GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF2428
          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:

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