GapMind for catabolism of small carbon sources

 

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

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate 353281 BT3755 acetyl-coenzyme A synthetase (NCBI ptt file)

Query= BRENDA::A4YDT1
         (564 letters)



>FitnessBrowser__Btheta:353281
          Length = 551

 Score =  357 bits (915), Expect = e-103
 Identities = 210/528 (39%), Positives = 308/528 (58%), Gaps = 20/528 (3%)

Query: 38  FNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGD 97
           FN+  DV  D    E+  K AL+W + + GE  + S+ ++   ++   S  +  G+ +GD
Sbjct: 29  FNFGYDVV-DAWAAEQPDKNALLWTN-DQGESRQFSFADMKRYTDMTASYFQSLGIGRGD 86

Query: 98  VVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFS--DLKPSAIISDSLRAS 155
           +V L+ K     W   +A+ K G  ++P+   LT  ++ YR +  D+K      + +   
Sbjct: 87  MVMLILKRRYEFWYSTIALHKLGATVIPATHLLTKKDIIYRCNAADIKMIVAAGEGIILQ 146

Query: 156 VMEEALGSL-KVEKFLIDGKR--ETWNSLEDESSNAEP-----EDTRGEDVIINYFTSGT 207
            +++AL     VEK +  G    E +        NA P          +D+ + YFTSGT
Sbjct: 147 HIKDALPECPSVEKLVSVGPEVPEGFEDFHQGIDNAAPFIRPRHANTNDDISLMYFTSGT 206

Query: 208 TGMPKRVIHTAVSYPVGSITTASIV-GVRESDLHLNLSATGWAKFAWSSFFSPLLVGATV 266
           TG PK V H   +YP+G I T S    + E+ LHL ++ TGW K  W   +   + GA +
Sbjct: 207 TGEPKMVAHD-FTYPLGHIVTGSFWHNLDENSLHLTIADTGWGKAVWGKLYGQWIAGANI 265

Query: 267 VGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLN 326
              ++E K      L +++   VTS CAPPT +R  I  DL ++    LR    AGE LN
Sbjct: 266 FVYDHE-KFTPAAILEKIQEYQVTSLCAPPTIFRFLIHEDLTKYDLSSLRYCTIAGEALN 324

Query: 327 PEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEI 386
           P V + +K    + + + +GQTETT  V   P+++ KPGSMG P+P YD+ L+D EG+ +
Sbjct: 325 PAVFETFKKLTGIKLMEGFGQTETTLTVATMPWMEPKPGSMGLPNPQYDVDLIDSEGRSV 384

Query: 387 TKPYEVGHITVKLNP-RPIGLFLGY-SDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGR 444
            +  E G I ++ +  +P+GLF  Y  D ++  E++ +G YYTGD A+ DE+GY +FVGR
Sbjct: 385 -EAGEQGQIVIRTSKGKPLGLFKEYYRDAERTHEAWHDGIYYTGDVAWKDEDGYLWFVGR 443

Query: 445 GDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGY--MPSK 502
            DDVIK+S YR+GPFEVESAL+ HPAV E A+ GVPD +R Q+VKA IVL K Y     +
Sbjct: 444 ADDVIKSSGYRIGPFEVESALMTHPAVIECAITGVPDEIRGQVVKATIVLSKDYKARAGE 503

Query: 503 ELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEE 550
           EL +E++  +K + +PYK PR+IEFVDELPKTISGKIRRVE+R+ +E+
Sbjct: 504 ELIKELQNHVKKVTAPYKYPRVIEFVDELPKTISGKIRRVEIRENDEK 551


Lambda     K      H
   0.318    0.137    0.402 

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: 795
Number of extensions: 36
Number of successful extensions: 6
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: 564
Length of database: 551
Length adjustment: 36
Effective length of query: 528
Effective length of database: 515
Effective search space:   271920
Effective search space used:   271920
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 (21.7 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 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