GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Marinobacter adhaerens HP15

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate GFF3052 HP15_2996 acetyl-CoA acetyltransferase

Query= SwissProt::P45369
         (394 letters)



>FitnessBrowser__Marino:GFF3052
          Length = 398

 Score =  573 bits (1476), Expect = e-168
 Identities = 280/390 (71%), Positives = 332/390 (85%)

Query: 4   NIVIVDAGRSAIGTFSGSLSSLSATEIGTAVLKGLLARTGLAPEQIDEVILGQVLTAGVG 63
           ++VIV A R+AIGTF G LSSLSA ++GTAV+K +L  TG+A +QI+EV+LGQVLTAG G
Sbjct: 9   DVVIVAARRTAIGTFGGGLSSLSADQLGTAVIKAILEETGVAGDQINEVVLGQVLTAGCG 68

Query: 64  QNPARQTTLKAGLPHSVPAMTINKVCGSGLKAVHLAMQAIACGDADIVIAGGQESMSQSS 123
           QNPARQ+ + AG+P SVPAMTINKVCGSGLKAVH+A+QAI CGDA+++IAGGQESMSQ+ 
Sbjct: 69  QNPARQSAINAGIPASVPAMTINKVCGSGLKAVHMAVQAIRCGDAEMMIAGGQESMSQAP 128

Query: 124 HVLPRSRDGQRMGDWSMKDTMIVDGLWDAFNNYHMGTTAENIAQKYGFTREQQDAFAAAS 183
           HVLP SR+GQRMG+WSM DTMI DGLWDAFN+YHMG TAENI +KYG +R++QD FAAAS
Sbjct: 129 HVLPNSRNGQRMGNWSMVDTMIKDGLWDAFNDYHMGITAENIVEKYGISRDEQDEFAAAS 188

Query: 184 QQKTEAAQKAGRFQDEIIPIEIPQRKGDPKVFDADEFPRHGTTAESLGKLRPAFSRDGSV 243
           QQK  AA++AG F  +I+P+ IPQRKGDP V D DE PR G TAE LGKLR AF +DG+V
Sbjct: 189 QQKAAAAREAGYFDGQIVPVSIPQRKGDPIVVDRDEGPRDGVTAEGLGKLRAAFKKDGTV 248

Query: 244 TAGNASGINDGAAMVVVMKESKAKELGLKPMARLVAFASAGVDPAIMGTGPIPASTKCLE 303
           TAGNAS +NDGAA V+V    KA+ELGL P+A + A+A+AGVDP IMGTGPIPAS +CL+
Sbjct: 249 TAGNASSLNDGAAAVMVCSAEKAEELGLTPIATIKAYANAGVDPTIMGTGPIPASQRCLK 308

Query: 304 KAGWTPADLDLIEANEAFAAQAMSVNQDMGWDLSKVNVNGGAIAIGHPIGASGARVLVTL 363
            AGW+  DLDL+EANEAFAAQA+SVN+DMGWD  KVNVNGGAIA+GHPIGASG R+LV+L
Sbjct: 309 LAGWSTEDLDLVEANEAFAAQAISVNRDMGWDTGKVNVNGGAIALGHPIGASGCRILVSL 368

Query: 364 LYEMQKRDAKKGLATLCIGGGQGVALAVER 393
           L+EM +RD  KGLATLCIGGG GVALAVER
Sbjct: 369 LHEMVRRDVHKGLATLCIGGGMGVALAVER 398


Lambda     K      H
   0.315    0.131    0.375 

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: 562
Number of extensions: 9
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: 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 (21.6 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