GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Marinobacter adhaerens HP15

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate GFF3052 HP15_2996 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Marino:GFF3052
          Length = 398

 Score =  320 bits (819), Expect = 6e-92
 Identities = 185/409 (45%), Positives = 257/409 (62%), Gaps = 22/409 (5%)

Query: 7   LKDAYIVDAIRTPIGRYGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQA 66
           ++D  IV A RT IG +GG LS++ AD LG   IKA+ E    +   +I++V+ G    A
Sbjct: 7   MRDVVIVAARRTAIGTFGGGLSSLSADQLGTAVIKAILEE-TGVAGDQINEVVLGQVLTA 65

Query: 67  GEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126
           G   ++ AR S + AG+P  VP  TIN++CGSG+ AV  A +AIR G+ ++MIAGG ESM
Sbjct: 66  G-CGQNPARQSAINAGIPASVPAMTINKVCGSGLKAVHMAVQAIRCGDAEMMIAGGQESM 124

Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKK----QYGIDSMPETAENVAADFGI 182
           S+AP V+       SR  +       W  V+ ++K      +    M  TAEN+   +GI
Sbjct: 125 SQAPHVLPN-----SRNGQRMGN---WSMVDTMIKDGLWDAFNDYHMGITAENIVEKYGI 176

Query: 183 SREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRE-TSLEKLA 241
           SR++QD FA  SQQ+ AAA++ G    +I PV+IP+RK DP+VVD DE PR+  + E L 
Sbjct: 177 SRDEQDEFAAASQQKAAAAREAGYFDGQIVPVSIPQRKGDPIVVDRDEGPRDGVTAEGLG 236

Query: 242 SLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPRIMG 301
            L   F+++GTVTAGNAS +NDGA A+++  A+  ++  L P A + A A AGV+P IMG
Sbjct: 237 KLRAAFKKDGTVTAGNASSLNDGAAAVMVCSAEKAEELGLTPIATIKAYANAGVDPTIMG 296

Query: 302 FGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAIALG 361
            GP PA+++ L  AG    D+D++E NEAFAAQA++V RD+G   D   VN NGGAIALG
Sbjct: 297 TGPIPASQRCLKLAGWSTEDLDLVEANEAFAAQAISVNRDMGW--DTGKVNVNGGAIALG 354

Query: 362 HPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIER 410
           HP+G SG R++ + L+E+ RR          L T+CIG G G+AL +ER
Sbjct: 355 HPIGASGCRILVSLLHEMVRR-----DVHKGLATLCIGGGMGVALAVER 398


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: 413
Number of extensions: 18
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: 398
Length adjustment: 31
Effective length of query: 384
Effective length of database: 367
Effective search space:   140928
Effective search space used:   140928
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.

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