GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Novosphingobium fuchskuhlense FNE08-7

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_067906010.1 AQZ52_RS00475 acetyl-CoA C-acyltransferase

Query= BRENDA::Q8VCH0
         (424 letters)



>NCBI__GCF_001519075.1:WP_067906010.1
          Length = 391

 Score =  278 bits (710), Expect = 3e-79
 Identities = 171/390 (43%), Positives = 237/390 (60%), Gaps = 9/390 (2%)

Query: 37  DVVVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDVKLKPEQLGDISVGNVLQPGA 96
           D V+V   RTPIGRA +G F  T    L +  L A +    ++  ++ D+  G+ LQ GA
Sbjct: 3   DAVIVAAARTPIGRAYKGAFNTTAGATLGALSLEAAVARAGIEGGEVDDVLWGSALQQGA 62

Query: 97  GA-IMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTL 155
            A  +AR     +G+P TV   +++RQCSSGL  +A  A  I     D+  A G ES++L
Sbjct: 63  QAGNIARQVALRAGLPVTVSGMSMDRQCSSGLMTIATAAKQIIVDRMDVVAAGGQESISL 122

Query: 156 SQRGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASAQS 215
            Q  +      R L         +PM  T+E V +R+ +SR+  D +AL SQQ+ A+AQ+
Sbjct: 123 VQTKDMRVAPDRSLVAMHGA-VYMPMLQTAETVGKRYNISREACDEYALQSQQRTAAAQA 181

Query: 216 RGCFHAEIVPVTTTVLNDKGDKKTITVSQ-----DEGVRPSTTMQGLAKLKPAFKDGGST 270
            G F AEIVP T+++     +   IT+ +     DEG RPSTT++ L  LKP   +GG  
Sbjct: 182 AGKFDAEIVPTTSSMGVQNKETGEITMQEVHLTKDEGNRPSTTLENLQALKPVI-EGGIV 240

Query: 271 TAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAALQ 330
           TAGN+SQ+SDG+AAV+L   + A + GL  LG     A  G  PD MGIGP +A+PA L+
Sbjct: 241 TAGNASQLSDGSAAVVLMEAAVAAKKGLTPLGRYVGMAAAGTEPDEMGIGPVFAVPALLK 300

Query: 331 KAGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVVTL 390
           + GL ++DI ++E+NEAFA Q +YC +KLGIP E +N  GGAI++GHP G TGAR V+  
Sbjct: 301 RFGLKMDDIGLWELNEAFAVQVLYCRDKLGIPNELLNVNGGAISIGHPYGMTGARGVMHA 360

Query: 391 LNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420
           L E KRRG + + VV+MC+G GMGAA +FE
Sbjct: 361 LIEGKRRGAK-HVVVTMCVGGGMGAAGLFE 389


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: 435
Number of extensions: 25
Number of successful extensions: 6
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: 391
Length adjustment: 31
Effective length of query: 393
Effective length of database: 360
Effective search space:   141480
Effective search space used:   141480
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