GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lldF in Burkholderia phytofirmans PsJN

Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate BPHYT_RS12805 BPHYT_RS12805 hypothetical protein

Query= uniprot:Q8EGS5
         (464 letters)



>FitnessBrowser__BFirm:BPHYT_RS12805
          Length = 471

 Score =  259 bits (662), Expect = 1e-73
 Identities = 152/425 (35%), Positives = 234/425 (55%), Gaps = 33/425 (7%)

Query: 62  EIKLHTLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSML 121
           E +   L NL  +LETFE+     G+ V +A+   E  R+V +I   H+VKK++K+KSM+
Sbjct: 54  ERRNRALENLDVWLETFEREAARRGVTVLFAETTQEAARLVGDIARRHEVKKVIKTKSMV 113

Query: 122 TEECHLNPYLEQRGIEVIDTDLGERIIQLA-KMPPSHIVVPAIHMKKEEVGDLFHDKLGT 180
           TEE  LN  L Q G++ I+TDLGE I+Q+    PPSHI+ P +H  K+E+ DLF  K   
Sbjct: 114 TEEMRLNEVLGQMGVQSIETDLGEYILQINDNEPPSHIIAPVVHKDKDEIADLFA-KTHN 172

Query: 181 KAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKL 240
           +   ++   +TR AR  LR  F++AD  +TG N  +A+ G+VV+ TNEGN  M   +P++
Sbjct: 173 RPRLTEITDMTREAREMLRPHFMTADMGVTGGNFVVAETGSVVLVTNEGNEGMCTVMPRV 232

Query: 241 QLHSMGIDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDGE------MHVIIV 294
            +   GI+KV+P ++  A  +R L R+ATGQ  + Y +   GP+ +G+      M+V++V
Sbjct: 233 HVAVTGIEKVLPTLEDLATAMRLLPRSATGQATSNYFSVLTGPRGEGDQDGPEHMYVVLV 292

Query: 295 DNGRTEMMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGATH---D 351
           D GRT ++      E L+CIRCG C+N CPVY++ GG++Y +  PGP+G  +  ++   D
Sbjct: 293 DGGRTGLIGGD-FQEMLRCIRCGACMNHCPVYQKVGGHAYGWVYPGPMGSVLTPSYVGID 351

Query: 352 NTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKLPYGKNAYMPLVGKFMA-- 409
               +  A TLCG C  VCP  +PL  ++   R  + E    P+ + A + + G F+A  
Sbjct: 352 KALDLPQAATLCGECNSVCPVGIPLSDLLRKLREKQVERRLRPWKERAGLAVWG-FLALH 410

Query: 410 ----------STTLLNCSMGAARTALRILPGSLLKPFSGA-WGKYRELPVAPNSSFEAWF 458
                     +  +L    G  R+  R+       P  GA W   R++P     +F   +
Sbjct: 411 PDAYALFTKLAVRVLERMGGRNRSIARL-------PLGGAGWTNTRDMPAPVGRTFRELY 463

Query: 459 KKHRS 463
              RS
Sbjct: 464 AAQRS 468


Lambda     K      H
   0.320    0.134    0.413 

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: 497
Number of extensions: 25
Number of successful extensions: 8
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: 464
Length of database: 471
Length adjustment: 33
Effective length of query: 431
Effective length of database: 438
Effective search space:   188778
Effective search space used:   188778
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: 51 (24.3 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:

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