GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Herbaspirillum seropedicae SmR1

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 HSERO_RS23535 HSERO_RS23535 acyl-CoA synthetase

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__HerbieS:HSERO_RS23535
          Length = 546

 Score =  557 bits (1435), Expect = e-163
 Identities = 282/543 (51%), Positives = 362/543 (66%), Gaps = 16/543 (2%)

Query: 17  ANYTALTPLWFLDRAAVVHPTRKSVIHGSREYTWRQTYDRCRRLASALADRSIGPGSTVA 76
           ANY ALTP+ F+ RAA V+  R ++IHG+    W QTY R RRLASAL    +G   TV+
Sbjct: 13  ANYAALTPIDFIARAAAVYGKRTAIIHGALRQDWDQTYRRTRRLASALQGLGVGKNDTVS 72

Query: 77  IIAPNIPAMYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMVDQEFFTLAEDS 136
            + PN PAM EAHFGVPM GAVLN +NIRL+A ++ F+L H ++ V+++D EF  LA+  
Sbjct: 73  AMLPNTPAMVEAHFGVPMAGAVLNALNIRLDAESIVFMLRHGEAKVLLIDSEFAALAQQ- 131

Query: 137 LRLMEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATGDPNYPWQPPADE 196
           LR       +      ++ + D    P         G +EYE  LA GD ++ WQ PADE
Sbjct: 132 LR-------TQLPALKIVEVFDELGPPPVAGERF--GHLEYEALLAGGDEHFDWQMPADE 182

Query: 197 WQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWTLPMFHCNGWCFP 256
           W +IAL YTSGTT  PKGVV HHRGA + A+SN L W +    VYLWTLPMFHCNGWCFP
Sbjct: 183 WDAIALNYTSGTTGDPKGVVYHHRGAALNAVSNILEWDLPKHPVYLWTLPMFHCNGWCFP 242

Query: 257 WSLAVLSGTSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKEDTILPLPHTVH 316
           W++A  +G ++CLR+   K V+ +IA++ +TH+CAAP+V  A+ NAP E     +   V 
Sbjct: 243 WTVAARAGVNVCLRKFEPKLVFDLIAEHGITHYCAAPIVHAALANAP-EGWRAGIRGPVK 301

Query: 317 VMTAGAAPPPSVLFSMNQKGFRVAHTYGLSETYGPSTVCAWKPEWDSLPPETQAKLNARQ 376
            M AGA PP +VL  M    F + H YGL+E YGP+ VCA + EW++L  + +A   +RQ
Sbjct: 302 AMVAGAPPPAAVLAKMEAMQFELTHVYGLTEVYGPAAVCAEQDEWNTLSVDQRAVQKSRQ 361

Query: 377 GVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEANKETFAGGWFHS 436
           GVRY     + V+   T  PV ADG+  GEI+FRGN+ MKGYLKN  A  E FAGGWFH+
Sbjct: 362 GVRYHLQSGVTVLSPDTMAPVAADGEEIGEIMFRGNICMKGYLKNDRATHEAFAGGWFHT 421

Query: 437 GDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEASVVARPDERWQES 496
           GD+ V + D YI+IKDRSKD+IISGGENISSVEVE+V+Y HPAVL A+VVA+PDE+W E+
Sbjct: 422 GDLGVMNADGYIKIKDRSKDIIISGGENISSVEVEDVLYRHPAVLAAAVVAQPDEKWGET 481

Query: 497 PCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVFGPLPKTATGKIQKHILRT 556
           PCAFV LK   E       A ++ +FCR  L  + VPK++ FGPLPKT+TGKIQK  LR 
Sbjct: 482 PCAFVELKEGAEVG-----AAELTEFCRSHLAGFKVPKAIYFGPLPKTSTGKIQKFELRK 536

Query: 557 KAK 559
           + K
Sbjct: 537 RMK 539


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: 893
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: 546
Length adjustment: 36
Effective length of query: 533
Effective length of database: 510
Effective search space:   271830
Effective search space used:   271830
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