GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella loihica PV-4

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 5210425 Shew_2866 acyl-CoA synthetase (RefSeq)

Query= SwissProt::P39062
         (572 letters)



>FitnessBrowser__PV4:5210425
          Length = 569

 Score =  191 bits (485), Expect = 7e-53
 Identities = 155/522 (29%), Positives = 253/522 (48%), Gaps = 63/522 (12%)

Query: 75  TFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEAFM 134
           T+ ++ E S R  NVLR  G V +GD V +FMP  P+ +   LG +K GA+  P+     
Sbjct: 60  TYAQLDEMSTRFANVLRGLG-VGQGDGVAVFMPNCPQFHIAFLGILKCGAVHMPVSPLSK 118

Query: 135 EGAVKDRLENSEAKVVVTTPELLERI-PVDKLPHLQHVFVVG------------------ 175
           E  ++ +L +S+ KV +    LL  + PV +   ++H+                      
Sbjct: 119 EMELRHQLGDSQPKVALCYDALLPTMRPVCQELGIEHIITTSYTDVRPRAITAVLPDLFE 178

Query: 176 -GEAESGTNIINYDEAAKQESTRLDIEWMDKKDGFL-LHYTSGSTGTPKGVLHVHEAMI- 232
             +      II++ EA    S  + ++++   D    ++YTSG+TG PKGV+H H  MI 
Sbjct: 179 IPKTPLADGIIDFFEAIDNASKEV-LDYIPALDDLAAINYTSGTTGMPKGVMHTHRNMIG 237

Query: 233 ---QQYQTGKWVLDLKEEDIYWCTADPG-WVTGTVYGIFAPWLNGATNVIVGGRFSPESW 288
                Y      +  +  D+   +  P  W+ G   G+  P  +GAT V++  R+  +++
Sbjct: 238 TMASYYPVTFGEVGPEGTDLVMLSFLPEFWIAGEDTGLLLPLYSGATLVLMA-RWDTKAF 296

Query: 289 YGTIEQLGVNVWYSAPTAFRMLMGAGDEMAA-----KYDLTSLRHV--LSVGEPLNPEVI 341
              +    VN+         ML+ + DE+       ++DLTSL  V  +S  + LN +  
Sbjct: 297 MELVHHHKVNMTI-------MLIDSVDEILNHPHLHQFDLTSLTTVPCISFIKKLNRDYR 349

Query: 342 -RWGHKVFNKRIHDTWWMTETGSQLICN-------YPCMDIK--PGSMGKPIPGVEAAIV 391
            RW            + MTET +   C+          MD+   P  +G P+PG E  I 
Sbjct: 350 QRWRELTGTTLFEVAYGMTETHT---CDTFTRGFQVDDMDLSFDPAFLGLPVPGTEIKIC 406

Query: 392 DNQGNELPPYRM-GNLAIKKGWPSMMHTIWNNPEKYESYFMPGGWYVSGDSAYMDEEGYF 450
           D    EL P  + G + I+   P+++   WN P+  ++ F  GGWY +GD   + EEG+F
Sbjct: 407 DFVTGELMPLGVEGEIQIRT--PTLLKGYWNKPDLNKNLFEEGGWYRTGDLGMITEEGFF 464

Query: 451 WFQGRVDDVIMTSGERVGPFEVESKLVEHPAIAEAGVIGKPDPVRGEIIKAFIALREGFE 510
            + GR  +++  +G  V P EVES L +HPAIA  GV+G+PD  +G++  AF+ L+ GF 
Sbjct: 465 RYLGRRKEMLKVNGMSVFPTEVESMLGQHPAIASCGVVGRPDERKGQVPVAFVTLKPGF- 523

Query: 511 PSDKLKEEIRLFVKQGLAAHAAPREIEFKDKLPKTRSGKIMR 552
             D+ +E ++ +    +A    P EI  +++LP T +GKI +
Sbjct: 524 --DETQESLQAWCVNAMAIFKVP-EIRIQERLPMTATGKIRK 562


Lambda     K      H
   0.318    0.136    0.425 

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: 804
Number of extensions: 46
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: 572
Length of database: 569
Length adjustment: 36
Effective length of query: 536
Effective length of database: 533
Effective search space:   285688
Effective search space used:   285688
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: 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