GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Burkholderia phytofirmans PsJN

Align Histidine transport system permease protein HisQ (characterized)
to candidate BPHYT_RS24045 BPHYT_RS24045 amino acid ABC transporter

Query= SwissProt::P0A2I9
         (228 letters)



>FitnessBrowser__BFirm:BPHYT_RS24045
          Length = 216

 Score =  115 bits (289), Expect = 5e-31
 Identities = 61/196 (31%), Positives = 103/196 (52%), Gaps = 11/196 (5%)

Query: 8   VILQGAIVTLELALSSVVLAVLIGLVGAGAKLSQNRVTGLIFEGYTTLIRGVPDLVLMLL 67
           ++L  A+ T+ ++L+ +++   + +    A+LS NR   +    Y    RGVP LV +LL
Sbjct: 13  LLLHAALATIGISLAGLLIGFFVAIGVCAARLSPNRAARMFGGAYVFFFRGVPMLVQLLL 72

Query: 68  IFYGLQIALNVVTDSLGIDQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGHIEAA 127
           ++Y L  A            I++ P+VA +  +     +Y  E  RG F++VP GH+EAA
Sbjct: 73  VYYLLPFA-----------GINVSPIVAALSAVSLCSASYIAEILRGGFLSVPPGHLEAA 121

Query: 128 TAFGFTHGQTFRRIMFPAMMRYALPGIGNNWQVILKATALVSLLGLEDVVKATQLAGKST 187
              G +     RRI+ P   R  LP + N   +++KA++L+S++G+ ++ +  Q    ST
Sbjct: 122 RMLGLSPFDMLRRILVPQAFRLTLPSLVNEMVLLIKASSLISVVGVAELTRTAQNIAAST 181

Query: 188 WEPFYFAVVCGLIYLV 203
           + P    V  GLIY V
Sbjct: 182 YRPLEAYVAAGLIYFV 197


Lambda     K      H
   0.328    0.144    0.422 

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: 128
Number of extensions: 4
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: 228
Length of database: 216
Length adjustment: 22
Effective length of query: 206
Effective length of database: 194
Effective search space:    39964
Effective search space used:    39964
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 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