Alignments for a candidate for acs in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Bacteroides thetaiotaomicron VPI-5482

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 352309 BT2782 long-chain-fatty-acid--CoA ligase (NCBI ptt file)

Query= SwissProt::Q8VZF1
         (569 letters)



>FitnessBrowser__Btheta:352309
          Length = 549

 Score =  146 bits (369), Expect = 2e-39
 Identities = 144/553 (26%), Positives = 226/553 (40%), Gaps = 53/553 (9%)

Query: 27  FLDRAAVVHPTRKSVIHGSRE--YTWRQTYDRCRRLASALADRSIGPGSTVAIIAPNIPA 84
           +L+  A   P ++ +++  R   +TW Q   R   +A  L    +  G+ V I A N+P 
Sbjct: 11  WLEHWAEETPDKEYIVYSDRNLRFTWSQLNQRVDDMAKGLIAVGVERGTHVGIWAANVPD 70

Query: 85  MYEAHFGVPMCGAVLNCVNIRLNAPTVAFLLSHSQSSVIMV-----DQEFFTLAEDSLRL 139
                +     GAV   VN       + +L  +S    + +     D +F  +    L  
Sbjct: 71  WLTLLYACAKIGAVYVTVNTNYKQAELEYLCQNSDMHTLCIVNGEKDSDFVQMTYTMLPE 130

Query: 140 MEEKAGSSFKRPLLIVIGDHTCAPESLNRALSKGAIEYEDFLATG-----DPNYPWQPPA 194
           ++       K      + +     +  +R +   A    + L  G     D     +   
Sbjct: 131 LKTCERGHLKSERFPYMKNVIYVGQEKHRGMYNTA----EILLLGNNVEDDRLTELKSKV 186

Query: 195 DEWQSIALGYTSGTTASPKGVVLHHRGAYIMALSNPLIWGMQDGAVYLWT--------LP 246
           D    + + YTSGTT  PKGV+L H   Y +A +     G   G    +T        +P
Sbjct: 187 DCHDVVNMQYTSGTTGFPKGVMLTH---YNIANN-----GFLTGEHMKFTADDKLCCCVP 238

Query: 247 MFHCNGWCFPWSLAVLSG-TSICLRQVTAKEVYSMIAKYKVTHFCAAPVVLNAIVNAPKE 305
           +FHC G        +  G T + + +     V + I K + T     P +  A ++ P  
Sbjct: 239 LFHCFGVVLATMNCLTHGCTQVMVERFDPLVVLASIHKERCTALYGVPTMFIAELHHPMF 298

Query: 306 DTILPLPHTVHVMTAGAAPPPSVLFSMNQKGF-RVAHTYGLSETYGPSTVCAWKPEWDSL 364
           D          +M AG+  P  ++  + +K + +V   YGL+E     T       +D  
Sbjct: 299 DLFDMSCLRTGIM-AGSLCPVELMKQVEEKMYMKVTSVYGLTEAAPGMTATRIDDSFD-- 355

Query: 365 PPETQAKLNARQGVRYTGMEQLDVIDTQTGKPVPADGKTAGEIVFRGNMVMKGYLKNPEA 424
                  +      R     ++ VID +TG+  P      GE+  RG   MKGY KNPEA
Sbjct: 356 -------VRCNTVGRDFEFTEVRVIDPETGEECPVG--VQGEMCNRGYNTMKGYYKNPEA 406

Query: 425 NKETF-AGGWFHSGDIAVKHPDNYIEIKDRSKDVIISGGENISSVEVENVVYHHPAVLEA 483
             E      + HSGD+ +K  D    I  R KD+II GGENI   E+E  +Y    V + 
Sbjct: 407 TAEVIDKDNFLHSGDLGIKDEDGNYRITGRIKDMIIRGGENIYPREIEEFLYKLDGVKDV 466

Query: 484 SVVARPDERWQESPCAFVTLKSDYEKHDQNKLAQDIMKFCREKLPAYWVPKSVVF-GPLP 542
            V   P +++ E+  AF+ L+   E H+      D+  FC+ K+  Y +PK V F    P
Sbjct: 467 QVAGIPSKKYGEAVGAFIILQEGVEMHE-----SDVRDFCKNKISRYKIPKYVFFVKEFP 521

Query: 543 KTATGKIQKHILR 555
            T +GKIQK  L+
Sbjct: 522 MTGSGKIQKFRLK 534


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: 644
Number of extensions: 34
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 569
Length of database: 549
Length adjustment: 36
Effective length of query: 533
Effective length of database: 513
Effective search space:   273429
Effective search space used:   273429
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)
SQLite3 databases

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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