GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdA in Caulobacter crescentus NA1000

Align 2-keto-isovalerate dehydrogenase component α subunit (EC 1.2.4.4) (characterized)
to candidate CCNA_01799 CCNA_01799 pyruvate dehydrogenase E1 component alpha subunit

Query= metacyc::MONOMER-11683
         (330 letters)



>FitnessBrowser__Caulo:CCNA_01799
          Length = 343

 Score =  145 bits (365), Expect = 2e-39
 Identities = 101/318 (31%), Positives = 158/318 (49%), Gaps = 10/318 (3%)

Query: 15  EAVDMYRTMLLARKIDERMWLLNRSGKIP-FVISCQGQEAAQVGAAFALDREMDYVLPYY 73
           E +  Y+ MLL R+ +ER   L   G I  F     GQEA  VG   ++ ++ D ++  Y
Sbjct: 27  ELLKFYQDMLLIRRFEERAGQLYGMGLIGGFCHLYIGQEAIAVGMQ-SISQKGDQIITGY 85

Query: 74  RDMGVVLAFGMTAKDLM--MSGFAKAADPNSGGRQMPGHFGQKKNRIVTGSSPVTTQVPH 131
           RD G +LA GM  +++M  ++G A  +    GG     H          G   V  QV  
Sbjct: 86  RDHGHMLAAGMDPREVMAELTGRAGGSSKGKGGSM---HMFDIATGFYGGHGIVGAQVAL 142

Query: 132 AVGIALAGRMEKKDIAAFVTFGEGSSNQGDFHEGANFAAVHKLPVIFMCENNKYAISVPY 191
             G+ALA         ++   G+G++NQG  +E  N A + KLPV+++ ENN+YA+    
Sbjct: 143 GTGLALANSYRNNGNVSYAYMGDGAANQGQVYESFNMAQLWKLPVVYVIENNQYAMGTAV 202

Query: 192 DKQVACENISDRAIGYGMPGVTVNGNDPLEVYQAVKEARERARRGEGPTLIETISYRLTP 251
           ++  +      R + + +PG  V+G D + V +A   A E AR G+GP ++E  +YR   
Sbjct: 203 ERAASETAFHKRGVSFRIPGEEVDGMDVIAVREAGARATEHARSGQGPYILEMKTYRYRG 262

Query: 252 HSSDDDDSSYRGREEVEEAKKS-DPLLTYQAYLKETGLLSDEIEQTMLDEIMAIVNEATD 310
           HS   D + YR +EEV+E K + DP+   +  L + G+  D+++     E+  IV EA +
Sbjct: 263 HSM-SDPAKYRTKEEVDEVKTTRDPIDHIKERLAKAGVTEDDLKGVDA-EVKRIVAEAAE 320

Query: 311 EAENAPYAAPESALDYVY 328
            A  +P   P      VY
Sbjct: 321 FARTSPEPDPSELYTDVY 338


Lambda     K      H
   0.316    0.132    0.377 

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: 278
Number of extensions: 19
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: 330
Length of database: 343
Length adjustment: 28
Effective length of query: 302
Effective length of database: 315
Effective search space:    95130
Effective search space used:    95130
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 (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