GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5210417
          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:

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