GapMind for catabolism of small carbon sources

 

Aligments for a candidate for scrK in Pseudomonas fluorescens FW300-N2E2

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate Pf6N2E2_1965 Fructokinase (EC 2.7.1.4)

Query= reanno::pseudo6_N2E2:Pf6N2E2_1965
         (306 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1965 Fructokinase (EC
           2.7.1.4)
          Length = 306

 Score =  612 bits (1577), Expect = e-180
 Identities = 306/306 (100%), Positives = 306/306 (100%)

Query: 1   MNMQLPSVVVFGEALTDVVQHSPGRWQGYPGGAPWNVARAMSRLGVPTAFAGSISTDSLG 60
           MNMQLPSVVVFGEALTDVVQHSPGRWQGYPGGAPWNVARAMSRLGVPTAFAGSISTDSLG
Sbjct: 1   MNMQLPSVVVFGEALTDVVQHSPGRWQGYPGGAPWNVARAMSRLGVPTAFAGSISTDSLG 60

Query: 61  DELAQQSKAAGLDMRFLQRVDADPLVAIVPSSHPPRYFFAGEADLLFDVDQLPAGWLDAA 120
           DELAQQSKAAGLDMRFLQRVDADPLVAIVPSSHPPRYFFAGEADLLFDVDQLPAGWLDAA
Sbjct: 61  DELAQQSKAAGLDMRFLQRVDADPLVAIVPSSHPPRYFFAGEADLLFDVDQLPAGWLDAA 120

Query: 121 RLCHFSCISLARQPLGDRLVEVARRVKEEDKLISYDPNWRNLMDTRYRELTFPAMVELAD 180
           RLCHFSCISLARQPLGDRLVEVARRVKEEDKLISYDPNWRNLMDTRYRELTFPAMVELAD
Sbjct: 121 RLCHFSCISLARQPLGDRLVEVARRVKEEDKLISYDPNWRNLMDTRYRELTFPAMVELAD 180

Query: 181 IIKLSDEDLRQIYPGLNEEQALHTLRTMNASAQILFTRGAKGMALYAADVKFEQPAIAVE 240
           IIKLSDEDLRQIYPGLNEEQALHTLRTMNASAQILFTRGAKGMALYAADVKFEQPAIAVE
Sbjct: 181 IIKLSDEDLRQIYPGLNEEQALHTLRTMNASAQILFTRGAKGMALYAADVKFEQPAIAVE 240

Query: 241 VADTVGAGDSSMAGWLASTLLGIQEPHARLEFSAACASVSCSHAGAYAPSREEVEDLLSN 300
           VADTVGAGDSSMAGWLASTLLGIQEPHARLEFSAACASVSCSHAGAYAPSREEVEDLLSN
Sbjct: 241 VADTVGAGDSSMAGWLASTLLGIQEPHARLEFSAACASVSCSHAGAYAPSREEVEDLLSN 300

Query: 301 RMQHQR 306
           RMQHQR
Sbjct: 301 RMQHQR 306


Lambda     K      H
   0.320    0.133    0.398 

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: 453
Number of extensions: 9
Number of successful extensions: 1
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: 306
Length of database: 306
Length adjustment: 27
Effective length of query: 279
Effective length of database: 279
Effective search space:    77841
Effective search space used:    77841
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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