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_RS09405 AZOBR_RS09405 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__azobra:AZOBR_RS09405
          Length = 544

 Score =  553 bits (1425), Expect = e-162
 Identities = 273/549 (49%), Positives = 365/549 (66%), Gaps = 15/549 (2%)

Query: 11  DLPKIPANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIG 70
           +L +  AN+  LTPL FL R+A+V+P + +V++G    +W +   R R LASA++   + 
Sbjct: 9   ELSRRTANHVPLTPLDFLRRSAMVYPDKTAVVYGPLRRSWLEVEHRARALASAVSRAGVR 68

Query: 71  PGSTVAIIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFF 130
           PG  V+++A N PAM EAHFGVP  GAVLN +N RL+ P VAF+L H++S + +VD+   
Sbjct: 69  PGEVVSVLAFNTPAMLEAHFGVPGAGAVLNAINTRLDPPAVAFILEHAESRLFLVDRGLS 128

Query: 131 TLAEDSLRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPW 190
            +A  +L  M          P ++ I D      +   A   G +EYEDFL TGDP  PW
Sbjct: 129 AVARAALERMTAP-------PRVVWIDD-----PAAQDADPVGDLEYEDFLKTGDPEAPW 176

Query: 191 QPPADEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHC 250
           + P DEW+SIAL YTSGTT +PKGV+ HHRGA++ AL N + +G++  +VYLWTLPMFHC
Sbjct: 177 RRPEDEWESIALNYTSGTTGNPKGVLYHHRGAHLNALGNVITFGLRPDSVYLWTLPMFHC 236

Query: 251 NGWCFPWSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILP 310
           NGW +PW++  +  T +CLR V    ++ +IA+ KVTH C APVVL  +++AP       
Sbjct: 237 NGWTYPWAVTAVGATHVCLRAVDPAAIFRLIAEEKVTHLCGAPVVLTMLIHAPDAVKRAF 296

Query: 311 LPHTVHVMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQA 370
               V V T GAAPP +V+  M + GFR+ H YG++E YGPST CAW+  W  LP E +A
Sbjct: 297 DHGPVQVATGGAAPPSAVIAGMERMGFRLTHLYGMTECYGPSTGCAWQEAWAELPLEERA 356

Query: 371 KLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFA 430
              ARQGV    M +  V+D  TG+ VPADG+T GE+  RGN VMKGYLKNP A  E   
Sbjct: 357 VKMARQGVPNVTMSEQTVLDPDTGREVPADGETLGELALRGNTVMKGYLKNPAATDEALR 416

Query: 431 GGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPD 490
            GW H+GD+AV HPD Y+EIKDR+KD+IISGGENI+S+EVE V+Y HP V+EA+VVARPD
Sbjct: 417 DGWLHTGDLAVLHPDRYVEIKDRAKDIIISGGENIASLEVEEVLYKHPHVMEAAVVARPD 476

Query: 491 ERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQ 550
            +W E+PCAFVTLK   E         +++ +CR+ L  +  P++VVFG LPKT+TGKIQ
Sbjct: 477 AKWGETPCAFVTLKPGSEGRVSE---AEVIGWCRDHLAHFKTPRTVVFGALPKTSTGKIQ 533

Query: 551 KHILRTKAK 559
           K +LR +A+
Sbjct: 534 KFVLREQAR 542


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: 890
Number of extensions: 31
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: 544
Length adjustment: 36
Effective length of query: 533
Effective length of database: 508
Effective search space:   270764
Effective search space used:   270764
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