GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Pedobacter sp. GW460-11-11-14-LB5

Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate CA265_RS02820 CA265_RS02820 acyl-CoA dehydrogenase

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



>FitnessBrowser__Pedo557:CA265_RS02820
          Length = 384

 Score =  326 bits (836), Expect = 6e-94
 Identities = 164/376 (43%), Positives = 247/376 (65%)

Query: 3   DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGG 62
           D   +E Q+ ++ M RDFA + I PH   W++A      L  Q+GELGL+G++VPEE+GG
Sbjct: 6   DFSETETQQSVKAMVRDFAEKNIRPHIMEWDEAQHFPVELFKQLGELGLMGVLVPEEYGG 65

Query: 63  SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIG 122
           S + Y  Y   + E++   G+ G  ++ HNS+  G +L + +  QK  WL +LA+   IG
Sbjct: 66  SGLGYQEYVDVIVEVARVCGSIGLSLAAHNSLCTGHILAFANPEQKQRWLPKLATAEWIG 125

Query: 123 CFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGL 182
            + LTE   GS+A  + T A      +++NG+K + ++ K   +A+V   T  +   KG+
Sbjct: 126 AWGLTEANTGSDALRMMTTAVEDGDDYIINGAKNWITHGKSGDIAVVMVRTGEQGSSKGI 185

Query: 183 SAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEG 242
           SA +V   TPGF   + E+K+G+RAS+T  +   +CR+P+ANLLG  G+G   A+  L+G
Sbjct: 186 SAIVVERGTPGFTAGKKENKLGMRASETTEMIFDNCRVPKANLLGNVGEGFKQAMKVLDG 245

Query: 243 GRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILH 302
           GRI I A ALGIA+ AF+AA+ Y+++R QFG+PI+  Q+I+  LADM T++ AA LLI  
Sbjct: 246 GRISIAALALGIAKGAFDAAVAYSKQRQQFGQPISSFQAISFKLADMATEIEAAELLIRQ 305

Query: 303 AARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQI 362
           AA LK+  LP   E++ AK FASE++ +V + AVQI GGYGY +D+PVE++YRD+++  I
Sbjct: 306 AADLKNRHLPMTKESAMAKYFASEVSVRVATDAVQIFGGYGYTKDFPVEKFYRDSKLCTI 365

Query: 363 YEGSSEIQRLLIAREL 378
            EG+SEIQ+++IARE+
Sbjct: 366 GEGTSEIQKIVIAREV 381


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: 357
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: 384
Length adjustment: 30
Effective length of query: 353
Effective length of database: 354
Effective search space:   124962
Effective search space used:   124962
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.

Links

Downloads

Related tools

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