GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Halobacillus alkaliphilus FP5

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_089751845.1 BMZ06_RS09710 acyl--CoA ligase

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_900113125.1:WP_089751845.1
          Length = 524

 Score =  353 bits (906), Expect = e-102
 Identities = 204/508 (40%), Positives = 297/508 (58%), Gaps = 13/508 (2%)

Query: 52  ERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLKKGDVVYLMTKVHPMHWA 111
           E   + AL+W     G   +++Y +L   +N++ +    HGL+KGD + +M       + 
Sbjct: 23  EDPDRKALLWLS-EAGGRKEVTYEQLLHQANKMGNAFLDHGLQKGDKILVMIPRLIEAYQ 81

Query: 112 VFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKFLI 171
           V++A +K G V++PS+  L   +++YR +     A+IS       ++E   S ++ KF +
Sbjct: 82  VYIAALKAGLVIIPSSEMLRAKDLQYRITHGDVRAVISYHPFTEHLDEVKESDQLLKFSV 141

Query: 172 DGKRETW----NSLEDESSNAEPEDTRGEDVIINYFTSGTTGMPKRVIHTAVSYPVGSIT 227
            G +E W      LED SS  E  DT  +D+    +TSGTTG PK V+HT   +    + 
Sbjct: 142 GGSKEGWFDFDGLLEDYSSTLETADTASDDMAFLSYTSGTTGNPKGVVHTH-GWGYAHLK 200

Query: 228 TASI--VGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGEVE 285
           TA+   + +++ D     +  GW K+ WS F S L  GA   G+ Y+GK + + YL  ++
Sbjct: 201 TAAYKWLAIQDGDTVWATAGPGWQKWVWSPFLSVLGTGAR--GLVYQGKFNPKTYLSLMD 258

Query: 286 NLGVTSFCAPPTAWRQFITLD-LDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRDF 344
              V   C  PT +R    +D LD ++   L S VSAGEPLN EVI  +K+ FN+T+RD 
Sbjct: 259 EHNVNVLCCTPTEYRLMAKVDNLDDYQLAGLHSAVSAGEPLNREVIDTFKNHFNVTVRDG 318

Query: 345 YGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLNPRPI 404
           YGQTE T +VG    ++V+PGSMG+P P   + ++D+  + + +  EVG I V L+  P 
Sbjct: 319 YGQTENTLLVGILKDMEVRPGSMGRPTPGNQVEIIDELAEPV-ETGEVGDIAVHLDT-PA 376

Query: 405 GLFLGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVESA 464
                Y D ++   S R  YY TGD+A  DE+GYF+F GR DD+I +S Y +GPFEVE A
Sbjct: 377 LFKEYYKDPERTKMSHRGHYYVTGDQARKDEDGYFWFEGRSDDIIISSGYTIGPFEVEDA 436

Query: 465 LLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYKVPRI 524
           L++H AV E AVV  PD VR  +VKA+IVL+  Y P+  L +E+++ +K   +PYK PR 
Sbjct: 437 LVKHKAVQECAVVSSPDEVRGNVVKAFIVLQNNYEPTDSLVKELQDHVKNTTAPYKYPRK 496

Query: 525 IEFVDELPKTISGKIRRVELRKREEEKR 552
           IEF +ELPKT SGKIRRVELRK+E   R
Sbjct: 497 IEFTEELPKTTSGKIRRVELRKKENASR 524


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: 741
Number of extensions: 44
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: 524
Length adjustment: 35
Effective length of query: 529
Effective length of database: 489
Effective search space:   258681
Effective search space used:   258681
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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