GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Herbaspirillum seropedicae SmR1

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate HSERO_RS23440 HSERO_RS23440 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__HerbieS:HSERO_RS23440
          Length = 394

 Score =  228 bits (582), Expect = 2e-64
 Identities = 138/375 (36%), Positives = 212/375 (56%), Gaps = 8/375 (2%)

Query: 20  DDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDY 79
           +D   +R+A  A+A  ++APR  E  R +     +++++G++G+LG T+ E+YGG GL Y
Sbjct: 13  EDIAALREAVAAFAHSEIAPRAAEIDRSDQFPMDLWKKLGDLGVLGITVSEEYGGAGLGY 72

Query: 80  VSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLT 139
           +++ +   E+ R  +         S+L +  I   G++ QK KYLP+L +G++IG   ++
Sbjct: 73  LAHIIAMEEISRASASVGLSYGAHSNLCVNQIKRNGNEEQKRKYLPRLISGDFIGALAMS 132

Query: 140 EPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDEIRGFIL 198
           EPN GSD  SM  RA K    Y L+GSKMWITN P ADV VV+AK D E G   +  F++
Sbjct: 133 EPNAGSDVVSMKLRADKKGDRYVLNGSKMWITNGPDADVLVVYAKTDLEAGARGMTAFLV 192

Query: 199 EKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHV-KGLRGPFTCLNSARYGI 257
           EKG KG S      K+G+R S TGE+V  +  VPEEN+L  V +G+    + L+  R  +
Sbjct: 193 EKGYKGFSVAQKLDKLGMRGSHTGELVFQDCEVPEENVLGGVGRGVNVLMSGLDFERSVL 252

Query: 258 AWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMK 317
           + G LG  ++C  +   YV DRKQFG+ +   QL+Q KLADM + +      V  +G+  
Sbjct: 253 SGGPLGIMQACMDVVVPYVHDRKQFGQAIGEFQLMQGKLADMYSTMMACKAYVYAVGQAC 312

Query: 318 DEGTAAVEITSIMK------RNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVN 371
           D   +A ++ ++ K        S  KA  +A  A   LGGNG  +E+ V R   + ++  
Sbjct: 313 DRADSADKVRALRKDAAGAILYSAEKATWMAGEAIQSLGGNGYINEYPVGRLWRDAKLYE 372

Query: 372 TYEGTHDIHALILGR 386
              GT +I  +++GR
Sbjct: 373 IGAGTSEIRRMLIGR 387


Lambda     K      H
   0.320    0.138    0.414 

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: 341
Number of extensions: 15
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: 395
Length of database: 394
Length adjustment: 31
Effective length of query: 364
Effective length of database: 363
Effective search space:   132132
Effective search space used:   132132
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