GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Azospirillum brasilense Sp245

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.21573.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: 00:00:00.03
# Mc/sec: 20.17
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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