GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Methylovulum miyakonense HT12

Align D-specific alpha-keto acid dehydrogenase; Vancomycin resistance protein VanH; EC 1.1.1.- (characterized)
to candidate WP_019867135.1 METMI_RS0115120 formate dehydrogenase

Query= SwissProt::Q05709
         (322 letters)



>NCBI__GCF_000384075.1:WP_019867135.1
          Length = 400

 Score =  104 bits (259), Expect = 4e-27
 Identities = 80/236 (33%), Positives = 116/236 (49%), Gaps = 24/236 (10%)

Query: 68  KRAGVKYISTRSIGCNHIDTTAAKRMGITVDNVAY-SPDSVADYTMMLILMAVRNVKSIV 126
           K   +K I T  IG +H D  AA   GITV  V Y + +SVA++ +M+ L  VRN     
Sbjct: 111 KAKNLKMIVTAGIGSDHTDLQAAMERGITVAEVTYCNSNSVAEHVVMMTLALVRNYLPSY 170

Query: 127 RSVEKHDFRLDS--DRGKVLSDMTVGVVGTGQIGKAVIERLRGFGCKVLAYSRSRSIEV- 183
             V K  + +     R   L  M VG V  G+IG  V+  L+ F  K+    R R  E  
Sbjct: 171 HWVIKGGWNIADCVARSYDLEAMHVGTVAAGRIGLRVLRLLKPFDVKLHYLDRHRLPEAV 230

Query: 184 -------NYVPFDELLQNSDIVTLHVPLNTDTHYIISHEQIQRMKQGAFLINTGRGPLVD 236
                   +   + L +  D+VTL+ PL+ +T ++I+   ++  K+GA+LINT RG L D
Sbjct: 231 EQELNLTYHSSLESLTKVCDVVTLNCPLHPETEHMINEASLKNFKRGAYLINTARGKLCD 290

Query: 237 TYELVKALENGKLGGAALDVLEGEEEFFYSDCTQKPIDNQFLLKLQRMPNVIITPH 292
              +V ALE+G+L G A DV   +           P D+ +    + MPN  +TPH
Sbjct: 291 RDAIVNALESGQLAGYAGDVWFPQ---------PAPNDHPW----RTMPNHGMTPH 333


Lambda     K      H
   0.319    0.135    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: 239
Number of extensions: 12
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: 322
Length of database: 400
Length adjustment: 29
Effective length of query: 293
Effective length of database: 371
Effective search space:   108703
Effective search space used:   108703
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: 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