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

GapMind for catabolism of small carbon sources

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

Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate Ac3H11_4184 Aldehyde dehydrogenase B (EC 1.2.1.22)

Query= reanno::MR1:200453
         (482 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4184
          Length = 498

 Score =  591 bits (1523), Expect = e-173
 Identities = 299/484 (61%), Positives = 365/484 (75%), Gaps = 7/484 (1%)

Query: 2   LLNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAAL 61
           LLNDP+LL+    INGQW   +S+  V   +PATG  +A V  +G A+ +AAIAAA AA 
Sbjct: 10  LLNDPTLLKTDGLINGQWVVGSSRFDV--NDPATGLKLADVANLGPADAEAAIAAANAAW 67

Query: 62  PAWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAE 121
             W+  TAKER   LR+WF+LL  N DDL  +MT+EQGKPL EAKGEV Y ASF+EWFAE
Sbjct: 68  GPWKTKTAKERSIILRKWFDLLMANQDDLGRIMTAEQGKPLAEAKGEVAYGASFVEWFAE 127

Query: 122 EAKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKP 181
           EAKRI G+T+P    ++R+MV+KQP+GV AAITPWNFP AMITRK APALAAGC +V+KP
Sbjct: 128 EAKRINGETLPQFDNNRRLMVLKQPIGVCAAITPWNFPLAMITRKVAPALAAGCPVVIKP 187

Query: 182 APQTPFTALALAVLAERAGIPAGVFSVITGD---AIAIGNEMCTNPIVRKLSFTGSTNVG 238
           A  TP TALA A LA RAGIPAGVF+++  D   +IAIG  +C + +VR +SFTGST VG
Sbjct: 188 AELTPLTALAAAELAIRAGIPAGVFNILPADSDNSIAIGKVLCASDVVRHISFTGSTEVG 247

Query: 239 IKLMAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQ 298
             LMAQ APT+KK+SLELGGNAPFIVFDDA+ID+AVEGA  +KYRNAGQTCVC NR YVQ
Sbjct: 248 RILMAQSAPTVKKMSLELGGNAPFIVFDDADIDSAVEGAFASKYRNAGQTCVCTNRFYVQ 307

Query: 299 AGVYDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGG 358
            GVYDEF  K +  V   KVG G  AGV  GPLI  AA+ KVQ H++DA+ KG  V+AGG
Sbjct: 308 EGVYDEFVAKFAAKVKTAKVGNGFEAGVNQGPLIEEAALTKVQRHVDDALAKGGQVVAGG 367

Query: 359 -KVHELG-GNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAA 416
            ++  LG G FFEPTV+ NA   M  AREETFGP AP+FKF    + I  AN+TEFGLA+
Sbjct: 368 QRLTALGSGQFFEPTVVANATADMLCAREETFGPFAPVFKFKTEQEAIDAANNTEFGLAS 427

Query: 417 YFYGRDISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIK 476
           YFY RD+  +++V E+LEYGMVG N G+++TE  PFGG+K SGLGREGS +G+++Y+EIK
Sbjct: 428 YFYSRDVGRIFRVTEALEYGMVGANVGILATEHVPFGGVKQSGLGREGSHHGMDDYVEIK 487

Query: 477 YICM 480
           Y+C+
Sbjct: 488 YLCL 491


Lambda     K      H
   0.318    0.133    0.390 

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: 718
Number of extensions: 20
Number of successful extensions: 4
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: 482
Length of database: 498
Length adjustment: 34
Effective length of query: 448
Effective length of database: 464
Effective search space:   207872
Effective search space used:   207872
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 (21.7 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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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