GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Pseudomonas fluorescens FW300-N2E3

Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate AO353_05480 AO353_05480 1-phosphofructokinase

Query= reanno::BFirm:BPHYT_RS02045
         (305 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05480
          Length = 313

 Score = 49.3 bits (116), Expect = 1e-10
 Identities = 71/269 (26%), Positives = 105/269 (39%), Gaps = 43/269 (15%)

Query: 37  GAGWNVARCVARLGLPTACAGSLGVDNFSDELWNASVAAGLDMRFMQRVERPPLLAIVHQ 96
           G G NVA+ +A LG     +G LG DN              +  F +R      + +  +
Sbjct: 39  GKGINVAQVLADLGHQLTVSGFLGEDNLQ----------AFEALFAKRGFVDAFIRVPGE 88

Query: 97  THPPAYFFMGENSADLAFDPAQLPAGW--------MGQVKWAHFGCI---SLVRQPIGNT 145
           T         +        P  + +          + Q+   H   +   SL R      
Sbjct: 89  TRSNIKLAEADGRITDINGPGPVVSAAAQQALLDRLDQITLGHDAVVVAGSLPRGVSAQW 148

Query: 146 LATLAAELRSQGVKISFDPNYRNLMEHGYEPTLRKMAALADLIKVSDEDLRLIFKTDDEA 205
           L  L   L+S+G+K++ D +   L           ++A   LIK + E+L      D EA
Sbjct: 149 LHGLLLRLKSRGLKVALDTSGEALRAG--------LSAGPWLIKPNTEELSEAL--DCEA 198

Query: 206 GALAQLRAMNPAATVLVTRGPETAVLIDGA---------MVTEARPPRVEVVDTVGAGDA 256
            ++A   A   AA+ L   G E  V+  GA             A PPRV VV TVGAGD+
Sbjct: 199 ISVA---AQAEAASRLHAHGIEHVVISHGAEGVNWFSVGSAMHATPPRVSVVSTVGAGDS 255

Query: 257 SIGGLLFSLMTAPQRAWPEHLAFALAAGA 285
            + G+L  L++A         A A+AA A
Sbjct: 256 LLAGMLHGLLSADTPEQTLRTATAIAAMA 284


Lambda     K      H
   0.321    0.134    0.412 

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: 182
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 305
Length of database: 313
Length adjustment: 27
Effective length of query: 278
Effective length of database: 286
Effective search space:    79508
Effective search space used:    79508
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 (21.9 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:

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