Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 3608920 Dshi_2311 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= reanno::Marino:GFF2744
(1209 letters)
>lcl|FitnessBrowser__Dino:3608920 Dshi_2311
delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
Length = 1221
Score = 1263 bits (3267), Expect = 0.0
Identities = 665/1209 (55%), Positives = 848/1209 (70%), Gaps = 19/1209 (1%)
Query: 15 RQAIRDYYLADEHKVIHEMIAGAQLSQAERDAISARAAELVRSVRKNAKSTIMEKFLAEY 74
R +R +Y A+E ++ + A +LS ER+ +A A V VR + ++ME FLAEY
Sbjct: 16 RAQVRAHYTAEETALLKSLAARIKLSAHEREKAAAAGARYVTRVRNETRPSMMEAFLAEY 75
Query: 75 GLTTKEGVALMCLAEALLRVPDNTTIHELIEDKITSGAWGTHVGKASSGLINTATVALLM 134
GL+T EGV LMCLAEALLRVPD TI +LIEDK+ WG H+G +SS L+N +T AL++
Sbjct: 76 GLSTSEGVGLMCLAEALLRVPDADTIDDLIEDKVAPSNWGAHLGHSSSSLVNASTWALML 135
Query: 135 TSNLLKDSERNTVGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVLGRDIDEAQDEAKEY 194
T +L + R LR L+KR GEPV+RT GQ+MK +GRQFVLG+ I+E A+E
Sbjct: 136 TGKVLDEDPRGPA-RALRGLVKRLGEPVVRTAVGQSMKVLGRQFVLGQTIEEGLKNAREL 194
Query: 195 MAKGYTYSYDMLGEAARTDDDAKRYYDSYSNAIDSIAKASKGDVRKNPGISVKLSALLAR 254
KG+TYSYDMLGEAARTD DA+RY+ +Y+ AI +IA+ + GDVR +PGISVKLSAL R
Sbjct: 195 EKKGFTYSYDMLGEAARTDADARRYHAAYAQAITAIARQATGDVRSSPGISVKLSALHPR 254
Query: 255 YEYGNKERVMNELLPRARELVKKAAAANMGFNIDAEEQDRLDLSLDVIEELVADPELAGW 314
YEY ++ VM +L+PRA LVK+AA A +GFN+DAEEQDRLDLSLDVIE +++DP+L GW
Sbjct: 255 YEYTHRHSVMADLVPRAAALVKQAAQAGIGFNVDAEEQDRLDLSLDVIEAMMSDPDLDGW 314
Query: 315 DGFGVVVQAYGKRSSFVLDWLYGLAEKYDRKFMVRLVKGAYWDAEIKRAQVMGLNGFPVF 374
DGFGVVVQAYG+R+ V++ LY +AE+YDRK MVRLVKGAYWD EIK AQ +G+ FPVF
Sbjct: 315 DGFGVVVQAYGRRAGPVIETLYDMAERYDRKIMVRLVKGAYWDTEIKLAQELGVERFPVF 374
Query: 375 TRKACSDVSFLSCATKLLNMTNRIYPQFATHNAHSVSAILEMAKTKGVDNYEFQRLHGMG 434
TRK +DVS+++CA LL+ +RIYPQFATHNAH+ +A+L+MA D +EFQRLHGMG
Sbjct: 375 TRKNNTDVSYMACAQMLLDRRDRIYPQFATHNAHTCAAVLQMAGNAR-DCFEFQRLHGMG 433
Query: 435 ESLHNEVLKVSGVPCRIYAPVGPHKDLLAYLVRRLLENGANSSFVNQIVDKRITPEEIAK 494
SLH V + G CRIYAPVG H+DLLAYLVRRLLENGANSSFVNQIVD I E I+
Sbjct: 434 ASLHQIVKETEGTRCRIYAPVGAHQDLLAYLVRRLLENGANSSFVNQIVDPDIPAEAISA 493
Query: 495 DPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDPVTVNEIEKGRGAYKDYRWKG 554
DP+ +E++G+ I + AI P LF RRNS+G+ + +P ++ + R A+ + W
Sbjct: 494 DPVSEMEKLGDQIPNPAIRQPSDLFAPDRRNSRGYRVNEPASILPLMTAREAFAETTWHA 553
Query: 555 GPLIAGEVAGT-EIQVVRNPADPDDLVGHVTQASDADVDTAITSAAAAFESWSAKSAEER 613
P++AG T + V +PAD LVG V +AS DV A+ +A F WSA+ ER
Sbjct: 554 RPMLAGGRDPTGPTREVHSPADKTRLVGTVQEASAEDVACALDAAETGFRDWSARPVSER 613
Query: 614 AACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYYANEAIRYK--DSG 671
A +RK+ D+YE+N AEL A+TTREAGK++LD +AE+REAVDF ++YANEA R + D G
Sbjct: 614 ADMLRKLADMYEDNIAELTAITTREAGKTVLDGIAEVREAVDFLRFYANEAERLEEEDPG 673
Query: 672 DARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAVELMHQAGIPKD 731
RG+ CISPWNFPLAIFTGQI A L GN V+AKPAEQT ++A RAV++M G+P
Sbjct: 674 RPRGIFVCISPWNFPLAIFTGQIAAALVMGNAVLAKPAEQTPIIAARAVQMMRDCGLPDA 733
Query: 732 AIQLVPGTGATVGAALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDAPLVAETGGLNA 791
A+QL+PG G VG LTSD R++GVCFTGST A I+K + +N P+A LVAETGGLNA
Sbjct: 734 ALQLLPGDGPMVGGPLTSDPRIAGVCFTGSTEVAMIIHKALAKNAGPEAVLVAETGGLNA 793
Query: 792 MIVDSTALPEQVVRDVLASSFQSAGQRCSALRMLYVQRDIADGLLEMLYGAMEELGIGDP 851
MIVDSTAL EQ VRD+L SSFQSAGQRCSALR+LYVQ D+ D L+EML GA++ L IGD
Sbjct: 794 MIVDSTALHEQAVRDILISSFQSAGQRCSALRILYVQEDVHDKLMEMLSGALDALVIGDS 853
Query: 852 WLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPEKGLFVSPAVLSVSGIEELEE 911
W L DV PVID +A+ I+ + ++ + G L+K + P+ G +V+PA++ V GI ++E
Sbjct: 854 WNLDVDVSPVIDADAQSDILGYIDQHRKAGTLIKTLAAPDSGTYVTPAIVKVGGIADMER 913
Query: 912 EIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSRIKVGNTYVNRN 971
EIFGPVLHVATF+A ID+VVD INA+ YGLTFG+H+R+D RVE+I RI+VGN YVNRN
Sbjct: 914 EIFGPVLHVATFKANEIDQVVDAINARRYGLTFGLHTRIDDRVEQIVERIQVGNVYVNRN 973
Query: 972 QIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLK-GETVEREADSNARKVDAKQLQKLIG 1030
QIGAIVGSQPFGGEGLSGTGPKAGGP Y+ RF K G++ A A + L +
Sbjct: 974 QIGAIVGSQPFGGEGLSGTGPKAGGPLYLTRFRKVGKSTSHPAPQGA-VLGKAALNTALS 1032
Query: 1031 QLDKLK-ASRPE----ARMDAIRPIFGNVPEPL------DAHVEALPGPTGETNRLSNHA 1079
LD A+RP+ RM A+ G V L D + LPGPTGE+NRLS
Sbjct: 1033 SLDARNWAARPDRVHILRM-ALSGSTGVVRRALSETAAFDMSPQTLPGPTGESNRLSMVP 1091
Query: 1080 RGVVLCLGPDKETALEQAGTALSQGNKVVVIAPGTQDVVDQANKAGLPIVGAQGLLEPEA 1139
RG VLCLGP E A+ QA AL G VV+ PG+ + + AG P+V G ++
Sbjct: 1092 RGTVLCLGPTPEIAMAQAVQALGAGCAVVIALPGSTPLSQPLSDAGAPVVTLDGTVDCVT 1151
Query: 1140 LATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEHTLDQRFVIERHLCVDTTAAG 1199
L + G E V + G + R AL++RDG ++PLI + +R+V+ERHLC+DTTAAG
Sbjct: 1152 LTELTGIEVVAAAGASDWTRTLRVALSQRDGPIIPLIVDEIAPERYVLERHLCIDTTAAG 1211
Query: 1200 GNASLIAAS 1208
GNA L+AAS
Sbjct: 1212 GNAKLLAAS 1220
Lambda K H
0.316 0.133 0.378
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: 3465
Number of extensions: 168
Number of successful extensions: 6
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: 1209
Length of database: 1221
Length adjustment: 47
Effective length of query: 1162
Effective length of database: 1174
Effective search space: 1364188
Effective search space used: 1364188
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 (21.6 bits)
S2: 59 (27.3 bits)
Align candidate 3608920 Dshi_2311 (delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq))
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.5403.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.2e-194 633.4 3.2 7.9e-194 630.7 0.1 2.1 2 lcl|FitnessBrowser__Dino:3608920 Dshi_2311 delta-1-pyrroline-5-ca
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608920 Dshi_2311 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 630.7 0.1 7.9e-194 7.9e-194 1 498 [. 516 1008 .. 516 1010 .. 0.99
2 ! 2.9 0.6 0.0017 0.0017 158 272 .. 1089 1190 .. 1075 1198 .. 0.82
Alignments for each domain:
== domain 1 score: 630.7 bits; conditional E-value: 7.9e-194
TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaae 75
dl++ r+ns G ++ + +l + ++ a+ +++a p++++ g ++ v +pad+ +vG+v+ea+a++
lcl|FitnessBrowser__Dino:3608920 516 DLFAPDRRNSRGYRVNEPASILPLMTAREAFAETTWHARPMLAGGRDPTGPTREVHSPADKTRLVGTVQEASAED 590
799*9**************************************99999*************************** PP
TIGR01238 76 vqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakqve 150
v a+d+a + f wsa + era +l++lad+ e ++ el a++ reaGkt+ + iaevreavdflr+ya+++e
lcl|FitnessBrowser__Dino:3608920 591 VACALDAAETGFRDWSARPVSERADMLRKLADMYEDNIAELTAITTREAGKTVLDGIAEVREAVDFLRFYANEAE 665
**************************************************************************8 PP
TIGR01238 151 dvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpG 225
+e+ +++G +vcispwnfplaiftGqiaaal+ Gn+v+akpaeqt++iaarav+++++ G+p +++qllpG
lcl|FitnessBrowser__Dino:3608920 666 RLEEEDPGRPRGIFVCISPWNFPLAIFTGQIAAALVMGNAVLAKPAEQTPIIAARAVQMMRDCGLPDAALQLLPG 740
88888999******************************************************************* PP
TIGR01238 226 rGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvvadvlasafd 300
G vG ltsd+riaGv ftGsteva i+kalak ++++l+aetGG namivdstal eq v+d+l s+f+
lcl|FitnessBrowser__Dino:3608920 741 DGPMVGGPLTSDPRIAGVCFTGSTEVAMIIHKALAKNAGPEAVLVAETGGLNAMIVDSTALHEQAVRDILISSFQ 815
*************************************************************************** PP
TIGR01238 301 saGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvk 375
saGqrcsalr+l+vqedv d++++++ Ga+d l++g +l dv pvida+a+ ++l +i++ ++ + ++ +
lcl|FitnessBrowser__Dino:3608920 816 SAGQRCSALRILYVQEDVHDKLMEMLSGALDALVIGDSWNLDVDVSPVIDADAQSDILGYIDQHRKAGTLIKTLA 890
****************************************************************99999998887 PP
TIGR01238 376 leddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqie 450
d gt+v+p ++++ ++++++e+fGpvlhv +ka+e+d+vvd ina+ yglt+G+h+ri++ v qi
lcl|FitnessBrowser__Dino:3608920 891 APD-----SGTYVTPAIVKVGGIADMEREIFGPVLHVATFKANEIDQVVDAINARRYGLTFGLHTRIDDRVEQIV 960
777.....8****************************************************************** PP
TIGR01238 451 krakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrv 498
+r++vGnvyvnrn++Ga+vG qpfGGeGlsGtGpkaGGplyl r+ +v
lcl|FitnessBrowser__Dino:3608920 961 ERIQVGNVYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPLYLTRFRKV 1008
********************************************9886 PP
== domain 2 score: 2.9 bits; conditional E-value: 0.0017
TIGR01238 158 akalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGa 232
+ ++G+v+c+ p i + q + al aG +v+ t+l + l +aG p ++ G +
lcl|FitnessBrowser__Dino:3608920 1089 MVPRGTVLCLGPTP---EIAMAQAVQALGAGCAVVIALPGSTPLS-----QPLSDAGAPVVTL---DGTVD--CV 1150
55688888888853...5778899999999998765555678985.....45889**998775...57777..56 PP
TIGR01238 233 altsderiaGviftGstevarlinkalakredapvpliae 272
+lt+ + i+ v+ +G+++ +r ++ al++r+ + +pli +
lcl|FitnessBrowser__Dino:3608920 1151 TLTELTGIEVVAAAGASDWTRTLRVALSQRDGPIIPLIVD 1190
8*******************************99999975 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (500 nodes)
Target sequences: 1 (1221 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 14.43
//
[ok]
This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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