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_02091 H281DRAFT_02091 hypothetical protein

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__Burk376:H281DRAFT_02091
          Length = 378

 Score =  248 bits (632), Expect = 3e-70
 Identities = 140/379 (36%), Positives = 214/379 (56%), Gaps = 9/379 (2%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96
           L ++  ++ + +R      + P A   D   +FP       A+LG    LVP  YGG GM
Sbjct: 3   LDQDHLMVRDALRTFVREAVTPYAATWDRERTFPKDVHRQLAELGAYGVLVPETYGGAGM 62

Query: 97  DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRFGEKSTLMTAF 155
           D    A++LEEI      T+  +      + SI+L  G+ A K ++L     +  ++ AF
Sbjct: 63  DALALALILEEIAAGDGGTSTAISVNNCPVCSILLTYGNDAQKREWLTPLA-RGEMLGAF 121

Query: 156 AATEPGAGSDLLAMKTRAV--KKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGM 213
             TEP AGSD  A++T A   K GD YV+NG K FIT+G   D+  V A TD + G +G+
Sbjct: 122 CLTEPQAGSDASALRTTATRDKDGDAYVLNGVKQFITSGKNGDVAIVMAVTDKAAGKRGI 181

Query: 214 STFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSI 273
           S F+V   + G +    E K+G      +++ FED  VPA NL+G EG+G+   +  L  
Sbjct: 182 SAFIVPTDSKGYVVARVEDKLGQHSSDTAQIIFEDCRVPAANLIGAEGEGYRIALSGLEG 241

Query: 274 NRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRK 333
            R+  A+Q+VG+A+ A E A+ + +ERE FG+P+     +QF +ADMAT++EAAR L+  
Sbjct: 242 GRIGIAAQSVGMARAAYEAALTYAKERESFGQPLFSHQAVQFRLADMATQLEAARQLIWH 301

Query: 334 ATTLLDAKDKRGPLI--GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKL 391
           A +L   KD   P +    MAK FAS+ A ++ + A+Q+ GG GY+ ++ VER+ R+ ++
Sbjct: 302 AASL---KDAGQPCLTEAAMAKLFASEAAERICSAALQIHGGYGYLSDFPVERIYRDVRV 358

Query: 392 TQIYTGTNQITRMVTGRSL 410
            QIY GT+ I +++  R L
Sbjct: 359 CQIYEGTSDIQKILIARGL 377


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: 346
Number of extensions: 10
Number of successful extensions: 4
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: 378
Length adjustment: 31
Effective length of query: 383
Effective length of database: 347
Effective search space:   132901
Effective search space used:   132901
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