GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Pedobacter sp. GW460-11-11-14-LB5

Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate CA265_RS18405 CA265_RS18405 dehydrogenase

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



>FitnessBrowser__Pedo557:CA265_RS18405
          Length = 658

 Score =  249 bits (636), Expect = 1e-70
 Identities = 139/310 (44%), Positives = 192/310 (61%), Gaps = 23/310 (7%)

Query: 7   IEAVRSAMDVSMARDDNVVVFGEDVGYFGGVFRCTQGLQAKYGKTRCFDTPISESGIVGT 66
           ++A+   +D++M +  N+V+ G+D+  +GG F+ T G  AKYG+ R  +TPI ES IVG 
Sbjct: 344 LDAITDGLDLAMQKYPNLVLMGQDIADYGGAFKITDGFTAKYGRGRVRNTPICESAIVGA 403

Query: 67  AIGMAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTGGGIFGG 126
            +G++  G K  VE+QFAD++   ++Q+    A+  YR        +VVRMPTG G   G
Sbjct: 404 GLGLSINGYKAVVEMQFADFVTVGFNQIVNNLAKTHYRWGE--KADVVVRMPTGAGTGAG 461

Query: 127 QTHSQSPEALFTHVCGLKVVVPSNPYDAKGLLISAIEDPDPVMFLEPKRLYNGPFDGHHE 186
             HSQS EA FT   GLK+V P+ P DAKGLL++AIEDP+PV++ E K LY         
Sbjct: 462 PFHSQSNEAWFTKTPGLKIVYPAFPEDAKGLLLAAIEDPNPVLYFEHKYLY--------- 512

Query: 187 RPVTAWSKHELGDVPDGHYTIPIGKAEIRRKGSGVTVIAYGTMVHVALAAAE---ETGID 243
           R ++A        VPDG+YT  IGKA    +G   T+I YG  VH AL   E   E+G  
Sbjct: 513 RSLSA-------PVPDGYYTTEIGKAVRLAEGDKFTIITYGLGVHWALDYMEQYPESG-- 563

Query: 244 AEVIDLRSLLPLDLETIVQSAKKTGRCVVVHEATLTSGFGAELAALVQEHCFYHLESPVV 303
           A +IDLR+L P D ET+  + K TGR +++HE TLT+GFGAEL+A + EHCF +L++PV+
Sbjct: 564 ATLIDLRTLQPWDKETVSAAVKATGRVLILHEDTLTNGFGAELSAWIGEHCFAYLDAPVM 623

Query: 304 RLTGWDTPYP 313
           R    DT  P
Sbjct: 624 RCASLDTAIP 633


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: 577
Number of extensions: 29
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: 337
Length of database: 658
Length adjustment: 33
Effective length of query: 304
Effective length of database: 625
Effective search space:   190000
Effective search space used:   190000
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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