Alignments for a candidate for acs in Azospirillum brasilense Sp245

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Azospirillum brasilense Sp245

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 AZOBR_RS06255 AZOBR_RS06255 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__azobra:AZOBR_RS06255
          Length = 551

 Score =  612 bits (1578), Expect = e-179
 Identities = 298/551 (54%), Positives = 386/551 (70%), Gaps = 16/551 (2%)

Query: 11  DLPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIG 70
           DL +  AN   L+PL FL R A V+P R +VIHG    TW +TY+RC RLASALA R IG
Sbjct: 12  DLDQNAANTVPLSPLSFLRRTAAVYPQRIAVIHGPVRRTWAETYERCVRLASALAKRGIG 71

Query: 71  PGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFF 130
            G TVA++APN P  +EAHFGVPM GAVLN +NIRL+A  +AF+L H ++ V++ D+EF 
Sbjct: 72  LGDTVAVMAPNTPESFEAHFGVPMTGAVLNALNIRLDAEALAFILEHGEAKVLLTDREFS 131

Query: 131 TLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPW 190
            +   ++ ++E K     +RP++I I D    P++    L  G   YE FL TGDP Y W
Sbjct: 132 GVISKAVHMLEPK-----RRPIVIDIDD----PQAKGGELI-GEQTYEQFLETGDPAYEW 181

Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250
             PADEWQ+IAL YTSGTT +PKGVV HHRGAY+ A+ N L W M    VYLWTLPMFHC
Sbjct: 182 PMPADEWQAIALNYTSGTTGNPKGVVYHHRGAYLNAMGNVLTWAMPHHPVYLWTLPMFHC 241

Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310
           NGWCFPW++  ++GT++C+R +TAK +Y  +A   VTH C AP+++  IVNAP ED    
Sbjct: 242 NGWCFPWTVTAMAGTNVCVRTITAKGIYDALADLGVTHMCGAPIIMGLIVNAP-EDQKRE 300

Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370
           +P  V +MTAGAAPP +V+  + + GF V H YGL+E YGP T+CAW   W+ LP E +A
Sbjct: 301 IPRGVKMMTAGAAPPAAVIEKIERMGFDVTHVYGLTEVYGPVTICAWHEHWNDLPLEERA 360

Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430
            L ARQGV Y  +E L V D  T +P   DG T GEI  RGN VMKGYLKNP A +E F+
Sbjct: 361 ALKARQGVNYATLEGLMVADPNTLQPTRKDGVTMGEIFMRGNTVMKGYLKNPRATQEAFS 420

Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490
           GGWFH+GD+ V H D YIE+KDRSKD+IISGGENIS++EVE+V+Y HP ++EA+VVARPD
Sbjct: 421 GGWFHTGDLGVWHADGYIELKDRSKDIIISGGENISTIEVESVLYKHPDIVEAAVVARPD 480

Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550
           E+W E+PCAFVT+K   +  +      +++ +CRE L  +  P++VVF  LPKT+TGKIQ
Sbjct: 481 EKWGETPCAFVTVKEGKQLTE-----AEVIAYCREHLAHFKCPRTVVFTALPKTSTGKIQ 535

Query: 551 KHILRTKAKEM 561
           K++LR +A+ +
Sbjct: 536 KYVLRDQARAL 546


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: 912
Number of extensions: 35
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: 551
Length adjustment: 36
Effective length of query: 533
Effective length of database: 515
Effective search space:   274495
Effective search space used:   274495
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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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 paper from 2022 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

GapMind for catabolism of small carbon sources