GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Arenimonas metalli CF5-1

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_034211018.1 N787_RS04435 long-chain fatty acid--CoA ligase

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_000747155.1:WP_034211018.1
          Length = 560

 Score =  145 bits (365), Expect = 5e-39
 Identities = 137/511 (26%), Positives = 221/511 (43%), Gaps = 45/511 (8%)

Query: 72  LSYHELSLMSNRVLS-TLRKHGLKKGDVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNL 130
           ++Y E+  +S +  +  L +  LKKGD V LM      +      V++ G  +V +    
Sbjct: 51  ITYAEVDRLSTQFANYLLHELKLKKGDRVALMMPNVLQYPIAIFGVLRAGLTVVNTNPMY 110

Query: 131 TVAEMKYRFSDLKPSAIISDSLRASVMEEALGSLKVEKFLIDG--------KRETWNSLE 182
           T  E+K++  D   SAI+     A V+ + +   +V++ L+ G        K    N + 
Sbjct: 111 TARELKHQLVDSGASAIVVLENFAHVVADVVAETQVKQVLVTGVGDMLGFPKGALVNFVL 170

Query: 183 DESSNAEPE------------------------DTRGEDVIINYFTSGTTGMPKRVIHTA 218
                  PE                        D RG D+    +T GTTG+ K  + T 
Sbjct: 171 RHVKKQVPEYDLPGAIRFGDAVAMGAKHQLPDIDIRGHDIAFLQYTGGTTGVAKGAMLTH 230

Query: 219 VSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINY--EGKLD 276
            +       ++  +G      H  +  T    +   +  +  LV     G+N+      D
Sbjct: 231 RNLVANMQQSSVWLGSNAKPGH-EVIITALPLYHIFALTANCLVFMKFGGLNHLITNPRD 289

Query: 277 TRRYLGEVENLGVTSFCAPPTAWRQFI-TLDLDQFRFERLRSVVSAGEPLNPEVIKIWKD 335
            + ++ E+  +  T+     T +   + T   D+  F  +   +  G  +   V + WK 
Sbjct: 290 MKGFVAELSKIPFTAITGVNTLFNGLLNTPGFDKIDFSNMHLSLGGGMAVQRAVAERWKK 349

Query: 336 KFNLTIRDFYGQTETTAMVGNFPF-LKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGH 394
              +T+ + YG TET+      P  L+   G++G P P  D  + DD GK++    EVG 
Sbjct: 350 VTGITLVEAYGLTETSPAACMNPMDLEDFNGAIGLPIPSTDACVKDDAGKQLPVG-EVGE 408

Query: 395 ITVKLNPRPIGLFLGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDY 454
           + ++      G +    +  K +++  EG+ +TGD A  D  G+FY V R  D+I  S +
Sbjct: 409 LCIRGPQVMAGYWQRPEETAKVIDA--EGWLHTGDMAKMDAGGFFYIVDRKKDMILVSGF 466

Query: 455 RVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKT 514
            V P EVE  +   P V E A VGVPD    + VK  IV K   +     A+++R   K 
Sbjct: 467 NVYPNEVEDVIALMPGVLEVAAVGVPDDKSGEAVKVVIVRKDPAL----TADQVRAFCKE 522

Query: 515 LLSPYKVPRIIEFVDELPKTISGKIRRVELR 545
            L+ YK PR++EF  ELPK+  GKI R ELR
Sbjct: 523 NLTGYKQPRLVEFRTELPKSNVGKILRRELR 553


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: 628
Number of extensions: 25
Number of successful extensions: 6
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: 564
Length of database: 560
Length adjustment: 36
Effective length of query: 528
Effective length of database: 524
Effective search space:   276672
Effective search space used:   276672
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 24 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