GapMind for catabolism of small carbon sources

 

Aligments for a candidate for D-LDH in Magnetospirillum magneticum AMB-1

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_043743064.1 AMB_RS00985 D-glycerate dehydrogenase

Query= BRENDA::O66939
         (334 letters)



>lcl|NCBI__GCF_000009985.1:WP_043743064.1 AMB_RS00985 D-glycerate
           dehydrogenase
          Length = 328

 Score =  142 bits (358), Expect = 1e-38
 Identities = 92/287 (32%), Positives = 153/287 (53%), Gaps = 22/287 (7%)

Query: 40  LKKAELISVFVYDKLTEELLSKM-PRLKLIHTRSVGFDHIDLDYCKKKGILVTHIPAYSP 98
           +K A+++   V D++   +LS+  P LKL+     G DHIDL   +++GI VT+ P    
Sbjct: 46  VKIADVLVPTVTDRIDAGILSQAGPNLKLVANFGTGVDHIDLATARQRGITVTNTPGVLT 105

Query: 99  ESVAEHTFAMILTLVKRLKRIEDRVKKLNFSQDSE--ILARELNRLTLGVIGTGRIGSRV 156
           E  A+   A+I+++ +R+   E  ++  ++   S   +L   +    LG+IG GRIG  V
Sbjct: 106 EDTADMAMALIMSVPRRIAEGERLIRSGDWKGWSPTFMLGHRIWGKRLGIIGMGRIGQAV 165

Query: 157 AMYGLAFGMKVLCYD---VVKREDLKEKGCVYTSLDELLKESDVISLHVPYTKETHHMIN 213
           A    AFGM +  ++   V    + + +   + SLD++L   DV+++H P+T  T H+++
Sbjct: 166 ARRAKAFGMSIHYHNRKRVHPDIETELEATYWESLDQMLARMDVVTVHCPHTPATFHLLS 225

Query: 214 EERISLMKDGVYLINTARGKVVDTDALYRAYQRGKFSGLGLDVFEDEEILILKKYTEGKA 273
             R+ L+    Y++NTARG++VD +AL R   RG  +G GLDVFE E  +          
Sbjct: 226 ARRLELLPKHAYVVNTARGEIVDENALTRMLIRGDLAGAGLDVFEHEPAV---------- 275

Query: 274 TDKNLKILELACKDNVIITPHIAYYTDKSLERIREETVKVVKAFVKG 320
              N K+L L   DNV++ PH+   T +    + E+ +  +K F  G
Sbjct: 276 ---NPKLLAL---DNVVLLPHLGSATIEGRVDMGEKVLVNIKTFADG 316


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: 216
Number of extensions: 5
Number of successful extensions: 4
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: 328
Length adjustment: 28
Effective length of query: 306
Effective length of database: 300
Effective search space:    91800
Effective search space used:    91800
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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