Alignments for a candidate for acs in Jannaschia aquimarina GSW-M26

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Jannaschia aquimarina GSW-M26

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 WP_043916943.1 jaqu_RS00350 AMP-binding protein

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_000877395.1:WP_043916943.1
          Length = 539

 Score =  529 bits (1362), Expect = e-154
 Identities = 272/553 (49%), Positives = 350/553 (63%), Gaps = 21/553 (3%)

Query: 8   DIDDLPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADR 67
           D   L K PAN+ ALTPL  L RAA + P R+++++G+   ++     R  RLASALA R
Sbjct: 6   DETGLDKGPANHVALTPLSHLARAAAIWPDREALVYGTVRRSYSDYQARVSRLASALAAR 65

Query: 68  SIGPGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQ 127
            + PG  VA + PN+PA  EA FGVP CGAVLN +N RL+  TV ++L H  + V++VD 
Sbjct: 66  GVTPGDVVAPLLPNVPAQVEAGFGVPACGAVLNTINTRLDLETVQYILGHGGAKVLLVDS 125

Query: 128 EFFTLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPN 187
               LAE++  + +         PL+I + D     E+  R L+     YED +A GDP 
Sbjct: 126 ALIELAEEAAAVQKTP-------PLIIEVPDPVAGIEATGRHLT-----YEDLVAEGDPA 173

Query: 188 YPWQPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPM 247
           + W  P DEW+S+AL YTSGTT  PKGVV HHRGAY++     + W M      L  +P+
Sbjct: 174 FRWIMPEDEWESLALNYTSGTTGRPKGVVYHHRGAYLITFGTVVSWRMVLHPRLLTVVPL 233

Query: 248 FHCNGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDT 307
           FHCNGWC  W + ++ GT +CLR+VTAK ++  IA   VTHF  AP+VLN + NA  +D 
Sbjct: 234 FHCNGWCHFWMMPLVGGTVVCLREVTAKGIFDAIADEGVTHFGGAPIVLNTLANAG-DDE 292

Query: 308 ILPLPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPE 367
             PLPH V V TAGA PP + L      G  V H YGL+ETYG      W+ +WD   P+
Sbjct: 293 RRPLPHVVEVYTAGAPPPAATLAKAEALGLNVTHCYGLTETYGHVVENVWQDKWDGSAPD 352

Query: 368 TQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKE 427
            +A L ARQGV Y  ME + V D   G PVP DG+T GE+  RGN VMKGY +NPEA  E
Sbjct: 353 ERAALKARQGVAYPMMEGVGVFDAD-GSPVPLDGETQGEVGMRGNAVMKGYYRNPEATAE 411

Query: 428 TFAGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVA 487
            F GGWF SGDIAV HPD Y++IKDR+KD+IISGGEN+SSVEVE V+ HHPAV   +VVA
Sbjct: 412 AFEGGWFRSGDIAVVHPDGYLQIKDRAKDIIISGGENVSSVEVEGVLMHHPAVDLCAVVA 471

Query: 488 RPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATG 547
           +PDE+W E PCAFV  + +  +       ++++ F RE+L  +  PK VVFG LPKT+TG
Sbjct: 472 QPDEKWGEVPCAFVETRGEVTE-------EELIAFARERLAGFKTPKRVVFGELPKTSTG 524

Query: 548 KIQKHILRTKAKE 560
           KIQK  LR +AK+
Sbjct: 525 KIQKFELRNRAKD 537


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: 909
Number of extensions: 40
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: 539
Length adjustment: 36
Effective length of query: 533
Effective length of database: 503
Effective search space:   268099
Effective search space used:   268099
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources