Aligments for a candidate for atoB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for atoB in Phaeobacter inhibens BS107

Align Acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate GFF3382 PGA1_c34350 acetyl-CoA acetyltransferase PhbA

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2411
         (393 letters)



>FitnessBrowser__Phaeo:GFF3382
          Length = 391

 Score =  464 bits (1193), Expect = e-135
 Identities = 232/389 (59%), Positives = 290/389 (74%)

Query: 5   EIYVVSAARTAIGTFGGSLKDVPLADLATTAVKAALERAAVDPALVGHLVMGNVIPTETR 64
           +I ++  ARTAIGTFGGSL      DLAT A KAA+ER+ V P  +G++V G+VI TE R
Sbjct: 3   DIVILDGARTAIGTFGGSLAGTTPIDLATVASKAAMERSGVAPEQIGNVVFGHVINTEPR 62

Query: 65  DAYISRVAAMNAGIPKETPAYNVNRLCGSGLQAIINAAQTLMLGDADIVVGAGAESMSRG 124
           D Y+SRVAAM AGIP  TPA NVNRLCGSG QAI++  Q+LMLGDA+  +  GAE+MSR 
Sbjct: 63  DMYLSRVAAMQAGIPNGTPAMNVNRLCGSGAQAIVSGIQSLMLGDAEFALTGGAENMSRS 122

Query: 125 PYLMPAARWGSRMGNAQVIDYMLGILHDPFHGIHMGITAENVAARNGITREMQDALAFED 184
           P+++P+ARWG +MG+A+ +D MLG L+ PF   HMG+TAENVA  + ITR   D  A   
Sbjct: 123 PFIVPSARWGQKMGDARALDMMLGALNCPFGTGHMGVTAENVADEHDITRAQMDEFALAS 182

Query: 185 QQRAAHAIANGYFSEQIATVEIQDRKGVKLFSVDEHPRATSLEQLAAMKPAFKKDGSVTA 244
           Q RAA AI  GYF+ QI  VE++ ++ +  F VDEHP+A++LE L  +K  FKKDG VTA
Sbjct: 183 QTRAAAAIEAGYFASQITPVEVKVKRDMVPFDVDEHPKASTLETLGGLKAVFKKDGRVTA 242

Query: 245 GNASGLNDGAAALVMASGNAVQANNLKPLARLVSYAHAGVEPEFMGLGPIPATRLALKRA 304
           GNASG+NDGAAA+VMA+ +A +   LKP AR++ YAHAGV PE MG+GP+PA +  LK+ 
Sbjct: 243 GNASGINDGAAAIVMATADAARQAGLKPKARILGYAHAGVRPEVMGIGPVPAVQNLLKKT 302

Query: 305 GLTVADLDVIEANIAFAAQACAVSQELDLDPAKVNPNGSGIALGHPVGATGAIIATKAIH 364
           GL+ +D DV+E+N AFAAQA AV++EL LDPAKVNPNG  IALGHPVGATGAII  K ++
Sbjct: 303 GLSASDFDVVESNEAFAAQALAVNKELGLDPAKVNPNGGAIALGHPVGATGAIITLKTLY 362

Query: 365 ELHRTGGRYALVTMCIGGGQGIAAIFERV 393
           EL R GG   L+TMCIGGGQGIA   ER+
Sbjct: 363 ELERIGGSKGLITMCIGGGQGIALAIERL 391


Lambda     K      H
   0.318    0.133    0.378 

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: 487
Number of extensions: 24
Number of successful extensions: 1
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: 393
Length of database: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
Effective search space:   130320
Effective search space used:   130320
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources