GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Shewanella sp. ANA-3

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 7023590 Shewana3_0819 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= reanno::ANA3:7023590
         (1064 letters)



>FitnessBrowser__ANA3:7023590
          Length = 1064

 Score = 2077 bits (5382), Expect = 0.0
 Identities = 1064/1064 (100%), Positives = 1064/1064 (100%)

Query: 1    MEAITMFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTR 60
            MEAITMFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTR
Sbjct: 1    MEAITMFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTR 60

Query: 61   RAHELVNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIED 120
            RAHELVNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIED
Sbjct: 61   RAHELVNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIED 120

Query: 121  KLSGAKWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIR 180
            KLSGAKWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIR
Sbjct: 121  KLSGAKWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIR 180

Query: 181  QAMMAAMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYA 240
            QAMMAAMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYA
Sbjct: 181  QAMMAAMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYA 240

Query: 241  NAITELGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNI 300
            NAITELGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNI
Sbjct: 241  NAITELGAQSYNENESPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNI 300

Query: 301  GISIDAEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQG 360
            GISIDAEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQG
Sbjct: 301  GISIDAEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQG 360

Query: 361  DEIPVRLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQ 420
            DEIPVRLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQ
Sbjct: 361  DEIPVRLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQ 420

Query: 421  FASHNAQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLP 480
            FASHNAQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLP
Sbjct: 421  FASHNAQTVAAISDMAGDRNHEFQRLHGMGQELYDTILSEAGAKAVRIYAPIGAHKDLLP 480

Query: 481  YLVRRLLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRK 540
            YLVRRLLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRK
Sbjct: 481  YLVRRLLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRK 540

Query: 541  NSKGLNMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVA 600
            NSKGLNMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVA
Sbjct: 541  NSKGLNMNIISEAEPFFAALDKFKSTQWQAGPLVNGQTLTGEHKTVVSPFDTTQTVGQVA 600

Query: 601  FADKAAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQ 660
            FADKAAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQ
Sbjct: 601  FADKAAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSIQ 660

Query: 661  DGIDEVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAI 720
            DGIDEVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAI
Sbjct: 661  DGIDEVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLAI 720

Query: 721  FLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTA 780
            FLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTA
Sbjct: 721  FLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALTA 780

Query: 781  DERIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVS 840
            DERIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVS
Sbjct: 781  DERIGGVCFTGSTGTAKLINRTLANREGAIIPLIAETGGQNAMVVDSTSQPEQVVNDVVS 840

Query: 841  SSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKAN 900
            SSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKAN
Sbjct: 841  SSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAKAN 900

Query: 901  LDAHIDHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKAS 960
            LDAHIDHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKAS
Sbjct: 901  LDAHIDHIKQVGKLIKQMSLPAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRYKAS 960

Query: 961  ELAHVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQG 1020
            ELAHVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQG
Sbjct: 961  ELAHVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQG 1020

Query: 1021 LSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSDA 1064
            LSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSDA
Sbjct: 1021 LSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGDSDA 1064


Lambda     K      H
   0.317    0.133    0.377 

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: 3210
Number of extensions: 109
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: 1064
Length of database: 1064
Length adjustment: 45
Effective length of query: 1019
Effective length of database: 1019
Effective search space:  1038361
Effective search space used:  1038361
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: 58 (26.9 bits)

Align candidate 7023590 Shewana3_0819 (bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq))
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

Software error:

../bin/blast/fastacmd -i /tmp/list.28905.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28905.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.