSSLVNASTWALM 143
YGLSTDEGVALMCLAEALLRVPDA+TIDALIEDKIAPS+WGKHLG S+SSLVNASTWALM
Sbjct: 67 YGLSTDEGVALMCLAEALLRVPDAETIDALIEDKIAPSDWGKHLGHSSSSLVNASTWALM 126
Query: 144 LTGKVLDEKRSPVSALRGAMKRLGEPVIRTAVSRAMKEMGRQFVLGETIEGAMKRAAGME 203
LTGKVLDE RSPV ALR A+KRLGEPVIRTAV RAMKEMGRQFVLGETIE AM RA GME
Sbjct: 127 LTGKVLDEGRSPVGALRSAIKRLGEPVIRTAVGRAMKEMGRQFVLGETIESAMTRARGME 186
Query: 204 AKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAAACNSADIRQNPGISVKLSALHPR 263
KGYTYSYDMLGEAARTEADAARYHL+YS+AISAIA AC S DIR+NPGISVKLSALHPR
Sbjct: 187 DKGYTYSYDMLGEAARTEADAARYHLSYSKAISAIANACTSDDIRKNPGISVKLSALHPR 246
Query: 264 YELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEEADRLSLSLEVIEEVISDPALAGW 323
YELAQET V E+LVPRL+ALALLAKAA MGLNVDAEEA+RLSLSLEVIE V+SDPALAGW
Sbjct: 247 YELAQETLVMEELVPRLKALALLAKAAKMGLNVDAEEANRLSLSLEVIEAVVSDPALAGW 306
Query: 324 DGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLVKGAYWDTEVKRAQVEGVDGFPVF 383
DGFG+VVQAYGPRTG ALDALY+MA+RYDR+ M+RLVKGAYWDTEVK AQVEG+DGFPV+
Sbjct: 307 DGFGIVVQAYGPRTGVALDALYEMADRYDRKFMIRLVKGAYWDTEVKLAQVEGIDGFPVY 366
Query: 384 THKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVSAILHMAKDTDKGAYEFQRLHGMG 443
T+K+LTDVSYIANARKLL++TDRIYPQFATHNAHTVSAI+HMA++ A+EFQRLHGMG
Sbjct: 367 TNKALTDVSYIANARKLLNMTDRIYPQFATHNAHTVSAIVHMAQEGQ--AFEFQRLHGMG 424
Query: 444 ETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDENVPPELVAA 503
ETLH +VLEQN+T+CRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDE+V PE VA
Sbjct: 425 ETLHQLVLEQNKTNCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDESVAPERVAT 484
Query: 504 DPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPTLAAIDAARAPWKSHSWAAEPLLA 563
DPF Q+ DL + GP+L+ ERPNS GFDL HAPTL AID+AR PW++H+W A PLLA
Sbjct: 485 DPFDQIGDLKRQIPTGPELYGAERPNSKGFDLAHAPTLTAIDSARTPWRAHNWVARPLLA 544
Query: 564 KAPETATTTDEPVRNPADLTTVGRVQTAGQAEIETALSAATPWNASAETRAEVLNRAADL 623
+T + + V NP+D VG ++E AL+ A W+A A+ RAE+LNRAADL
Sbjct: 545 S--DTTGSAPQNVMNPSDHALVGESSECRLEDVEQALNDAARWSAPAQERAEILNRAADL 602
Query: 624 YEANYGELFALLTREAGKTLPDCVAELREAVDFLRYYAARISAEPPVGVFTCISPWNFPL 683
YEA+YGELFALL REAGKTL D VAELREAVDFLRYYAA I A P G+FTCISPWNFPL
Sbjct: 603 YEAHYGELFALLHREAGKTLMDAVAELREAVDFLRYYAANIPAADPAGIFTCISPWNFPL 662
Query: 684 AIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLHEAGVPRSALQLLPGAG-AVGGAL 742
AIF+GQIAAALAVGN VLAKPAE T LIAHRA+ LLHEAGVPR+ALQL PG G +G L
Sbjct: 663 AIFTGQIAAALAVGNGVLAKPAESTTLIAHRAVQLLHEAGVPRTALQLTPGRGREIGPLL 722
Query: 743 TSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAETGGLNAMIVDSTALPEQAVQSI 802
T D RV GVAFTGSTATAL IR MA+ LRPGAPLIAETGGLNAMIVDSTALPEQAVQ+I
Sbjct: 723 TGDPRVSGVAFTGSTATALHIRTEMAKGLRPGAPLIAETGGLNAMIVDSTALPEQAVQAI 782
Query: 803 IESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDALHLGDPWNLSTDSGPVIDETAR 862
IESAFQSAGQRCSALRCLYLQEDIAD VL MLKGAMD LHLGDPWNLSTDSGPVID A+
Sbjct: 783 IESAFQSAGQRCSALRCLYLQEDIADTVLDMLKGAMDCLHLGDPWNLSTDSGPVIDSRAQ 842
Query: 863 AGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITGIQALEQEIFGPVLHVVRFKSQD 922
+GILAHI AR+EGRV+ E+ PQGGTFVAPTLIE++GI AL++EIFGPVLHV RFK++D
Sbjct: 843 SGILAHISTARSEGRVMHELHPPQGGTFVAPTLIEVSGIDALKEEIFGPVLHVARFKARD 902
Query: 923 LDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGNLYVNRNQIGAIVGSQPFGGEGL 982
LD++I IN TGYGLTFGLHTRIDDRVQ++CDRI AGN+YVNRNQIGAIVGSQPFGGEGL
Sbjct: 903 LDKVIEAINGTGYGLTFGLHTRIDDRVQHVCDRIKAGNIYVNRNQIGAIVGSQPFGGEGL 962
Query: 983 SGTGPKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTMLPAPTGQPMQEITTSLPGPTGES 1042
SGTGPKAGGP Y+ R+CAPDRQ S +++ + + ++PAPTG Q T +LPGPTGES
Sbjct: 963 SGTGPKAGGPLYLSRYCAPDRQTSAETFNN---STRVVPAPTGTAAQPTTQTLPGPTGES 1019
Query: 1043 NRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEATGPLDMRQLLTMEGTSGVIWWG 1102
NRL+ R PLLC+GPG +A QA+AVH+ GG AI+ LD+ QL T++ +GV+WWG
Sbjct: 1020 NRLTTAPRLPLLCMGPGKKAAAEQAKAVHSHGGLAIQMADNLDLDQLRTLDAIAGVLWWG 1079
Query: 1103 DETTAREIESWLARRNGPILPLIPGLPDKARVQAERHVCVDTTAAGGNAALLGGMG 1158
DE TAREIE LA R+G ILPLIPGLPD+ARV AE HVCVDTTAAGGNA+LLGG G
Sbjct: 1080 DEQTAREIEQHLAARDGAILPLIPGLPDRARVMAEHHVCVDTTAAGGNASLLGGQG 1135
Lambda K H
0.317 0.132 0.387
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3256
Number of extensions: 127
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1158
Length of database: 1135
Length adjustment: 46
Effective length of query: 1112
Effective length of database: 1089
Effective search space: 1210968
Effective search space used: 1210968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)
Align candidate WP_090216616.1 CV091_RS05315 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR01238.hmm
# target sequence database: /tmp/gapView.1362687.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01238 [M=500]
Accession: TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.8e-195 635.5 0.0 1.2e-192 626.8 0.0 2.4 2 NCBI__GCF_002796795.1:WP_090216616.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002796795.1:WP_090216616.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 626.8 0.0 1.2e-192 1.2e-192 1 495 [. 502 978 .. 502 982 .. 0.97
2 ! 6.1 0.0 0.00017 0.00017 237 270 .. 1069 1102 .. 1062 1123 .. 0.89
Alignments for each domain:
== domain 1 score: 626.8 bits; conditional E-value: 1.2e-192
TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseada 73
+lyg r ns+G dla +l +++ + + a+++ a p++ + q v+np d+ +vG+ se +
NCBI__GCF_002796795.1:WP_090216616.1 502 ELYGAERPNSKGFDLAHAPTLTAIDSARTPWRAHNWVARPLL-ASDTTGSAPQNVMNPSDHA-LVGESSECRL 572
79****************************************.55566667799******85.89*******9 PP
TIGR01238 74 aevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryya 146
++v++a++ +a wsa +a+era il+r+adl e h el all+reaGktl +a+ae+reavdflryya
NCBI__GCF_002796795.1:WP_090216616.1 573 EDVEQALN----DAARWSA-PAQERAEILNRAADLYEAHYGELFALLHREAGKTLMDAVAELREAVDFLRYYA 640
99998875....5689*98.9**************************************************** PP
TIGR01238 147 kqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagv 219
++ +a + G + cispwnfplaiftGqiaaala Gn v+akpae t+lia rav+ll+eaGvp ++
NCBI__GCF_002796795.1:WP_090216616.1 641 ANI------PAADPAGIFTCISPWNFPLAIFTGQIAAALAVGNGVLAKPAESTTLIAHRAVQLLHEAGVPRTA 707
*99......45789*********************************************************** PP
TIGR01238 220 iqllpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvva 292
+ql pGrG ++G lt d+r++Gv+ftGst++a i+ ++ak + +pliaetGG namivdstal+eq v+
NCBI__GCF_002796795.1:WP_090216616.1 708 LQLTPGRGREIGPLLTGDPRVSGVAFTGSTATALHIRTEMAKGLRPGAPLIAETGGLNAMIVDSTALPEQAVQ 780
************************************************************************* PP
TIGR01238 293 dvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmk 365
+++saf+saGqrcsalr l++qed+ad vl+++kGamd l++g p +l td Gpvid++a+ +lahi +
NCBI__GCF_002796795.1:WP_090216616.1 781 AIIESAFQSAGQRCSALRCLYLQEDIADTVLDMLKGAMDCLHLGDPWNLSTDSGPVIDSRAQSGILAHISTAR 853
************************************************************************* PP
TIGR01238 366 akakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGv 438
+ ++ ++++ + gtfvaptl+e+ +d+lk+e+fGpvlhv r+ka++ldkv++ in +Gyglt+G+
NCBI__GCF_002796795.1:WP_090216616.1 854 SEGRVMHELHPPQ-----GGTFVAPTLIEVSGIDALKEEIFGPVLHVARFKARDLDKVIEAINGTGYGLTFGL 921
*******998765.....9****************************************************** PP
TIGR01238 439 hsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrl 495
h+ri++ v+++ +r+k+Gn+yvnrn++Ga+vG qpfGGeGlsGtGpkaGGplyl r+
NCBI__GCF_002796795.1:WP_090216616.1 922 HTRIDDRVQHVCDRIKAGNIYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPLYLSRY 978
******************************************************997 PP
== domain 2 score: 6.1 bits; conditional E-value: 0.00017
TIGR01238 237 deriaGviftGstevarlinkalakredapvpli 270
++iaGv++ G ++ar i++ la r+ a pli
NCBI__GCF_002796795.1:WP_090216616.1 1069 LDAIAGVLWWGDEQTAREIEQHLAARDGAILPLI 1102
578************************9999998 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (500 nodes)
Target sequences: 1 (1135 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 53.51
//
[ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory