GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacC in Pseudomonas stutzeri RCH2

Align Tagatose-6-phosphate kinase; EC 2.7.1.144; Phosphotagatokinase (uncharacterized)
to candidate GFF3290 Psest_3354 1-phosphofructokinase

Query= curated2:Q8XNK5
         (310 letters)



>FitnessBrowser__psRCH2:GFF3290
          Length = 312

 Score =  140 bits (353), Expect = 4e-38
 Identities = 92/280 (32%), Positives = 143/280 (51%), Gaps = 4/280 (1%)

Query: 2   ILTITMNPSIDISYPLDVLNLDSVNRVTKVTKTAGGKGLNVTRVLKQLDADVLASGLLGG 61
           +LT+T+NP++D++  L  L L  VNR   +   A GKGLNV +VL  L   +  +G LG 
Sbjct: 4   VLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGFLGE 63

Query: 62  FFGDFIKNDLNINGIKHSFSDISGETRNCIAILH-EGNQTEILESGPNISEKEANNFLRH 120
                 +   +  G    F  ++GETR+ + +   +G  T+I   G  +SE +    L  
Sbjct: 64  GNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEADGRVTDINGPGLAVSEAQRAELLAR 123

Query: 121 FELLVDKANIISISGSLPLGISKDFYVKMLSICNKKDKRVVLDCSGEELRQVLKNDSKPF 180
            + LV    ++ ++GSLP GI   ++V++L+       RV LD SG  LR  L   ++P+
Sbjct: 124 LKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLA--TRPW 181

Query: 181 AIKPNIDELSDLLGVKVKDSIEDLKLILNTPMFNGIEWIVISMGAKGSFAKHNDKFYRVI 240
            IKPN +EL++  G+++  S   L          GIE +V+S GA G             
Sbjct: 182 LIKPNEEELAEARGIELSGS-SALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAALHAS 240

Query: 241 IPKIQVVNPVGSGDSTIAGLTKGLNDGETDENVLKIANTL 280
            PK++VV+ VG+GDS +AG+  GL +G   E  L  A  +
Sbjct: 241 PPKVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAI 280


Lambda     K      H
   0.317    0.137    0.385 

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: 175
Number of extensions: 8
Number of successful extensions: 5
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: 310
Length of database: 312
Length adjustment: 27
Effective length of query: 283
Effective length of database: 285
Effective search space:    80655
Effective search space used:    80655
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 (21.6 bits)
S2: 48 (23.1 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:

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