GapMind for catabolism of small carbon sources

 

Alignments 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:

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