GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__ANA3:7026089
          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:

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