GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Marinicella litoralis KMM 3900

Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate WP_099018480.1 CCS90_RS05525 pyruvate dehydrogenase

Query= reanno::Smeli:SMc03202
         (337 letters)



>NCBI__GCF_002591915.1:WP_099018480.1
          Length = 701

 Score =  244 bits (623), Expect = 5e-69
 Identities = 134/333 (40%), Positives = 196/333 (58%), Gaps = 17/333 (5%)

Query: 3   RMTMIEAVRSAMDVSMARDDNVVVFGEDVGYFGGVFRCTQGLQAKYGKTRCFDTPISESG 62
           R+ M+ A+R  +D  ++ ++ ++VFGEDVG  GGV   T GLQ K+G+ + FDT +SE G
Sbjct: 380 RINMVTAIRKTLDYELSHNNKMLVFGEDVGAKGGVHAVTLGLQEKHGEAQVFDTSLSEEG 439

Query: 63  IVGTAIGMAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTGGG 122
           I+G +IG+A  GL P  EIQF  Y  PA +QL  E   +R+R+N  F  P+VVRM  G  
Sbjct: 440 IIGRSIGLALAGLLPVPEIQFRKYADPAEEQLN-ETGSMRWRTNNRFAAPMVVRMAGGYF 498

Query: 123 IFGGQTHSQSPEALFTHVCGLKVVVPSNPYDAKGLLISAIEDPDPVMFLEPKRLYNGPFD 182
             G   HSQ  E  + H  G +V +PSN  DA GLL  A+ + +P +F E +++ +    
Sbjct: 499 GCGDPWHSQCAEVKWVHAIGWQVAMPSNAEDAVGLLRYALRNNNPTIFFEHRKMLDH--- 555

Query: 183 GHHERPVTAWSKHELGDVPDGHYTIPIGKAEIRRKGSGVTVIAYGTMVHVALAAAEETGI 242
                   AWS+      P   Y IP G+      G  VTV+++G MVH+   A E+TGI
Sbjct: 556 --------AWSRRPY---PGDQYIIPFGQGNKILSGDRVTVVSWGGMVHMCQTAIEQTGI 604

Query: 243 DAEVIDLRSLLPLDLETIVQSAKKTGRCVVVHEATLTSGFGAELAALVQEHCFYHLESPV 302
            A++IDLR+L P D   ++QS KKTGRC++VHE  +++GFGAE+AA++ +  F++L++P+
Sbjct: 605 QADLIDLRTLRPWDKAMVLQSVKKTGRCLIVHEDNMSAGFGAEIAAILAKEAFFYLDAPI 664

Query: 303 VRLTGWDTPYPHAQEW--DYFPGPARVGRALAE 333
            RL   D   PH  +      P P  + + L E
Sbjct: 665 ERLATADIGNPHDPKLMEHALPNPDSIAQRLME 697


Lambda     K      H
   0.321    0.138    0.424 

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: 592
Number of extensions: 28
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: 337
Length of database: 701
Length adjustment: 34
Effective length of query: 303
Effective length of database: 667
Effective search space:   202101
Effective search space used:   202101
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: 52 (24.6 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