GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Shewanella sp. ANA-3

Align Acetate/butyrate--CoA ligase AAE7, peroxisomal; AMP-binding protein 7; AtAMPBP7; Acetyl-CoA synthetase; Acyl-activating enzyme 7; Butyryl-CoA synthetase; Protein ACETATE NON-UTILIZING 1; EC 6.2.1.1; EC 6.2.1.2 (characterized)
to candidate 7026089 Shewana3_3231 AMP-dependent synthetase and ligase (RefSeq)

Query= SwissProt::Q8VZF1
         (569 letters)



>lcl|FitnessBrowser__ANA3:7026089 Shewana3_3231 AMP-dependent
           synthetase and ligase (RefSeq)
          Length = 534

 Score =  146 bits (368), Expect = 2e-39
 Identities = 151/510 (29%), Positives = 232/510 (45%), Gaps = 56/510 (10%)

Query: 68  SIGPGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQ 127
           ++ PG  +AI  PNI     A +G    G +L   N       +    + S +  ++V  
Sbjct: 62  NLKPGDRIAIQLPNITQFVIAAYGALRAGLILVNTNPLYTERELIHQFNDSGAKALVV-- 119

Query: 128 EFFTLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCA---PESLNRALSKGAIEYEDFLATG 184
                  D L  + +   ++   P+ +VI  H      P+   +   K  +E+   L  G
Sbjct: 120 -----LSDLLPTLAKVVATT---PIELVISTHPLDLIDPQVQPKTGLKN-VEFCQVLKQG 170

Query: 185 D--PNYPWQPPADEWQSIALGYTSGTTASPKGVVLHH-----RGAYIMALSNPLIWGMQD 237
              P   + P A++    AL YT GTT   KG +L H       A + +    +I   +D
Sbjct: 171 AELPFSRFVPAANDLA--ALQYTGGTTGLSKGAMLTHGNMLANAAQVKSRIGSVITEGED 228

Query: 238 GAVYLWTLPMFHCNGWCFPWSLAVL---SGTSICL---RQVTAKEVYSMIAKYKVTHFCA 291
             +++  LP++H   + F  +L +     G S+ +   R ++   +   +AKY  T F  
Sbjct: 229 --IFVAPLPIYHI--YAFMVNLVLYFECGGCSVLIPNPRDISG--LIKTLAKYPFTGFAG 282

Query: 292 APVVLNAIVNAPKEDTILPLPHTVHVMTAGAAPPPSVLFSMNQK-GFRVAHTYGLSETYG 350
              +  A+ + P E   L   H    ++ G A   +      Q  G  ++  YGLSET  
Sbjct: 283 LNTLFVALCHQP-EFKALDFSHLKITISGGTALTAAAANIWQQTTGNTISEGYGLSET-- 339

Query: 351 PSTVCAWKPEWDSLPPETQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFR 410
                   P      P  Q      + V  T ++ LD    + G  V A G+ AGE+  R
Sbjct: 340 -------SPVISLNAPGYQKIGTIGKPVLGTEVKLLD----ENGNEV-AQGE-AGELAAR 386

Query: 411 GNMVMKGYLKNPEANKETF-AGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVE 469
           G  VM GY  NP+       A G+F +GDIA+ + + + +I DR KD+II  G N+   E
Sbjct: 387 GPQVMLGYWNNPQETANVMTADGFFKTGDIAILNEEGFHQIVDRKKDMIIVSGFNVYPNE 446

Query: 470 VENVVYHHPAVLEASVVARPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPA 529
           VENV+  HP ++E +VV   DE   E+  AFV LK D + H+Q K A  I+ FCRE+L A
Sbjct: 447 VENVLASHPNIIECAVVGVKDEHSGEAVKAFVVLKDDSQDHEQMKTA--ILNFCREQLTA 504

Query: 530 YWVPKSVVFGP-LPKTATGKIQKHILRTKA 558
           Y +PK + F P LPK+  GKI +  L+ +A
Sbjct: 505 YKLPKLIEFMPQLPKSTVGKILRRELKHQA 534


Lambda     K      H
   0.319    0.134    0.422 

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: 654
Number of extensions: 39
Number of successful extensions: 5
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: 569
Length of database: 534
Length adjustment: 36
Effective length of query: 533
Effective length of database: 498
Effective search space:   265434
Effective search space used:   265434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 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