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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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