GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Sphingomonas koreensis DSMZ 15582

Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate Ga0059261_3284 Ga0059261_3284 acetyl-CoA acetyltransferases

Query= BRENDA::Q8VCH0
         (424 letters)



>FitnessBrowser__Korea:Ga0059261_3284
          Length = 391

 Score =  276 bits (705), Expect = 1e-78
 Identities = 173/389 (44%), Positives = 241/389 (61%), Gaps = 11/389 (2%)

Query: 39  VVVHGRRTPIGRASRGCFKDTTPDELLSAVLTAVLQDVKLKPEQLGDISVGNVLQPG--A 96
           V+V   RTPIGRA RG F       L +  + A +Q   ++  ++ D+  G  LQ G  A
Sbjct: 5   VIVSTARTPIGRAYRGAFNALPAQTLAARSIEAAVQRAGIEGGEVQDVVFGAALQQGHQA 64

Query: 97  GAIMARIAQFLSGIPETVPLSTVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMTLS 156
           G I AR A   +G+P +V   +V+RQC+SGL A+A  A  I   + DI +  GVES++L 
Sbjct: 65  GNI-ARQAALRAGLPVSVSGMSVDRQCASGLMAIATAAKQIIVDNMDIAIGGGVESISLV 123

Query: 157 QRGNHGNISSRLLENEKARDCLIPMGITSENVAERFGVSRQKQDAFALASQQKAASAQSR 216
           Q      I++         D  +PM  T+E VA R+ +SR+ QD ++L SQQ+ A+AQ+ 
Sbjct: 124 QTPQM-RIAADPELLAMHNDVYMPMLQTAEVVAARYNISREVQDEYSLQSQQRTAAAQAA 182

Query: 217 GCFHAEIVPVTTTV-LNDKGDK----KTITVSQDEGVRPSTTMQGLAKLKPAFKDGGSTT 271
           G F  EIVPVT T+ + +K  K    K +T+++DEG RP TT++GL  L+P   +G   T
Sbjct: 183 GKFDDEIVPVTATMNIVNKETKEVTQKEVTLTKDEGNRPETTLEGLQALQPVVPNG-VIT 241

Query: 272 AGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDVMGIGPAYAIPAALQK 331
           AGN+SQ+SDG+++ +L     AE+ GL  LG     AV G  PD MGIGP +AIPA L++
Sbjct: 242 AGNASQLSDGSSSSVLMEEKLAEKRGLTPLGRYVGMAVAGTKPDEMGIGPVFAIPALLER 301

Query: 332 AGLTVNDIDIFEINEAFASQAVYCVEKLGIPAEKVNPLGGAIALGHPLGCTGARQVVTLL 391
             L ++DI ++E+NEAFA Q +YC +KLGIP E +N  GG+I++GHP G TGAR     L
Sbjct: 302 FNLKMDDIGLWELNEAFAVQVLYCRDKLGIPNELLNVNGGSISIGHPYGMTGARCTGHAL 361

Query: 392 NELKRRGRRAYGVVSMCIGTGMGAAAVFE 420
            E KRRG + Y VV+MC+G GMGAA +FE
Sbjct: 362 IEGKRRGAK-YVVVTMCVGGGMGAAGLFE 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: 27
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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