GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dadA in Acidovorax sp. GW101-3H11

Align D-alanine dehydrogenase (EC 1.4.99.-) (characterized)
to candidate Ac3H11_832 D-amino acid dehydrogenase small subunit (EC 1.4.99.1)

Query= reanno::acidovorax_3H11:Ac3H11_4848
         (445 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_832 D-amino acid
           dehydrogenase small subunit (EC 1.4.99.1)
          Length = 414

 Score =  380 bits (975), Expect = e-110
 Identities = 197/414 (47%), Positives = 262/414 (63%), Gaps = 20/414 (4%)

Query: 26  VIVIDRQPDAALETSFANAAQISVSYCEPWANREAPLKALKWMFDKEAPLLFRPQMDWQQ 85
           V VIDRQ     ETSFAN  QISVS+ EPWAN  APLK L+W+  ++APLLFR + D +Q
Sbjct: 1   VTVIDRQGAPGAETSFANGGQISVSHAEPWANPSAPLKVLQWLGKEDAPLLFRIRADMRQ 60

Query: 86  WRWGLQFLAQCNDTAFERNVQQIVALGAYSHAALKDLVGTTGIEYNRLERGIAHFYTDQK 145
           W WGL FL  C       N++QIV LG YS   L+ L   TGI+Y++  +GI HFYT+QK
Sbjct: 61  WLWGLSFLRNCTPARTRHNIEQIVRLGTYSRDTLQQLRAATGIQYDQRTQGILHFYTNQK 120

Query: 146 SFDAAGHAVELMRKHGVQRRLVSRDELLQIEPAFRAYGDKITGGTYTSTDESGDARVFTQ 205
            FD A    E MR  G +R+++S DE +++EPA      ++ G TYT+ DESGDA  FT+
Sbjct: 121 EFDGALAPAEQMRALGCERQVISADEAVRLEPALAHIRPQLAGATYTAEDESGDANQFTR 180

Query: 206 ELARRCIARGAQFLYGHDVLRLNKIGNAIDSVAVMARQPGGGGKKDFILKADAVVVACGS 265
           ELA+ C A G QF  GH +  L + G  ID V V   +    G+ + + + DA V+A GS
Sbjct: 181 ELAKLCEAAGVQFRMGHHITALREAGGRIDHVEVTTAE----GRFERV-RGDAFVLAMGS 235

Query: 266 YSAPLLRSVGVDLPIYPGKGYSATFPLLRPEGAPMVSTIDDGKKIAMSRL-----GNHLR 320
           +S  L + +G+ LPIYP KGYS T P+     A  VS  DD  K+  SR      G+ LR
Sbjct: 236 FSPLLAQPLGIRLPIYPAKGYSVTMPVKDASKAHQVSLTDDEFKLVFSRYTSERGGDRLR 295

Query: 321 VAGTIELNGWDLTLDSSLARARCHMLSRRIEAILPGVCDTRTPEEGGDPQYWTGLRPATP 380
           +AGT ELNG+D  L+    + RC  + RR+E + PG  D          Q+W+GLRPATP
Sbjct: 296 IAGTAELNGYDRHLN----QVRCEAIVRRVEQLFPGAGD------ASQAQFWSGLRPATP 345

Query: 381 TNIPFIGRTRVGKLWVNAGHGTLGWTHGAGSGKALAELISGQVPAMNFGFCGME 434
           +N+P IG+T+VG L++N GHGTLGWTH  GSGKALA+++SG+VP ++F F G++
Sbjct: 346 SNVPLIGKTKVGNLFLNTGHGTLGWTHACGSGKALADIVSGRVPEVDFAFQGLQ 399


Lambda     K      H
   0.321    0.137    0.424 

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: 534
Number of extensions: 23
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: 445
Length of database: 414
Length adjustment: 32
Effective length of query: 413
Effective length of database: 382
Effective search space:   157766
Effective search space used:   157766
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 (21.8 bits)
S2: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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