GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Sinorhizobium meliloti 1021

Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate SMc01639 SMc01639 acyl-CoA dehydrogenase

Query= BRENDA::P26440
         (426 letters)



>FitnessBrowser__Smeli:SMc01639
          Length = 386

 Score =  208 bits (529), Expect = 3e-58
 Identities = 124/379 (32%), Positives = 201/379 (53%), Gaps = 9/379 (2%)

Query: 45  LSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLR--EFWKQLGNLGVLGITAPVQYG 102
           L+EEQ+ +  T+  F++  + P   E++R+         E  ++   LG      P + G
Sbjct: 5   LTEEQQMIVDTVRTFVETEIYPHENEVERTGVVPRELGLEIARKCKELGFFACNFPEEVG 64

Query: 103 GSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCINQLVRNGNEAQKEKYLPKLISGEYI 162
           G+GL +L   LV  E+ R S  + + +G  S + +       NE Q+E+YL   + G+  
Sbjct: 65  GAGLDHLTFTLVERELGRGSMGLTVFFGRPSGILMAC-----NEDQRERYLLPAVRGDKF 119

Query: 163 GALAMSEPNAGSDVVSMKLKAEKKGNHYILNGNKFWITNGPDADVLIVYAKTDLAAVPAS 222
            ALAM+EP+AGSDV  MK  A   G+ +I+NG K +I++   AD +IV+  T     P  
Sbjct: 120 DALAMTEPDAGSDVRGMKCFARPDGDDWIVNGTKHFISHADIADFVIVFIATGEEQTPRG 179

Query: 223 --RGITAFIVEKGMPGFSTSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLM 280
             + IT F+V++G PGF   +  + +  RG   C L F+DC++P+A ILG  +KG  +  
Sbjct: 180 PKKKITCFLVDRGTPGFEIREGYNSVSHRGYKNCILTFDDCRLPSAQILGEVHKGFDIAN 239

Query: 281 SGLDLERLVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLMACR 340
             L   RL +A   +G  +   D+ + Y   R+ FG+ I   Q +  K+ADM T + A  
Sbjct: 240 DWLYATRLTVAATSVGRARRAFDYALSYAAERKQFGKPISANQGVSFKLADMITEIDAAD 299

Query: 341 QYVYNVAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFGGNGYINDFPMGRFLRDA 400
               + A   D+G  + ++ A   +++ E   +V  + IQ +GG G ++D P+ RF RDA
Sbjct: 300 LLTLSAAWRLDQGLPSNREIASAKVFATEMLARVTDEAIQIYGGMGLMDDLPLARFWRDA 359

Query: 401 KLYEIGAGTSEVRRLVIGR 419
           ++  I  GTSE++R +I R
Sbjct: 360 RVERIWDGTSEIQRHIISR 378


Lambda     K      H
   0.321    0.137    0.410 

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: 394
Number of extensions: 17
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: 426
Length of database: 386
Length adjustment: 31
Effective length of query: 395
Effective length of database: 355
Effective search space:   140225
Effective search space used:   140225
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