Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate AZOBR_RS23695 AZOBR_RS23695 transcriptional regulator
Query= reanno::azobra:AZOBR_RS23695
(1235 letters)
>FitnessBrowser__azobra:AZOBR_RS23695
Length = 1235
Score = 2414 bits (6255), Expect = 0.0
Identities = 1235/1235 (100%), Positives = 1235/1235 (100%)
Query: 1 IDTRTAPPSAAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGV 60
IDTRTAPPSAAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGV
Sbjct: 1 IDTRTAPPSAAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGV 60
Query: 61 ITAAAATARKLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDAL 120
ITAAAATARKLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDAL
Sbjct: 61 ITAAAATARKLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDAL 120
Query: 121 IRDKIAGGDWQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLI 180
IRDKIAGGDWQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLI
Sbjct: 121 IRDKIAGGDWQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLI 180
Query: 181 RRGVDFAMRMMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADY 240
RRGVDFAMRMMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADY
Sbjct: 181 RRGVDFAMRMMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADY 240
Query: 241 VNAIHAIGTASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYD 300
VNAIHAIGTASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYD
Sbjct: 241 VNAIHAIGTASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYD 300
Query: 301 IGLNIDAEEADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRS 360
IGLNIDAEEADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRS
Sbjct: 301 IGLNIDAEEADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRS 360
Query: 361 GHRLMIRLVKGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQF 420
GHRLMIRLVKGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQF
Sbjct: 361 GHRLMIRLVKGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQF 420
Query: 421 ATHNAQTLATIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVVGPLKRPCRIYAPVGTHETL 480
ATHNAQTLATIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVVGPLKRPCRIYAPVGTHETL
Sbjct: 421 ATHNAQTLATIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVVGPLKRPCRIYAPVGTHETL 480
Query: 481 LAYLVRRLLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYA 540
LAYLVRRLLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYA
Sbjct: 481 LAYLVRRLLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYA 540
Query: 541 PERANSAGIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVV 600
PERANSAGIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVV
Sbjct: 541 PERANSAGIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVV 600
Query: 601 GSVTEASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAG 660
GSVTEASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAG
Sbjct: 601 GSVTEASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAG 660
Query: 661 KSLPNAIAEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAAL 720
KSLPNAIAEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAAL
Sbjct: 661 KSLPNAIAEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAAL 720
Query: 721 AAGNPVLAKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFT 780
AAGNPVLAKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFT
Sbjct: 721 AAGNPVLAKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFT 780
Query: 781 GSTEVARLIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAG 840
GSTEVARLIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAG
Sbjct: 781 GSTEVARLIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAG 840
Query: 841 QRCSALRILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEA 900
QRCSALRILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEA
Sbjct: 841 QRCSALRILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEA 900
Query: 901 MRAKGRNVEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVD 960
MRAKGRNVEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVD
Sbjct: 901 MRAKGRNVEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVD 960
Query: 961 SINATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPK 1020
SINATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPK
Sbjct: 961 SINATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPK 1020
Query: 1021 AGGPLYLSRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIG 1080
AGGPLYLSRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIG
Sbjct: 1021 AGGPLYLSRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIG 1080
Query: 1081 GGAELNGPVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLR 1140
GGAELNGPVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLR
Sbjct: 1081 GGAELNGPVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLR 1140
Query: 1141 GLPPALAARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALA 1200
GLPPALAARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALA
Sbjct: 1141 GLPPALAARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALA 1200
Query: 1201 AGRGEGYDLDLLLNERSVSVNTAAAGGNASLVAMS 1235
AGRGEGYDLDLLLNERSVSVNTAAAGGNASLVAMS
Sbjct: 1201 AGRGEGYDLDLLLNERSVSVNTAAAGGNASLVAMS 1235
Lambda K H
0.319 0.136 0.396
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: 4391
Number of extensions: 160
Number of successful extensions: 1
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: 1235
Length of database: 1235
Length adjustment: 48
Effective length of query: 1187
Effective length of database: 1187
Effective search space: 1408969
Effective search space used: 1408969
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: 59 (27.3 bits)
Align candidate AZOBR_RS23695 AZOBR_RS23695 (transcriptional regulator)
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.20797.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
2.9e-234 764.1 0.8 4.2e-234 763.6 0.8 1.2 1 lcl|FitnessBrowser__azobra:AZOBR_RS23695 AZOBR_RS23695 transcriptional re
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS23695 AZOBR_RS23695 transcriptional regulator
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 763.6 0.8 4.2e-234 4.2e-234 1 498 [. 537 1033 .. 537 1035 .. 0.98
Alignments for each domain:
== domain 1 score: 763.6 bits; conditional E-value: 4.2e-234
TIGR01238 1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGq 67
+ly+ r ns+G+dl+ e+el++l++ l ++a+ ++ aap++++ + g+aqpv+npadr+d+vG
lcl|FitnessBrowser__azobra:AZOBR_RS23695 537 NLYAPERANSAGIDLSDETELARLSAALSASAEMTWTAAPLLADG-ERAGQAQPVRNPADRRDVVGS 602
589999************************************655.55699**************** PP
TIGR01238 68 vseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiae 134
v+ea++a v ea + avaa++ w at+++eraa l r+ad ++++mp+l++l+vreaGk+l naiae
lcl|FitnessBrowser__azobra:AZOBR_RS23695 603 VTEASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAIAE 669
******************************************************************* PP
TIGR01238 135 vreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsl 201
vrea+dflryy+ qv+d +d+ ++++lG+vvcispwnfplaif GqiaaalaaGn v+akpae+t+l
lcl|FitnessBrowser__azobra:AZOBR_RS23695 670 VREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVLAKPAEETPL 736
******************************************************************* PP
TIGR01238 202 iaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap.. 266
iaa+av +l+ aG+pag++qllpG+Ge vGaal +e+++Gv+ftGstevarli+++la r ++
lcl|FitnessBrowser__azobra:AZOBR_RS23695 737 IAAEAVRILHAAGIPAGALQLLPGAGE-VGAALVGHEAVRGVMFTGSTEVARLIQRQLAGRLLPDga 802
***************************.*********************************865444 PP
TIGR01238 267 .vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamde 332
+pliaetGGqnamivds+alaeqvv dv+asafdsaGqrcsalr+lc+qedvadr+l ++kGam e
lcl|FitnessBrowser__azobra:AZOBR_RS23695 803 pIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRILCLQEDVADRTLAMLKGAMRE 869
4****************************************************************** PP
TIGR01238 333 lkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddld 399
l++g+p rl dvGpvi +ea+ + ahie+m+ak+++v + l + e+ gtf+apt++e+ ++
lcl|FitnessBrowser__azobra:AZOBR_RS23695 870 LRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRNVEFLPLPA--ETADGTFIAPTVIEIGGIH 934
*******************************************999..999**************** PP
TIGR01238 400 elkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvG 466
el++evfGpvlhvvr+++d+ld +vd ina+Gyglt+G+h+ri+ t+ ++++r+ +Gnvyvnrn +G
lcl|FitnessBrowser__azobra:AZOBR_RS23695 935 ELEREVFGPVLHVVRFHRDDLDALVDSINATGYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIG 1001
******************************************************************* PP
TIGR01238 467 avvGvqpfGGeGlsGtGpkaGGplylyrltrv 498
avvGvqpfGG+GlsGtGpkaGGplyl rl++
lcl|FitnessBrowser__azobra:AZOBR_RS23695 1002 AVVGVQPFGGHGLSGTGPKAGGPLYLSRLLSR 1033
*****************************986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (500 nodes)
Target sequences: 1 (1235 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 22.55
//
[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:
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