GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Pseudomonas fluorescens GW456-L13

Align Histidine transport system permease protein HisQ (characterized)
to candidate PfGW456L13_3700 Arginine/ornithine ABC transporter, permease protein AotQ

Query= SwissProt::P52094
         (228 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3700
          Length = 229

 Score =  234 bits (598), Expect = 8e-67
 Identities = 117/229 (51%), Positives = 166/229 (72%), Gaps = 1/229 (0%)

Query: 1   MLYGFSGVILQGALVTLELAISSVVLAVIIGLIGAGGKLSQNRLSGLIFEGYTTLIRGVP 60
           ML+G+   IL GA +T+ LA++S+ LA+ +GL+GA  +LS  +   L+ E YTTLIRG+P
Sbjct: 1   MLHGYGSSILDGAWLTINLALTSMSLAIALGLVGAAFRLSPLKWLALLGESYTTLIRGIP 60

Query: 61  DLVLMLLIFYGLQIALNTVTEAMGVGQ-IDIDPMVAGIITLGFIYGAYFTETFRGAFMAV 119
           DLVL+LLIFYG Q  +N +  A+G  + IDI+P +AG+ T+GFI+GAY +ETFRGAFMA+
Sbjct: 61  DLVLILLIFYGGQDLVNRIALALGYTRYIDINPFIAGVCTMGFIFGAYLSETFRGAFMAI 120

Query: 120 PKGHIEAATAFGFTRGQVFRRIMFPSMMRYALPGIGNNWQVILKSTALVSLLGLEDVVKA 179
           PKG  EA  A+G    QVF RI+ P M+R+A+PG  NNW V+ KSTAL+S++GL+D++  
Sbjct: 121 PKGQAEAGVAYGMGGAQVFWRILVPQMIRFAIPGFTNNWLVLTKSTALISVIGLQDMMFK 180

Query: 180 TQLAGKSTWEPFYFAIVCGVIYLVFTTVSNGVLLFLERRYSVGVKRADL 228
            + A  +T EPF F +    +YL+ T++S  VL +LE+ YSVG+K A+L
Sbjct: 181 AKNAADATHEPFTFFLAVAALYLMLTSLSLLVLRYLEKHYSVGIKAAEL 229


Lambda     K      H
   0.328    0.145    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: 188
Number of extensions: 7
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: 229
Length adjustment: 23
Effective length of query: 205
Effective length of database: 206
Effective search space:    42230
Effective search space used:    42230
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: 46 (22.3 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