GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Pseudomonas stutzeri RCH2

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate GFF374 Psest_0375 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::Q72IB9
         (516 letters)



>FitnessBrowser__psRCH2:GFF374
          Length = 480

 Score =  283 bits (723), Expect = 1e-80
 Identities = 177/458 (38%), Positives = 258/458 (56%), Gaps = 12/458 (2%)

Query: 36  RHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQ 95
           + Y  +I G+WV +     + NPS  S+V+G  A+A  A+ E A+ AA +AF  W  +  
Sbjct: 5   QRYDNFIDGQWVGSDRYQANTNPSDLSDVIGEYAQADAAQVEQAIAAARRAFPAWATFGI 64

Query: 96  EDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYP 155
           + R+  L K    +  R+ EL   L  E GK   EA  +VA A +  +Y+A   LR    
Sbjct: 65  QARADALEKVGLEILARREELGTLLAREEGKTLPEAIGEVARAGNIFKYFAGECLRQAGE 124

Query: 156 AVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVV 215
            ++ V  PG   E    PLG   +I PWNFP+AI    I   +A GN V+ KPA+     
Sbjct: 125 TLQSVR-PGVGVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAFGNCVVIKPADLVPGC 183

Query: 216 GAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRL 275
              + EI   AGFP GV N + G G EVG  +V       ++FTGS+ VG  I +    +
Sbjct: 184 AWAIAEIISRAGFPAGVFNLVMGKGREVGEAIVNAKDVDAVSFTGSVGVGRGIAQTC--V 241

Query: 276 APGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAY 335
           A G     +  +E GGK+  IV + AD ++A E    SA+   GQ+C+A+SR+I+T+G Y
Sbjct: 242 ARGA----KVQLEMGGKNPQIVLDDADLNVAVELCTQSAFYSTGQRCTASSRIIVTEGIY 297

Query: 336 EPVLERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLE 393
           +  +E +++R +++ VG A E+  D+GPVVS  Q  + L YIEIGK EG +L  GG+R++
Sbjct: 298 DRFVEAMVERIKKIKVGSALEQGVDVGPVVSEAQLEQDLRYIEIGKQEGARLACGGERVK 357

Query: 394 --GEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYS 451
              EGYF+APT+F +  P  RI++EEIFGPV +V++VKD+ EAL +ANDT +GL+ G+ +
Sbjct: 358 CGTEGYFLAPTLFVDSDPNMRISREEIFGPVANVVKVKDYDEALAMANDTEFGLSAGICT 417

Query: 452 RKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFK 489
              ++    +R    G +  N    G    V PFGG K
Sbjct: 418 TSLKYANHFKRHAQAGMVMINLPTAGVDYHV-PFGGRK 454


Lambda     K      H
   0.319    0.137    0.403 

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: 588
Number of extensions: 32
Number of successful extensions: 5
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: 516
Length of database: 480
Length adjustment: 34
Effective length of query: 482
Effective length of database: 446
Effective search space:   214972
Effective search space used:   214972
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 (21.7 bits)
S2: 52 (24.6 bits)

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