GapMind for catabolism of small carbon sources

 

Aligments for a candidate for atoB in Pseudomonas stutzeri RCH2

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate GFF2428 Psest_2476 acetyl-CoA acetyltransferases

Query= SwissProt::Q0KBP1
         (394 letters)



>lcl|FitnessBrowser__psRCH2:GFF2428 Psest_2476 acetyl-CoA
           acetyltransferases
          Length = 398

 Score =  408 bits (1048), Expect = e-118
 Identities = 209/393 (53%), Positives = 283/393 (72%), Gaps = 3/393 (0%)

Query: 3   REVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEP 62
           ++VV++SG RTAIG FG SL   +PAELG    R A+ RA V+ +++ H +FG++I T P
Sbjct: 8   QDVVILSGARTAIGDFGASLSGYSPAELGTFAGRAAIERAGVAAEEIDHCIFGHIITTSP 67

Query: 63  RDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSR 122
           +D YL R  A+N G+  ++ A+ VNRLCGS +Q+++SAAQ I  G + +A+ GGAESMS+
Sbjct: 68  QDAYLARHVALNCGLAEHSAAMNVNRLCGSSVQSLISAAQMIQAGASRLALAGGAESMSQ 127

Query: 123 APYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALE 182
             YL P  R+G RMGDA  VD+ +G L DPF   HMG+TAENVA  Y  +R Q D+ A +
Sbjct: 128 GAYLLPKLRFGQRMGDAAAVDLTIGILSDPFGSGHMGITAENVAARYGFTREQLDQYACD 187

Query: 183 SHRRASAAIKAGYFKDQIVPV-VSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENG 241
           SHR+A+ A+ AG+   QIV V ++KGR     F  DEHVR D T++ + KLR  F K++G
Sbjct: 188 SHRKAANAMAAGHLTTQIVSVPINKGRAAG-EFSQDEHVRPDTTLEGLQKLRAAF-KKDG 245

Query: 242 TVTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIA 301
            VTAGNAS LND AAA+V+    EA R GL+P AR +SY  AGV+P+ MG+GP+PA + A
Sbjct: 246 MVTAGNASPLNDGAAALVLGSAQEAARLGLRPRARFLSYAFAGVEPQLMGLGPIPAVQRA 305

Query: 302 LERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITV 361
           L  A L+++D+D+IE+NEAFAAQA AV ++L  DP KVN NG  I+ GHP+G+TG+++T+
Sbjct: 306 LTAANLRLADIDIIESNEAFAAQALAVAQSLEFDPDKVNVNGGAIAHGHPVGSTGSILTL 365

Query: 362 KALHELNRVQGRYALVTMCIGGGQGIAAIFERI 394
           KAL+EL R+  R+AL+TMCIGGGQGIA I ER+
Sbjct: 366 KALYELERLGKRHALITMCIGGGQGIALILERL 398


Lambda     K      H
   0.318    0.134    0.381 

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: 418
Number of extensions: 13
Number of successful extensions: 2
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: 394
Length of database: 398
Length adjustment: 31
Effective length of query: 363
Effective length of database: 367
Effective search space:   133221
Effective search space used:   133221
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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