GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Xanthobacter autotrophicus Py2

Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_012116241.1 XAUT_RS21625 isovaleryl-CoA dehydrogenase

Query= reanno::psRCH2:GFF2392
         (383 letters)



>NCBI__GCF_000017645.1:WP_012116241.1
          Length = 390

 Score =  266 bits (681), Expect = 6e-76
 Identities = 140/376 (37%), Positives = 217/376 (57%)

Query: 3   DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGG 62
           D +L E   M+RD  R F+  EIAP A   ++       L  ++G LGLLG+   EE+GG
Sbjct: 10  DFDLGETADMLRDTVRSFSDAEIAPRAAEIDRTNQFPRDLWPKLGALGLLGVTAEEEYGG 69

Query: 63  SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIG 122
           S + Y+ + +A+EEIS    + G     H+++    +   G+  QK ++L +L SG  +G
Sbjct: 70  SGLGYLEHVIAMEEISRASASVGLSYGAHSNLCINQISRNGTAEQKAKYLPKLISGEHVG 129

Query: 123 CFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGL 182
             A++EP AGS+  ++RTRA+     ++LNGSK + +N   ++  +V+A TDP  G KG+
Sbjct: 130 ALAMSEPGAGSDVVSMRTRADKKGDRYILNGSKMWITNGPIAETLVVYAKTDPAAGPKGM 189

Query: 183 SAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEG 242
           +AFLV  D PGF+  +   K+G+R SDT  +   DC +PE N+LG  G+G+ + +S L+ 
Sbjct: 190 TAFLVERDFPGFSTAQKLDKLGMRGSDTGELVFQDCEVPEENVLGAVGRGVNVLMSGLDY 249

Query: 243 GRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILH 302
            R  +     GI +A  +  L Y  ER QFG+PI   Q +   +ADM   +NA +  +  
Sbjct: 250 ERAVLAGGPTGIMQACMDIVLPYVHERKQFGQPIGTFQLMQGKIADMYVTMNATKAYVYA 309

Query: 303 AARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQI 362
            A+    G     +A+ A L+A+E A  +  +A+Q  GG GY+ DYP  R  RDA++ +I
Sbjct: 310 VAKACDRGATTREDAAGAILYAAEKATWMALEAIQTLGGNGYINDYPTGRLLRDAKLYEI 369

Query: 363 YEGSSEIQRLLIAREL 378
             G+SEI+R+LI R+L
Sbjct: 370 GAGTSEIRRMLIGRQL 385


Lambda     K      H
   0.318    0.133    0.390 

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: 334
Number of extensions: 18
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: 390
Length adjustment: 30
Effective length of query: 353
Effective length of database: 360
Effective search space:   127080
Effective search space used:   127080
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 Apr 09 2024. 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