GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Paraburkholderia bryophila 376MFSha3.1

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate H281DRAFT_01204 H281DRAFT_01204 hypothetical protein

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__Burk376:H281DRAFT_01204
          Length = 377

 Score =  261 bits (668), Expect = 2e-74
 Identities = 151/374 (40%), Positives = 217/374 (58%), Gaps = 7/374 (1%)

Query: 38  TEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMD 97
           TEEQ+++ +  R+ A   +AP A + D +   P        DLG L  +VP ++GG+  D
Sbjct: 6   TEEQRMIRDAARDFATERLAPNAAQWDRDAQLPADVVRQMGDLGFLGMIVPSQWGGSYTD 65

Query: 98  ITTFAMVLEEIGKVCASTA-LMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFA 156
              +A+ LEEI   CA+ A LM +  + G   I+  GS A K++YL        +  AF 
Sbjct: 66  YVAYALALEEIAAGCAACATLMSVHNSVGCGPILNFGSDAQKDRYLHDLATGRRI-GAFC 124

Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTF 216
            TEP AGS+   ++TRAV    K+++NG K F+TNG+ ADI  V+A TDP +G +G+S F
Sbjct: 125 LTEPQAGSEANNLRTRAVLCDGKWILNGSKQFVTNGARADIAIVFAVTDPDRGKRGLSAF 184

Query: 217 VVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRV 276
           +V   TPG   G  E K+G+R      +  +D  VP  NL+GE G+G    +  L   R+
Sbjct: 185 IVPTDTPGFNVGKPEHKLGIRASDTCPISLDDCAVPDANLLGEPGEGLRIALSNLEGGRI 244

Query: 277 FCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATT 336
             A+QAVGIA+ A + A  +  ER QFGK +     I  M+ADMAT + AARLLV  A  
Sbjct: 245 GIAAQAVGIARAAFDAARAYASERMQFGKALKDHQTIANMLADMATRLNAARLLVHHAAR 304

Query: 337 LLDAKDKRGPLI--GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394
           L  A +   P +     AK FAS+ A +V ++A+Q+ GG GY+++Y VER  R+A++TQI
Sbjct: 305 LRSAGE---PCLSEASQAKLFASEVAEEVCSNAIQIHGGYGYLEDYAVERHYRDARITQI 361

Query: 395 YTGTNQITRMVTGR 408
           Y GT+++ RMV  R
Sbjct: 362 YEGTSEVQRMVIAR 375


Lambda     K      H
   0.318    0.133    0.375 

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: 354
Number of extensions: 9
Number of successful extensions: 3
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: 414
Length of database: 377
Length adjustment: 31
Effective length of query: 383
Effective length of database: 346
Effective search space:   132518
Effective search space used:   132518
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