GapMind for catabolism of small carbon sources

 

Alignments for a candidate for putA in Acidovorax sp. GW101-3H11

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Ac3H11_3961 Aldehyde dehydrogenase B (EC 1.2.1.22)

Query= BRENDA::Q72IB9
         (516 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3961
          Length = 512

 Score =  258 bits (659), Expect = 4e-73
 Identities = 169/459 (36%), Positives = 243/459 (52%), Gaps = 19/459 (4%)

Query: 42  IGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRL 101
           IGG W D      + NPS   +V+G  A A + +A  A+ AA  AF  W     + R  +
Sbjct: 39  IGGAWTDGVRTYQNTNPSDTRDVIGDYAVASREQALDAVAAAHAAFPAWSLSTPQQRFDI 98

Query: 102 LLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVP 161
           L      +  RK EL   L  E GK   EA  +V  A    +++A  ALR   P  EV+P
Sbjct: 99  LDAVGNEIIARKAELGDLLAREEGKTLPEAIGEVGRAAAIFKFFAGEALR---PGGEVMP 155

Query: 162 Y--PGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKV 219
              PG   E    PLG   +I PWNFP+AI    I   +A GN V+ KPAE        +
Sbjct: 156 SVRPGVGIEITREPLGTIGIITPWNFPIAIPAWKIAPALAYGNCVVFKPAEVVPGSAWAL 215

Query: 220 FEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQ 279
            +I H AG P GV N + G G +VGA L+E  R   ++FTGS+  G ++  AA  +  G 
Sbjct: 216 ADILHRAGLPAGVFNLVMGRGSDVGAVLLEDERIAGVSFTGSVGTGQRV--AAACVPRG- 272

Query: 280 TWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVL 339
               +  +E GGK+  +V + AD ++A    + S +   GQ+C+A+SR+I+T+G ++  +
Sbjct: 273 ---AKVQLEMGGKNPFVVLDDADLNVAVGAAINSGFFSTGQRCTASSRVIVTEGIHDRFV 329

Query: 340 ERVLKRAERLSVGPAEE-NPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLE---- 393
             ++++ + L V  A +   D+GPVV   Q  + L YI IG+ EG +L  GG+ LE    
Sbjct: 330 AAMVEKMKTLKVDDARKAGTDIGPVVDDRQLAQDLEYIGIGQQEGAKLAYGGEALEKNAD 389

Query: 394 -GEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSR 452
              G+++ P +FTE  P  RI +EEIFGPV+SV+R K++ EAL +ANDTP+GL  G+ + 
Sbjct: 390 GAPGFYLRPALFTETTPGMRINREEIFGPVVSVLRAKNYEEALALANDTPFGLASGIATT 449

Query: 453 KREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLS 491
             +H    +R    G +  N    G    V PFGG K S
Sbjct: 450 SLKHATHFKRHAQAGMVMVNLPTAGVDYHV-PFGGRKSS 487


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: 650
Number of extensions: 36
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: 512
Length adjustment: 35
Effective length of query: 481
Effective length of database: 477
Effective search space:   229437
Effective search space used:   229437
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