GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Marinobacter guineae M3B

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_099617459.1 CLH62_RS07455 acetyl-CoA C-acetyltransferase

Query= reanno::Marino:GFF2751
         (415 letters)



>NCBI__GCF_002744735.1:WP_099617459.1
          Length = 392

 Score =  323 bits (827), Expect = 7e-93
 Identities = 190/406 (46%), Positives = 256/406 (63%), Gaps = 16/406 (3%)

Query: 7   LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66
           ++D  IV A RT IG +GG LS++RAD LG   IKAL E    +   +I++V+ G    A
Sbjct: 1   MRDVVIVAARRTAIGIFGGGLSSLRADQLGTAVIKALLEE-TGVAGDQINEVVLGQVLTA 59

Query: 67  GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126
           G   ++ AR S + AG+P  VP  TIN++CGSG+ AV  A +AIR G+ ++MIAGG ESM
Sbjct: 60  G-CGQNPARQSAINAGIPASVPAMTINKVCGSGLKAVHMAVQAIRCGDAEMMIAGGQESM 118

Query: 127 SRAPFVMGKADSAFSR-KAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRE 185
           S++P V+  + +        + DT I     N  L   +    M  TAEN+   +G+SRE
Sbjct: 119 SQSPHVLPNSRNGQRMGNWSMVDTMI-----NDGLWDAFNDYHMGVTAENIVERYGVSRE 173

Query: 186 DQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRE-TSLEKLASLP 244
           +QD FA  SQQ+  AA++ G    +I PV+IP+RK DP+VVD DE PR   S E L  L 
Sbjct: 174 EQDEFAAASQQKAVAAREAGYFDGQIVPVSIPQRKGDPIVVDQDEGPRGGVSAEGLGKLR 233

Query: 245 TPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMGFGP 304
             F+++GTVTAGNAS +NDGA A+L+  AD  K+  L P A + A A AGV+P IMG GP
Sbjct: 234 PAFKKDGTVTAGNASSLNDGAAAVLVCSADKAKELGLTPLATIRAHANAGVDPSIMGTGP 293

Query: 305 APATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALGHPL 364
            PA+++ L  AG  + D+D++E NEAFAAQA++V RDLG   D   VN NGGAIALGHP+
Sbjct: 294 IPASQRCLKLAGWSVDDLDLVEANEAFAAQAISVNRDLGW--DTGKVNVNGGAIALGHPI 351

Query: 365 GMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIER 410
           G SG R++ + L+E+ RR          L T+CIG G G+AL +ER
Sbjct: 352 GASGCRILVSLLHEMVRR-----DVHKGLATLCIGGGMGVALAVER 392


Lambda     K      H
   0.318    0.133    0.382 

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: 412
Number of extensions: 22
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: 415
Length of database: 392
Length adjustment: 31
Effective length of query: 384
Effective length of database: 361
Effective search space:   138624
Effective search space used:   138624
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 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