GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate Pf1N1B4_4396 Arginine/ornithine ABC transporter, ATP-binding protein AotP

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4396 Arginine/ornithine
           ABC transporter, ATP-binding protein AotP
          Length = 254

 Score =  439 bits (1130), Expect = e-128
 Identities = 222/254 (87%), Positives = 239/254 (94%)

Query: 1   MYKLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKI 60
           MYKLEVQDLHK YG+H+VLKGVSL+A AGDVISIIGSSGSGKSTFLRCINLLEQP+AG I
Sbjct: 1   MYKLEVQDLHKSYGAHQVLKGVSLQAQAGDVISIIGSSGSGKSTFLRCINLLEQPNAGNI 60

Query: 61  LLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLG 120
           +LN E LKLVANK G LKAA+PKQLQRMRS+LSMVFQHFNLWSHM+A+EN+MEAPVHV G
Sbjct: 61  VLNGEPLKLVANKLGGLKAAEPKQLQRMRSQLSMVFQHFNLWSHMSALENVMEAPVHVQG 120

Query: 121 MSKTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSAL 180
           + K EAREKAEHYL+KVGVAHR +A+P HMSGGEQQRVAIARALAMEP+VMLFDEPTSAL
Sbjct: 121 LGKKEAREKAEHYLDKVGVAHRMNAWPAHMSGGEQQRVAIARALAMEPQVMLFDEPTSAL 180

Query: 181 DPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNP 240
           DPELVG+VLKVMQ LAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEE G+P EVLVNP
Sbjct: 181 DPELVGEVLKVMQDLAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEERGDPSEVLVNP 240

Query: 241 QSERLQQFLSGSLK 254
           QSERLQQFLSGSLK
Sbjct: 241 QSERLQQFLSGSLK 254


Lambda     K      H
   0.317    0.131    0.366 

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: 306
Number of extensions: 4
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: 254
Length of database: 254
Length adjustment: 24
Effective length of query: 230
Effective length of database: 230
Effective search space:    52900
Effective search space used:    52900
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