GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA 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))

Software error:

../bin/blast/fastacmd -i /tmp/list.12876.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12876.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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