GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Chryseobacterium arthrosphaerae CC-VM-7

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_065397667.1 BBI00_RS04610 acetyl-CoA C-acyltransferase

Query= BRENDA::Q8VCH0
         (424 letters)



>NCBI__GCF_001684965.1:WP_065397667.1
          Length = 392

 Score =  290 bits (743), Expect = 4e-83
 Identities = 165/387 (42%), Positives = 238/387 (61%), Gaps = 8/387 (2%)

Query: 40  VVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDV-KLKPEQLGDISVGNVL-QPGAG 97
           +V G R+ +G+A +G  + T PD + + V+  ++ ++ +L   ++ D+ VGN + +   G
Sbjct: 6   IVKGFRSAVGKAPKGSLRFTRPDVMAATVIEKLMAELPQLDKNRIDDLIVGNAMPEAEQG 65

Query: 98  AIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTLSQ 157
             +AR+   +    + VP  TVNR C+SG +A+A  +  I+ G  D  +A G ESM+   
Sbjct: 66  LNVARLISLMGLNTDKVPGVTVNRYCASGSEAIAIASAKIQAGMADCIIAGGTESMSYIP 125

Query: 158 RGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASAQSRG 217
            G +  +    +      D    MG T+E VA+++ +SR++QD FA  S  KA  A   G
Sbjct: 126 MGGYKPVPETDIAKTNP-DYYWGMGYTAEEVAKQYNISREEQDQFAFESHMKALKANQEG 184

Query: 218 CFHAEIVPVTTTVL----NDKGDKKTITVSQDEGVRPSTTMQGLAKLKPAFKDGGSTTAG 273
            F  +IVP+         N K   K    S DEG R  T++ GLAKL+P F +GGS TAG
Sbjct: 185 KFANQIVPIPVQYNFLDENQKMQTKKFDFSVDEGPRADTSLAGLAKLRPVFANGGSVTAG 244

Query: 274 NSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAALQKAG 333
           NSSQ+SDGAA V++      +ELGL     L +YA  G+ P +MG+GP YAIP AL++AG
Sbjct: 245 NSSQMSDGAAFVMVMSEEMVKELGLEPEARLVAYAAAGLEPRIMGMGPIYAIPKALKQAG 304

Query: 334 LTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVVTLLNE 393
           L + DID+ E+NEAFASQ+V   ++LG+  E +N  GGAIALGHPLGCTG +  V LL+E
Sbjct: 305 LELKDIDLIELNEAFASQSVAIKKELGLNPEILNVNGGAIALGHPLGCTGTKLTVQLLDE 364

Query: 394 LKRRGRRAYGVVSMCIGTGMGAAAVFE 420
           ++RRG + YG+VSMC+GTG GAA++FE
Sbjct: 365 MRRRGNK-YGMVSMCVGTGQGAASIFE 390


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: 396
Number of extensions: 15
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: 392
Length adjustment: 31
Effective length of query: 393
Effective length of database: 361
Effective search space:   141873
Effective search space used:   141873
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 24 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