GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuA in Sphingomonas koreensis DSMZ 15582

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate Ga0059261_4052 Ga0059261_4052 Acyl-CoA dehydrogenases

Query= reanno::Smeli:SM_b21121
         (387 letters)



>FitnessBrowser__Korea:Ga0059261_4052
          Length = 385

 Score =  509 bits (1312), Expect = e-149
 Identities = 262/378 (69%), Positives = 300/378 (79%), Gaps = 3/378 (0%)

Query: 6   LNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMS-LWREMGELGLLGITADEAH 64
           ++FAL E  + +R + +RFA ERI PLA   D  + FP   LW  MGELGL GIT DE  
Sbjct: 6   MDFALSETAEMIRDTTQRFAKERIEPLAAKIDAEDWFPRDELWTAMGELGLHGITVDEEF 65

Query: 65  GGAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEH 124
           GG GLGYL H +A EE+SRASAS+GLSYGAHSNLCVNQI+R   PAQK++YLP+LISGEH
Sbjct: 66  GGLGLGYLEHVIACEEVSRASASIGLSYGAHSNLCVNQISRWASPAQKAKYLPRLISGEH 125

Query: 125 VGALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPR 184
           VG+LAMSE GAGSDVVSMKL+A+ +GDRYVLNG+K WITN   AD LVVYAKT    G R
Sbjct: 126 VGSLAMSEAGAGSDVVSMKLRAEHKGDRYVLNGTKFWITNAAYADTLVVYAKT--GEGSR 183

Query: 185 GITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGL 244
           GIT FL+EK  PGFS GQK+DK+GMRGS T+EL+F DCEVPEENV+G +  GV VLMSGL
Sbjct: 184 GITTFLIEKDMPGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENVMGPLNGGVGVLMSGL 243

Query: 245 DYERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYV 304
           DYER VL+   LGIM ACLDVV+PYL ERKQFGQ IG FQLMQ K+ADMYV +N+ARAYV
Sbjct: 244 DYERTVLAGIQLGIMQACLDVVLPYLRERKQFGQAIGSFQLMQAKVADMYVALNSARAYV 303

Query: 305 YAVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLY 364
           YAVA ACD G+T R DAAG IL A+E A  +A EA+QALGG GYT D+P  R LRDAKL 
Sbjct: 304 YAVAQACDAGKTTRFDAAGAILLASENAFRVAGEAVQALGGAGYTKDWPVERFLRDAKLL 363

Query: 365 EIGAGTSEIRRMLIGREL 382
           +IGAGT+EIRRMLIGREL
Sbjct: 364 DIGAGTNEIRRMLIGREL 381


Lambda     K      H
   0.318    0.135    0.391 

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: 413
Number of extensions: 12
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: 387
Length of database: 385
Length adjustment: 30
Effective length of query: 357
Effective length of database: 355
Effective search space:   126735
Effective search space used:   126735
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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