GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3961 Aldehyde
           dehydrogenase B (EC 1.2.1.22)
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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