Alignments for a candidate for acs in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Halomonas desiderata SP1

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_086511178.1 BZY95_RS17500 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>NCBI__GCF_002151265.1:WP_086511178.1
          Length = 543

 Score =  614 bits (1583), Expect = e-180
 Identities = 300/549 (54%), Positives = 386/549 (70%), Gaps = 16/549 (2%)

Query: 11  DLPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIG 70
           DLPK  AN+ AL+PL F++R+A ++P   +VIHG    +WR+T+ RCRRLASAL  R I 
Sbjct: 9   DLPKTQANHVALSPLTFIERSASIYPDYPAVIHGDIRRSWRETWARCRRLASALEKRGIK 68

Query: 71  PGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFF 130
           PG TVA + PN+PAM+EAHFGVP+ G VLN +NIRL+A  +A++L H ++  ++VD EF 
Sbjct: 69  PGETVAAMLPNVPAMFEAHFGVPLAGCVLNTLNIRLDAEAIAYMLEHGEAQAVLVDPEFA 128

Query: 131 TLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPW 190
            + ED++  +  K       PL+I + D     E+ +     G +EYE  LA GDP Y +
Sbjct: 129 GVIEDAVSRLAIK-------PLVIDVDDALYEGETRHI----GELEYEALLAEGDPEYAY 177

Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250
           Q P DEWQ+I+L YTSGTT  PKGVV HHRGAY+ A+SN L W M    VYLWTLPMFHC
Sbjct: 178 QLPEDEWQAISLNYTSGTTGKPKGVVYHHRGAYLNAVSNILEWAMPHHPVYLWTLPMFHC 237

Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310
           NGWCFPW++A  +G S+CLR+V  K++  +I   KVTHF  AP+VLN +VN P E     
Sbjct: 238 NGWCFPWTIAANAGVSVCLRRVDPKKIMDLIVDEKVTHFSGAPIVLNGLVNLPAEQK-RA 296

Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370
             H V V TAGAAPP SV+  + + G  V H YGL+E YGP TVCAW+  WD LP E +A
Sbjct: 297 FDHPVKVTTAGAAPPASVIAGVEKLGIEVTHVYGLTEVYGPVTVCAWREAWDELPLEERA 356

Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430
           ++ ARQGVRY  +E L V D  T +PVP DG+T GEI+ RGN VMKGYLKN  A ++   
Sbjct: 357 RIKARQGVRYHMLEALCVADPNTLEPVPKDGETIGEILMRGNNVMKGYLKNEAATEQALE 416

Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490
           GGW+H+GD+AV HPD YIEIKDRSKD+IISGGENIS++EVE+ +Y HPAV EA+VVA+PD
Sbjct: 417 GGWYHTGDLAVWHPDGYIEIKDRSKDIIISGGENISTIEVEDAIYSHPAVEEAAVVAKPD 476

Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550
           E+W E+PCAFV LK  Y +  +     DI++ CR+ L  + VPK+V+F  LPKT+TGKIQ
Sbjct: 477 EKWGETPCAFVKLKVGYGEVTE----ADIIEHCRQHLARFKVPKTVIFTELPKTSTGKIQ 532

Query: 551 KHILRTKAK 559
           K +LR +A+
Sbjct: 533 KFVLREEAR 541


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: 914
Number of extensions: 43
Number of successful extensions: 4
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: 543
Length adjustment: 36
Effective length of query: 533
Effective length of database: 507
Effective search space:   270231
Effective search space used:   270231
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)
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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 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