GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AO353_03050 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate Pf1N1B4_4399 Arginine/ornithine ABC transporter, permease protein AotQ

Query= reanno::pseudo3_N2E3:AO353_03050
         (229 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4399 Arginine/ornithine
           ABC transporter, permease protein AotQ
          Length = 230

 Score =  364 bits (935), Expect = e-106
 Identities = 179/229 (78%), Positives = 206/229 (89%)

Query: 1   MLKGYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIP 60
           ML GYG+ ILDGAWLT+ LAL+SM+LAI LGLIG A RLSP++WLA LG+ Y+T+IRGIP
Sbjct: 2   MLHGYGSSILDGAWLTINLALTSMSLAIALGLIGAAFRLSPLKWLAVLGESYTTLIRGIP 61

Query: 61  DLVLILLIFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAI 120
           DLVLILLIFYGGQDL+NR+A  LGY  YID+NP +AG+ T+GFIFGAYLSETFRGAFMAI
Sbjct: 62  DLVLILLIFYGGQDLVNRIALALGYTRYIDINPFIAGVCTMGFIFGAYLSETFRGAFMAI 121

Query: 121 PKGQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFK 180
           PKGQAEAG AYGM   QVF+R+LVPQMIR AIPGFTNNWLVLTK+TALISV+GLQDMMFK
Sbjct: 122 PKGQAEAGVAYGMGGAQVFWRILVPQMIRFAIPGFTNNWLVLTKSTALISVIGLQDMMFK 181

Query: 181 AKQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAADL 229
           AK AADAT EPFTFFLAVAA+YL++TS+SLL LR+LEK YSVG++AA+L
Sbjct: 182 AKNAADATHEPFTFFLAVAALYLMLTSLSLLVLRYLEKHYSVGIKAAEL 230


Lambda     K      H
   0.329    0.144    0.421 

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: 281
Number of extensions: 11
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: 229
Length of database: 230
Length adjustment: 23
Effective length of query: 206
Effective length of database: 207
Effective search space:    42642
Effective search space used:    42642
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 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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