GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Shewanella loihica PV-4

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 5210417 Shew_2858 acetyl-CoA acetyltransferase (RefSeq)

Query= BRENDA::Q8VCH0
         (424 letters)



>lcl|FitnessBrowser__PV4:5210417 Shew_2858 acetyl-CoA
           acetyltransferase (RefSeq)
          Length = 394

 Score =  277 bits (708), Expect = 5e-79
 Identities = 171/394 (43%), Positives = 238/394 (60%), Gaps = 14/394 (3%)

Query: 37  DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDVKLKPEQLGDISVGNVLQPG- 95
           + V+V   RT + ++ RG   +T    +L   +   +Q   ++  ++ D  +G VL  G 
Sbjct: 3   EAVIVSTARTGMAKSFRGSLNNTKSPTMLGHCIKQAVQRAGVEGGEIDDAIMGTVLTAGT 62

Query: 96  AGAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTL 155
           AG  +AR A   +G+P TV   T++RQCSSGL A+   A  I      I +A G E++T 
Sbjct: 63  AGMNIARNAVLAAGLPNTVSAQTIDRQCSSGLMAIGMAAKQIIVDQQQIVVAGGQENITA 122

Query: 156 SQ----RGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAA 211
            Q    +    N    +++ E      +PM  T+E+VA+ +GVSR+ QD +AL SQQ+ A
Sbjct: 123 VQNEYMKWAADNADPNVMQFEP--HAYMPMLKTAEHVAKVYGVSREAQDIYALMSQQRTA 180

Query: 212 SAQSRGCFHAEIVPVTTTV-LNDKGDK----KTITVSQDEGVRPSTTMQGLAKLKPAFKD 266
           +AQ  G F  EIVP TTT+ + D+  K    + +T+ +DE  RPSTTM+ L  L P   +
Sbjct: 181 AAQEAGYFDDEIVPFTTTMAIQDRETKAISYQQVTLDRDECNRPSTTMESLQNLAPVI-E 239

Query: 267 GGSTTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIP 326
           GG  TAGN+SQ+SDGA+A ++  R  AE+ GL  LG+ R  AV G  P+ MGIGP YAIP
Sbjct: 240 GGFITAGNASQLSDGASACVVMERKLAEQRGLAPLGIYRGIAVAGCAPEEMGIGPIYAIP 299

Query: 327 AALQKAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQ 386
             L++ GLT++DI ++EINEAFA QA+YC + LGI   + N  GG I++GHP G TG+R 
Sbjct: 300 KLLKQHGLTIDDIGLWEINEAFAVQALYCRDHLGIDPARYNVNGGGISIGHPYGMTGSRL 359

Query: 387 VVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420
           V   L E KRRG + Y VV MCIG GMGAA +FE
Sbjct: 360 VGHALIEGKRRGVK-YVVVGMCIGGGMGAAGLFE 392


Lambda     K      H
   0.317    0.133    0.377 

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: 406
Number of extensions: 19
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: 424
Length of database: 394
Length adjustment: 31
Effective length of query: 393
Effective length of database: 363
Effective search space:   142659
Effective search space used:   142659
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 (21.6 bits)
S2: 50 (23.9 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 preprint 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