GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Bacillus altitudinis 41KF2b

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_017367983.1 BA79_RS04725 D-glycerate dehydrogenase

Query= BRENDA::F8A9V0
         (325 letters)



>NCBI__GCF_000691145.1:WP_017367983.1
          Length = 322

 Score =  131 bits (330), Expect = 2e-35
 Identities = 96/305 (31%), Positives = 156/305 (51%), Gaps = 24/305 (7%)

Query: 24  WDVEMTPDFLDETTVEKAKGAQVVSLFVSDKADGPVLEALHSYGVGLLALRSAGYDHIDI 83
           W  E  P   +E   + A+   ++++ +SD+ D  +L   ++  + ++A  + GYD+ID+
Sbjct: 29  WTSEDEPCPREELEKQAAQADGLLTM-LSDQVDEALLS--NAPNLKVVANLAVGYDNIDL 85

Query: 84  ETAKRLGIKVVNVPAYSPHAIADHTLAIMLALIRRLHRAHDKVRLGDFDLDG---LMGFD 140
           + AK+ GI V + P     + AD   A+++A  RR+  A D ++ G++   G   L G D
Sbjct: 86  KAAKKHGITVCHTPDVLTESTADLAFALLMASARRIVEASDWIKDGNWTGWGPLLLAGAD 145

Query: 141 LNGKVAGVIGLGKIGRLVATRLKAFGCKVLGYDPYIQPEI-----VENVDLDTLITQADI 195
           ++ K  G++G+G IG  +A R K F   VL ++   +PE      V     D L+TQ+D 
Sbjct: 146 VHHKTLGIVGMGSIGTALAKRAKGFDMNVLYHNRSRKPEAEAQLGVTYAAFDELLTQSDF 205

Query: 196 ISIHCPLTRENFHMFNEETFKRMKPGAILVNTARGGLIDTKALLEALKSGKLGGAALDVY 255
           I    PLT E   MFN++ F++MK  A  +N +RG  +D  AL +A+ +GK+ GA LDV+
Sbjct: 206 IVCLTPLTPETKEMFNKKAFEQMKNTAYFINVSRGQTVDEDALYDAVTTGKIAGAGLDVF 265

Query: 256 EYERGLFFKNHQKEGIKDPYLAQLLGLANVVLTGHQAFLTREAVKNIEETTVENILEWQK 315
                       KE +   +   L  L NV +  H    + E  KN+     ENI    +
Sbjct: 266 -----------SKEPVSPDH--PLTTLPNVTVLPHIGSASVETRKNMMHLCAENIALVLQ 312

Query: 316 NPQAK 320
           + QAK
Sbjct: 313 DQQAK 317


Lambda     K      H
   0.321    0.140    0.407 

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: 238
Number of extensions: 13
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: 325
Length of database: 322
Length adjustment: 28
Effective length of query: 297
Effective length of database: 294
Effective search space:    87318
Effective search space used:    87318
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: 48 (23.1 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