GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acdH in Paraburkholderia bryophila 376MFSha3.1

Align isobutyryl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate H281DRAFT_01204 H281DRAFT_01204 hypothetical protein

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_01204 H281DRAFT_01204
           hypothetical protein
          Length = 377

 Score =  550 bits (1418), Expect = e-161
 Identities = 267/372 (71%), Positives = 323/372 (86%)

Query: 7   TEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDALVAKMGELGLLGMVVPEEWGGTYVD 66
           TEEQ MIRD ARDFA   +AP+A  W++   +   +V +MG+LG LGM+VP +WGG+Y D
Sbjct: 6   TEEQRMIRDAARDFATERLAPNAAQWDRDAQLPADVVRQMGDLGFLGMIVPSQWGGSYTD 65

Query: 67  YVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQTWLADLASGQAIGCFCL 126
           YVAYALA+EEI+AG  A   LMS+HNSVGCGP+LN+G++ QK  +L DLA+G+ IG FCL
Sbjct: 66  YVAYALALEEIAAGCAACATLMSVHNSVGCGPILNFGSDAQKDRYLHDLATGRRIGAFCL 125

Query: 127 TEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGRRAKLAIVFAVTDPDLGKKGLSAFL 186
           TEPQAGSEA+NLRTRA L DG+W++NG+KQFV+NG RA +AIVFAVTDPD GK+GLSAF+
Sbjct: 126 TEPQAGSEANNLRTRAVLCDGKWILNGSKQFVTNGARADIAIVFAVTDPDRGKRGLSAFI 185

Query: 187 VPTDTPGFIVDRSEHKMGIRASDTCAVTLNNCTIPEANLLGERGKGLAIALSNLEGGRIG 246
           VPTDTPGF V + EHK+GIRASDTC ++L++C +P+ANLLGE G+GL IALSNLEGGRIG
Sbjct: 186 VPTDTPGFNVGKPEHKLGIRASDTCPISLDDCAVPDANLLGEPGEGLRIALSNLEGGRIG 245

Query: 247 IAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSVANMLADMHTRLNAARLLILHAARL 306
           IAAQA+GIARAAF+AA AYA +R+QF K + +HQ++ANMLADM TRLNAARLL+ HAARL
Sbjct: 246 IAAQAVGIARAAFDAARAYASERMQFGKALKDHQTIANMLADMATRLNAARLLVHHAARL 305

Query: 307 RSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARITQIYEGS 366
           RSAG+PCLSEASQAKLFASE+AE+VCS+AIQIHGGYGYLEDY VER+YRDARITQIYEG+
Sbjct: 306 RSAGEPCLSEASQAKLFASEVAEEVCSNAIQIHGGYGYLEDYAVERHYRDARITQIYEGT 365

Query: 367 SEIQRMVIAREL 378
           SE+QRMVIAR +
Sbjct: 366 SEVQRMVIARHV 377


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: 451
Number of extensions: 12
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: 383
Length of database: 377
Length adjustment: 30
Effective length of query: 353
Effective length of database: 347
Effective search space:   122491
Effective search space used:   122491
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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