GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Caulobacter crescentus NA1000

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate CCNA_03322 CCNA_03322 D-3-phosphoglycerate dehydrogenase

Query= BRENDA::F8A9V0
         (325 letters)



>FitnessBrowser__Caulo:CCNA_03322
          Length = 526

 Score =  146 bits (369), Expect = 1e-39
 Identities = 93/265 (35%), Positives = 137/265 (51%), Gaps = 21/265 (7%)

Query: 54  KADGPVLEALHSYGVGLLALRSAGYDHIDIETAKRLGIKVVNVPAYSPHAIADHTLAIML 113
           K D  V+ A +   V  +A    G D++DI  A   GI V+N P  +    A+H +A+M 
Sbjct: 55  KLDKDVIAAANKLRV--IARAGIGVDNVDIPAATAKGIVVMNTPFGNSITTAEHAIAMMF 112

Query: 114 ALIRRLHRAHDKVRLGDFDLDGLMGFDLNGKVAGVIGLGKIGRLVATRLKAFGCKVLGYD 173
           AL R++  A    + G ++ +  MG +L  K  G+IG G IG +VA R      KV+ YD
Sbjct: 113 ALARQIPAADVSTQGGKWEKNRFMGVELYAKTLGLIGAGNIGGIVADRALGLKMKVVAYD 172

Query: 174 PYIQPEI-----VENVDLDTLITQADIISIHCPLTRENFHMFNEETFKRMKPGAILVNTA 228
           P++ PE      VE V+LD L+ +AD+I++H PLT +  ++ + E   + K G ++VN A
Sbjct: 173 PFLSPERAVEMGVEKVELDELLARADVITLHTPLTDKTRNILSAENLAKTKKGVMIVNCA 232

Query: 229 RGGLIDTKALLEALKSGKLGGAALDVYEYERGLFFKNHQKEGIKDPYLAQLLGLANVVLT 288
           RGGL+D  AL + L  G +GGAA DV+  E         KE         L G   VV T
Sbjct: 233 RGGLVDEAALRKLLDEGHVGGAAFDVFTVEPA-------KEN-------PLFGSDKVVAT 278

Query: 289 GHQAFLTREAVKNIEETTVENILEW 313
            H    T EA +N+     E + ++
Sbjct: 279 PHLGASTNEAQENVALQVAEQVSDY 303


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: 345
Number of extensions: 19
Number of successful extensions: 2
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: 526
Length adjustment: 31
Effective length of query: 294
Effective length of database: 495
Effective search space:   145530
Effective search space used:   145530
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: 50 (23.9 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