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.

Links

Downloads

Related tools

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