GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Pseudomonas stutzeri RCH2

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF3021 Psest_3079 delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain)

Query= reanno::psRCH2:GFF3021
         (1053 letters)



>FitnessBrowser__psRCH2:GFF3021
          Length = 1053

 Score = 2078 bits (5384), Expect = 0.0
 Identities = 1053/1053 (100%), Positives = 1053/1053 (100%)

Query: 1    MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL 60
            MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL
Sbjct: 1    MFKAGHVLDGAFANQKAAEFFPAISANYSVDEAQYLTELLQLADPGEAGIAAIRERARSL 60

Query: 61   IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW 120
            IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW
Sbjct: 61   IEAVRGRDNAVDTLDALLRQYSLDTQEGLMLMCLAEALLRVPDAATADALIRDKLNAAEW 120

Query: 121  ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK 180
            ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK
Sbjct: 121  ERHLGQSDNVLVNFAAWGLVMTGKVVDPETADGRPKNVIGRLLKRSGEPVIRGAMNQAMK 180

Query: 181  LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA 240
            LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA
Sbjct: 181  LMGKQFVLGRTISEALKNGRPEREKGYTYSFDMLGEAALTAEDAAKYMADYRQAVETVGA 240

Query: 241  EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA 300
            EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA
Sbjct: 241  EPQVGKGPRPSVSIKLSALHPRYELAQRERVLTELFGSVRELAILARRLNVGITIDAEEA 300

Query: 301  DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK 360
            DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK
Sbjct: 301  DRLELSLELYEKLLRDPAIAGWGEFGLVIQAYSKRCLPVLVWLTLLGRELGERIPLRLVK 360

Query: 361  GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV 420
            GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV
Sbjct: 361  GAYWDSEIKQCQVQGLDGYPVYTRKEGTDTSYLACARYLLSEHTRGVIYPQFASHNAHTV 420

Query: 421  SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL 480
            SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL
Sbjct: 421  SCILAMAEETAQPREFEFQRLHGMGDALYDTVIEKYARNVRIYAPVGAHKDLLPYLVRRL 480

Query: 481  LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM 540
            LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM
Sbjct: 481  LENGANSSFVHQLVDPRVPVESLIDHPVTQLRRFAAPGNPRIPLPPALFGNRKNSQGINM 540

Query: 541  NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA 600
            NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA
Sbjct: 541  NIQNQWTELASAYQPFLERQWQAAPVISGRTLAGTPSEVRCPYELNKVVGQAQFASADQA 600

Query: 601  RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR 660
            RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR
Sbjct: 601  RQAIDRLAAYWPIWNATPVEARAAVLERLGDLLEQHRAELMALCTVEAGKSLQDGIDEVR 660

Query: 661  EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA 720
            EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA
Sbjct: 661  EAVDFCRYYAQQARLKLGREELKGPTGERNELFHEGRGVFVCVSPWNFPLAIYLGQITAA 720

Query: 721  LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC 780
            LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC
Sbjct: 721  LVAGNTVLAKPAEQTSLIAARALELMFEAGLPQEAIAFLPGDGATLGGVFCRDPRVVGVC 780

Query: 781  FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ 840
            FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ
Sbjct: 781  FTGSTDTARIINRQLAEKEGPIATLIAETGGQNAMIVDSTALPEQVIKDAVGSAFTSAGQ 840

Query: 841  RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL 900
            RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL
Sbjct: 841  RCSALRVLYVQRDIADRVIDLLKGAMAELRVGPTHLRENDIGPVIDQEAREGLLAHIQQL 900

Query: 901  KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960
            KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI
Sbjct: 901  KSEGRLIAEATVPAGLNGHFVAPVAFEIDGIHQLKKEHFGPVLHVVRYDAADLEKVVAAI 960

Query: 961  NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG 1020
            NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG
Sbjct: 961  NGTGYGLTLGVHSRNEETAERIEQLARVGNLYVNRNQIGAVVGVQPFGGCRLSGTGPKAG 1020

Query: 1021 GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD 1053
            GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD
Sbjct: 1021 GPSYLLRFANERTTSTNTTAVGGNASLLSLGDD 1053


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: 3243
Number of extensions: 94
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: 1053
Length of database: 1053
Length adjustment: 45
Effective length of query: 1008
Effective length of database: 1008
Effective search space:  1016064
Effective search space used:  1016064
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: 58 (26.9 bits)

Align candidate GFF3021 Psest_3079 (delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain))
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

Software error:

../bin/blast/fastacmd -i /tmp/list.6554.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6554.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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