GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Klebsiella michiganensis M5al

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BWI76_RS13120 BWI76_RS13120 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__Koxy:BWI76_RS13120
          Length = 262

 Score =  145 bits (366), Expect = 8e-40
 Identities = 95/262 (36%), Positives = 136/262 (51%), Gaps = 7/262 (2%)

Query: 1   MSELIVSR-QQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFF 59
           M   I+S  +Q V+ +TLNRP   N+ N+ +  QL   L+ A  D  +   ++TG  R F
Sbjct: 1   MEAFILSEVEQGVMTITLNRPDRLNSFNDLMHQQLAACLKQAERDDDVRCLLLTGAGRGF 60

Query: 60  AAGADLNEM------AEKDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALL 113
            AG DLN+          DL  ++      L  RL A  KP+I AVNG A GAG  LAL 
Sbjct: 61  CAGQDLNDRNVDPSGPAPDLGLSVERFYNPLVRRLAALPKPVICAVNGVAAGAGATLALG 120

Query: 114 CDVVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGL 173
           CD+V+A  +A+F +    LG++P  GG+  L R  G++ A  + L G+S++A+QA Q G+
Sbjct: 121 CDIVLAARSAKFVMAFSKLGLVPDCGGSWFLPRVAGRARAMGLALLGDSLSAEQAAQWGM 180

Query: 174 VSDVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAA 233
           +  V       +  L LA  +A      L   K+AL+ ++   L   L  ER    L   
Sbjct: 181 IWQVVDDAELKDTGLALARHLAAQPTYGLGLIKKALQLAETQTLDQQLDLERDYQRLAGR 240

Query: 234 TEDRHEGISAFLQKRTPDFKGR 255
           + D  EG+SAFL KR P F G+
Sbjct: 241 SADYREGVSAFLAKRPPQFSGK 262


Lambda     K      H
   0.318    0.130    0.356 

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: 141
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: 255
Length of database: 262
Length adjustment: 24
Effective length of query: 231
Effective length of database: 238
Effective search space:    54978
Effective search space used:    54978
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 (21.8 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