Aligments for a candidate for acs in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
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