GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Pseudomonas fluorescens FW300-N2E2

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate Pf6N2E2_1934 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= BRENDA::Q5SLK3
         (254 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1934
          Length = 264

 Score =  188 bits (478), Expect = 8e-53
 Identities = 108/253 (42%), Positives = 156/253 (61%), Gaps = 8/253 (3%)

Query: 10  VLVLTLNRPEKLNAITGELLDALYAALKEGEEDREVRALLLTGAGRAFSAGQDL------ 63
           V+V  LNRPEK NA++  +LD+L  AL   +E+ ++   ++TGAG AF +G DL      
Sbjct: 12  VMVAKLNRPEKKNALSESMLDSLRTALLAADENDDIGCFVITGAGDAFCSGGDLGRRAAE 71

Query: 64  TEFGDRKP-DYEAHLRRY-NRVVEALSGLEKPLVVAVNGVAAGAGMSLALWGDLRLAAVG 121
           +  GD  P + +  L++  ++V  A+   EKPL+ AVNG A GAGM L+L  D+R A+  
Sbjct: 72  SAEGDPTPLERKIRLQKVTHQVALAIENFEKPLIAAVNGAAVGAGMDLSLQCDMRFASES 131

Query: 122 ASFTTAFVRIGLVPDSGLSFLLPRLVGLAKAQELLLLSPRLSAEEALALGLVHRVVPAEK 181
           A F  A++R+GL+P +G  +LLPR+VG AKA ELL     +SAEEALALG+V+RV   ++
Sbjct: 132 ARFAEAYIRVGLIPGNGGCYLLPRIVGTAKALELLWTGDFVSAEEALALGIVNRVFSDDE 191

Query: 182 LMEEALSLAKELAQGPTRAYALTKKLLLETYRLSLTEALALEAVLQGQAGQTQDHEEGVR 241
           LM++ L  A  LA GP       KKLL ++ R  L  +L   A        T D++E ++
Sbjct: 192 LMQQTLDFATRLADGPPIQQRSIKKLLYQSLRTDLRTSLESVAAQMAVVQSTDDYKEAIK 251

Query: 242 AFREKRPPRFQGR 254
           A++EKR PRF G+
Sbjct: 252 AYKEKRKPRFIGK 264


Lambda     K      H
   0.318    0.135    0.371 

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: 152
Number of extensions: 5
Number of successful extensions: 2
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: 254
Length of database: 264
Length adjustment: 24
Effective length of query: 230
Effective length of database: 240
Effective search space:    55200
Effective search space used:    55200
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. 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