GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Fibrella aestuarina BUZ 2

Align L-lactate dehydrogenase; EC 1.1.1.27 (uncharacterized)
to candidate WP_015333884.1 FAES_RS24460 Ldh family oxidoreductase

Query= curated2:Q07251
         (349 letters)



>NCBI__GCF_000331105.1:WP_015333884.1
          Length = 355

 Score =  142 bits (358), Expect = 1e-38
 Identities = 110/345 (31%), Positives = 166/345 (48%), Gaps = 33/345 (9%)

Query: 16  LAAQQVPADIADDVAEHLVESDRCGYISHGLSILPNYRTALDGHSVNPQGRAKCVLDQGT 75
           +   +  A +A DV   LV +D  G  SHG++ LP Y    D   +NP    K V +  +
Sbjct: 18  IGCSEADARLAADV---LVSADLRGVDSHGVARLPGYVRLYDNGRLNPTPAIKIVHETPS 74

Query: 76  LMVFDGDGGFGQHVGKSVMQAAIERVRQHGHCIVTLRRSHHLGRMGHYGEMAAAAGFVLL 135
             V DGD G G  VG   MQ AI++ R  G   V +R S+H G  G++  +A     +  
Sbjct: 75  TAVVDGDRGLGLVVGPWAMQVAIDKARVAGTGWVAVRNSNHFGIAGYHALLATDHDMIGQ 134

Query: 136 SFTNVINRAPVVAPFGGRVARLTTNPLCFAGPMPNGRPPLVVDIATSAIAINKARVLAEK 195
           + T+    AP+VAP       L TNP+  A P     PP + D A++A+A  K  +L  K
Sbjct: 135 AMTHA---APLVAPTFSLDKLLGTNPIAVAIPAAT-EPPFLADFASTAVAYGKLEILQRK 190

Query: 196 GEPAPEGSIIGADGNPTTDASTMFGEHPGALLPF------GGHKGYALGVVAELLAGVLS 249
           G+PAP G    ADG PTTD++ +  ++ GALLP       G HKGY LG + ++ +GVLS
Sbjct: 191 GQPAPLGWAQDADGQPTTDSNAV--KNGGALLPLGSDREHGSHKGYGLGAIVDIFSGVLS 248

Query: 250 G---GGTIQPDNPRG--------GVATNNLFAVLLNPALDLGLDWQSAEVEAFVRYLHDT 298
           G   G  + P    G        GV T + F  +   A     ++++  ++ +++     
Sbjct: 249 GANYGPWVPPFATAGFMSANEGVGVGTGHFFGAMRIDAFRPAAEFKN-HMDTWIQRFRSA 307

Query: 299 PPAPGVDRVQYPGEYE---AANRAQASDTLNINPAIWRNLERLAQ 340
               G  +V  PG+ E    A R QA   + ++  + + LE L +
Sbjct: 308 KAVAG-KQVLVPGDPERLMEAERLQAG--IPVHETVVQQLEHLGE 349


Lambda     K      H
   0.319    0.136    0.409 

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: 347
Number of extensions: 21
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: 349
Length of database: 355
Length adjustment: 29
Effective length of query: 320
Effective length of database: 326
Effective search space:   104320
Effective search space used:   104320
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: 49 (23.5 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