GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ch1CoA in Pseudomonas fluorescens FW300-N1B4

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate Pf1N1B4_4787 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= SwissProt::Q2LQN9
         (414 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4787 Butyryl-CoA
           dehydrogenase (EC 1.3.99.2)
          Length = 375

 Score =  258 bits (659), Expect = 2e-73
 Identities = 150/374 (40%), Positives = 213/374 (56%), Gaps = 5/374 (1%)

Query: 39  EEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDI 98
           +EQ  + +  R  A   + P A E D  H FP  A    A LG    LVP ++GG     
Sbjct: 5   DEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64

Query: 99  TTFAMVLEEI--GKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFA 156
             +AM LEEI  G    ST +M +  + G + I+  G+   KE++L        ++ AFA
Sbjct: 65  LAYAMALEEIAAGDGACST-IMSVHNSVGCVPILKFGNDDQKERFLKPLAS-GAMLGAFA 122

Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTF 216
            TEP AGSD  ++KTRA   GD YV+NG K FIT+G  A ++ V+A TDPS G +G++  
Sbjct: 123 LTEPQAGSDASSLKTRARLDGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGITAL 182

Query: 217 VVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRV 276
           +V   +PG      E K+G       ++ FED++VP  N +GEEG+G+   +  L   RV
Sbjct: 183 IVPTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPVANRLGEEGEGYKIALANLEGGRV 242

Query: 277 FCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATT 336
             ASQ+VG+A+ A E A  + RERE FGKPI     + F +ADMAT++  AR +V  A  
Sbjct: 243 GIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAA 302

Query: 337 LLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYT 396
           L D+  K   +   MAK FAS+ A KV + A+Q +GG GY+ ++ +ER+ R+ ++ QIY 
Sbjct: 303 LRDS-GKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPLERIYRDVRVCQIYE 361

Query: 397 GTNQITRMVTGRSL 410
           GT+ I RMV  R+L
Sbjct: 362 GTSDIQRMVISRNL 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: 335
Number of extensions: 12
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: 375
Length adjustment: 31
Effective length of query: 383
Effective length of database: 344
Effective search space:   131752
Effective search space used:   131752
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 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