GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lldF in Paraburkholderia bryophila 376MFSha3.1

Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate H281DRAFT_00473 H281DRAFT_00473 iron-sulfur cluster-binding protein

Query= uniprot:Q8EGS5
         (464 letters)



>FitnessBrowser__Burk376:H281DRAFT_00473
          Length = 471

 Score =  261 bits (667), Expect = 4e-74
 Identities = 160/422 (37%), Positives = 236/422 (55%), Gaps = 27/422 (6%)

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

Query: 122 TEECHLNPYLEQRGIEVIDTDLGERIIQL-AKMPPSHIVVPAIHMKKEEVGDLFHDKLGT 180
           TEE  LN  L Q G++ I+TDLGE I+Q+    PPSHI+ P +H  K+E+ DLF    G 
Sbjct: 114 TEEMRLNEVLGQMGVQSIETDLGEYILQINGNEPPSHIIAPVVHKDKDEIADLFAKTHGR 173

Query: 181 KAGESDPLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKL 240
                 P  +T  AR  LR  FLSAD  +TG N  IA+ G+VV+ TNEGN  M   +P++
Sbjct: 174 PRLTEIP-DMTLEARQVLRPHFLSADMGVTGGNFVIAETGSVVLVTNEGNEGMCTVMPRV 232

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

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

Query: 352 NTNSIAWACTLCGSCTYVCPTKVPLDKIIHHHRRLKAEAGKLPYGKNAYMPLVGKFMAST 411
               +  A TLCG C  VCP  +PL  ++   R  + E    P+ + A + + G FMA  
Sbjct: 352 KALDLPQAATLCGECNSVCPVGIPLSDLLRKLREKQVERRLRPWKERAGLAVWG-FMA-- 408

Query: 412 TLLNCSMGA--ARTALRILP------GSLLK-PFSGA-WGKYRELPVAPNSSFEAWFKKH 461
             L+  M A   + A+R+L        S+ K P +GA W   R++P     +F   +   
Sbjct: 409 --LHPGMYALVTKLAVRVLERLGGSNRSIAKLPLAGAGWTDTRDMPAPVGRTFRELYAAQ 466

Query: 462 RS 463
           RS
Sbjct: 467 RS 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: 490
Number of extensions: 26
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