GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Pedobacter sp. GW460-11-11-14-LB5

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate CA265_RS12240 CA265_RS12240 phosphoglycerate dehydrogenase

Query= BRENDA::O66939
         (334 letters)



>FitnessBrowser__Pedo557:CA265_RS12240
          Length = 311

 Score =  152 bits (384), Expect = 1e-41
 Identities = 98/325 (30%), Positives = 168/325 (51%), Gaps = 31/325 (9%)

Query: 3   VLFTSVPQEDVPFYQEALKDLSLKIYTTDVSKVPENELKKAELISVFVYDK--LTEELLS 60
           +L  ++ +E +   QE     ++ ++T       ++ L   E+ ++    K  + + L+ 
Sbjct: 6   LLLETIAEEALALLQE-----NVNVFTGYDEAGLKDTLNNVEVHAIITRGKKHIDKTLMD 60

Query: 61  KMPRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSPESVAEHTFAMILTLVKRLKRIE 120
             P L++     VG D++D+D    + I V + P  +  ++AEHT A++L L++ + R  
Sbjct: 61  ACPHLEVAARCGVGLDNVDVDEASARKIRVINAPGSNAATIAEHTLALMLMLMRDMHRSV 120

Query: 121 DRVKKLNFSQDSEILARELNRLTLGVIGTGRIGSRVAMYGLAFGMKVLCYDVVKREDLKE 180
           + VK+ N++  ++    ELN  TLG++G G IG RVA  G AFGMKVLC+          
Sbjct: 121 NHVKQNNWNWRNQYAGDELNGKTLGILGLGNIGKRVAKLGDAFGMKVLCW---------S 171

Query: 181 KGCVYTSLDELLKESDVISLHVPYTKETHHMINEERISLMKDGVYLINTARGKVVDTDAL 240
           +      LDE+L++SDV+SLH+P + ET+ +I   +++LMK   +LINTARG ++D  AL
Sbjct: 172 RSVQDLPLDEVLQQSDVVSLHLPLSNETNEIIGASQLALMKPKAFLINTARGALIDHAAL 231

Query: 241 YRAYQRGKFSGLGLDVFEDEEILILKKYTEGKATDKNLKILELACKDNVIITPHIAYYTD 300
             A   G  +G   DV  DE                 L+ L +    N ++TPH A  T 
Sbjct: 232 LDALNAGTIAGFAADVLPDE---------------PPLQSLAVVQHPNALVTPHAASLTA 276

Query: 301 KSLERIREETVKVVKAFVKGDLEQI 325
            + +++   TV+ V + + G   ++
Sbjct: 277 STYKQMCLLTVRNVLSVLAGQQPEL 301


Lambda     K      H
   0.319    0.138    0.383 

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: 196
Number of extensions: 6
Number of successful extensions: 3
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: 334
Length of database: 311
Length adjustment: 28
Effective length of query: 306
Effective length of database: 283
Effective search space:    86598
Effective search space used:    86598
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: 48 (23.1 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