GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Leeuwenhoekiella blandensis MED217

Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_009779945.1 MED217_RS07745 acyl-CoA dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_25670
         (383 letters)



>NCBI__GCF_000152985.1:WP_009779945.1
          Length = 602

 Score =  228 bits (581), Expect = 3e-64
 Identities = 141/392 (35%), Positives = 215/392 (54%), Gaps = 26/392 (6%)

Query: 5   ELTEEQVMIRDMARDFARGEIAPHAQAWEKAGW-IDDALVAKMGELGLLGMVVPEEWGGT 63
           +  EEQ M+++  ++F   EI P+ + +E   + + + ++ K GELGLLG+ VP+E+ G 
Sbjct: 31  DFNEEQKMMKETVKEFVDREIVPNKERFEHKDYALTEEVMRKAGELGLLGIAVPDEYDGL 90

Query: 64  YVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAIGC 123
            + +V+  L  + IS   G+       H  +G  P+  YGTEEQK+ ++  LA+G+  G 
Sbjct: 91  GMGFVSTMLVCDYISGATGSIATAFGAHTGIGTMPITLYGTEEQKKKYVPKLATGEWFGA 150

Query: 124 FCLTEPQAGSEAHNLRTRAEL-RDGQ-WVINGAKQFVSNGRRAKLAIVFAVTDPDLGKKG 181
           +CLTEP AGS+A++ +T+AEL  DG+ + ING K ++SN     L IVFA  + D   K 
Sbjct: 151 YCLTEPGAGSDANSGKTKAELSADGKSYKINGQKMWISNAGFCNLFIVFARIEDD---KN 207

Query: 182 LSAFLVPTDTP-GFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNL 240
           ++ F+V  D+  G  +   E K+GI +S T  V  N+  +P  N+L  RG+G  IA++ L
Sbjct: 208 ITGFIVENDSSNGISLGEEEKKLGIHSSSTRQVFFNDTVVPVENMLAGRGEGFKIAMNAL 267

Query: 241 EGGRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRLNAARLLI 300
             GRI +AA  L   R   +  + YA +RVQF  PI +  ++   LA+M T         
Sbjct: 268 NVGRIKLAAACLDAQRRIIDMGVKYANERVQFKTPIAQFGAIKYKLAEMATNAYVCESAS 327

Query: 301 LHAAR-------LRSAGKPCLSEA------------SQAKLFASEMAEKVCSSAIQIHGG 341
             AA+       +R A      EA            S  K+ ASE  +      IQI+GG
Sbjct: 328 YRAAKNIEDRIAIRMADGNSHQEAELKGVEEYAIECSILKVAASEDMQNCADEGIQIYGG 387

Query: 342 YGYLEDYPVERYYRDARITQIYEGSSEIQRMV 373
            G+  D P+E  +RDARI++IYEG++EI RM+
Sbjct: 388 MGFSADAPMEAAWRDARISRIYEGTNEINRML 419


Lambda     K      H
   0.319    0.134    0.394 

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: 482
Number of extensions: 21
Number of successful extensions: 5
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: 383
Length of database: 602
Length adjustment: 34
Effective length of query: 349
Effective length of database: 568
Effective search space:   198232
Effective search space used:   198232
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: 51 (24.3 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