GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artJ in Pseudomonas fluorescens GW456-L13

Align ABC transporter for L-Arginine, periplasmic substrate-binding component (characterized)
to candidate PfGW456L13_4635 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)

Query= reanno::BFirm:BPHYT_RS07735
         (264 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4635
           Lysine-arginine-ornithine-binding periplasmic protein
           precursor (TC 3.A.1.3.1)
          Length = 260

 Score =  245 bits (626), Expect = 6e-70
 Identities = 131/257 (50%), Positives = 167/257 (64%), Gaps = 6/257 (2%)

Query: 1   MKMNWRNIAALALFAAASATAGTAAAADIKEVHFGVEASYAPFESKSPSGELQGFDIDVG 60
           MK     ++ALAL  AA    G+A A + KE+ FGV+ SYAPFESK+  G L GFDID+G
Sbjct: 1   MKKALLTLSALALCMAA----GSAMAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLG 56

Query: 61  NAVCAKLKAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQM 120
           NA+CA+LK KC WVE+ FDG+IP L+A KF+ + S MT+T  R + +DF+  +++ P   
Sbjct: 57  NAICAELKVKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKVIDFSSELFSGPTAY 116

Query: 121 IAKKGSGLLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGR 180
           + KKGSGL    ASLKGK VG  QGTIQE YAKA    AGV    YQ QDQ+Y+DL SGR
Sbjct: 117 VFKKGSGLTEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYSDLTSGR 176

Query: 181 LDAAFQDAEAASKGFLKKPQGAGFEFAGPAVTDEKLLGAGVGFGVRKGDKALKDALNQAL 240
           LDAA QD   A  GFLK P+G G+E + P   D +LL A    G++KG+  LK  L++ +
Sbjct: 177 LDAAIQDMLQAELGFLKSPKGEGYEVSKP--VDSELLPAKTAVGIKKGNTELKALLDKGI 234

Query: 241 KELKADGTIDRFAAKYF 257
           K L  DGT      K+F
Sbjct: 235 KALHDDGTYATIQKKHF 251


Lambda     K      H
   0.317    0.133    0.383 

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: 234
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: 264
Length of database: 260
Length adjustment: 25
Effective length of query: 239
Effective length of database: 235
Effective search space:    56165
Effective search space used:    56165
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 (21.7 bits)
S2: 47 (22.7 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