Alignments for a candidate for adh in Azoarcus sp. BH72

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Azoarcus sp. BH72

Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate WP_011765850.1 AZO_RS10715 aldehyde dehydrogenase

Query= SwissProt::Q64057
         (539 letters)



>NCBI__GCF_000061505.1:WP_011765850.1
          Length = 501

 Score =  462 bits (1190), Expect = e-134
 Identities = 241/484 (49%), Positives = 320/484 (66%), Gaps = 10/484 (2%)

Query: 60  GGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGD 119
           GG  EV +   P +   +A++R AS ++ +  IG+A +AW  W  IPAP RG +VR   D
Sbjct: 19  GGELEVRS---PIDGRTVAQLRPASHRETDAAIGRAHEAWLEWRTIPAPARGTLVRHYAD 75

Query: 120 ALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSERPGHALM 179
           ALR     L  L++LE GKI  E +GEVQE +D+CD+AAGLSR + G T+ SERPGH L 
Sbjct: 76  ALRRHKTALAELITLESGKIRQESLGEVQEMIDICDFAAGLSRQLHGLTIASERPGHRLQ 135

Query: 180 EQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKIIAKVLE 239
           E W+P G+VG+I+AFNFP AV+ WN A+A + G+  +WK +P T L ++A   +      
Sbjct: 136 ELWHPAGVVGVISAFNFPAAVWAWNAALAWVCGDTVIWKPSPRTPLTALACASLFNDACA 195

Query: 240 DNLLP-GAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSLLELG 298
            +      +  +  GG +    +A D RV +LS TGST +G+++A +V  RFG+S+LELG
Sbjct: 196 THSQGCEGLLEVLIGGNEPARQLAADRRVAVLSATGSTAMGREIAPVVASRFGRSILELG 255

Query: 299 GNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNAYSQIR 358
           GNNA I    ADL L   + LFAA GTAGQRCTT+RRL +HE IHD ++ RL+ A++Q+R
Sbjct: 256 GNNAAIVTPSADLDLTERAVLFAAAGTAGQRCTTLRRLIVHEHIHDTLLARLQAAWAQLR 315

Query: 359 VGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMDHP----GNYVEPTIV 414
           +GNP +P++L GPL    A      A+ EA+ EGG  V+GG+    P    G Y  P +V
Sbjct: 316 IGNPMEPDVLVGPLIEASAGEAMTAALAEAEAEGGR-VFGGEAYPVPGLGSGCYRRPALV 374

Query: 415 TGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPK 474
             +    P+V +ETFAPILYV +++  E+    NN V QGL+S+IFT+DLG    ++   
Sbjct: 375 -AMPAQTPVVMRETFAPILYVLRYRTLEDAIAMNNAVPQGLASAIFTRDLGEAEAFISAS 433

Query: 475 GSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSTALPLAQ 534
           GSDCGIVNVN   SGAEIGGAFGGEK TGGGRE+GSD WK YMRR+TCTIN S +LPLAQ
Sbjct: 434 GSDCGIVNVNTGPSGAEIGGAFGGEKDTGGGREAGSDVWKTYMRRATCTINGSGSLPLAQ 493

Query: 535 GIKF 538
           GI+F
Sbjct: 494 GIRF 497


Lambda     K      H
   0.319    0.137    0.417 

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: 834
Number of extensions: 33
Number of successful extensions: 3
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: 539
Length of database: 501
Length adjustment: 35
Effective length of query: 504
Effective length of database: 466
Effective search space:   234864
Effective search space used:   234864
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources