GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Algiphilus aromaticivorans DG1253

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_043768478.1 U743_RS11515 isovaleryl-CoA dehydrogenase

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



>NCBI__GCF_000733765.1:WP_043768478.1
          Length = 387

 Score =  584 bits (1505), Expect = e-171
 Identities = 289/381 (75%), Positives = 319/381 (83%)

Query: 6   LNFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHG 65
           LN  LG ++DALR +   FA   IAP+A+  D  N FP  LW ++GELG LG+TA E  G
Sbjct: 6   LNHDLGPDLDALREAAADFARREIAPIAESTDADNVFPRQLWPKLGELGALGMTAGEDVG 65

Query: 66  GAGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHV 125
           G G+GYLAH V MEEISRAS S+GLSYGAHSNLCVNQ+++NG P Q+ +YLPKLISGEHV
Sbjct: 66  GMGMGYLAHVVLMEEISRASGSIGLSYGAHSNLCVNQLDKNGSPDQRQKYLPKLISGEHV 125

Query: 126 GALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRG 185
           GALAMSEPGAGSDVVSMKL+ADK+GDRYVLNGSKMWITNGPDAD LVVYAKTDP AGPRG
Sbjct: 126 GALAMSEPGAGSDVVSMKLRADKKGDRYVLNGSKMWITNGPDADTLVVYAKTDPEAGPRG 185

Query: 186 ITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLD 245
           ITAF+VEK   GFS  QKLDKLGMRGSNT EL+F +CEVPEENVLG VG+GV VLMSGLD
Sbjct: 186 ITAFIVEKGMAGFSTAQKLDKLGMRGSNTCELVFDNCEVPEENVLGAVGKGVNVLMSGLD 245

Query: 246 YERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVY 305
           YERVVLS GP+G+M A LD+V PY+HER+QFG PIG FQLMQGKLADMYV  +  R+YVY
Sbjct: 246 YERVVLSGGPVGLMQAALDIVTPYVHERQQFGDPIGSFQLMQGKLADMYVGTSVCRSYVY 305

Query: 306 AVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLYE 365
           AVA ACDRGET RKDAAG ILYAAEKAT    +AIQALGGNGY N+Y  GRL RDAKLYE
Sbjct: 306 AVARACDRGETTRKDAAGAILYAAEKATWACGQAIQALGGNGYINEYATGRLWRDAKLYE 365

Query: 366 IGAGTSEIRRMLIGRELFAET 386
           IGAGTSEIRRMLIGRELF ET
Sbjct: 366 IGAGTSEIRRMLIGRELFDET 386


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: 469
Number of extensions: 14
Number of successful extensions: 1
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: 387
Length adjustment: 30
Effective length of query: 357
Effective length of database: 357
Effective search space:   127449
Effective search space used:   127449
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 24 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