GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-Arginine, putative ATPase component (characterized)
to candidate Pf1N1B4_3175 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)

Query= reanno::BFirm:BPHYT_RS07685
         (263 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3175 Histidine ABC
           transporter, ATP-binding protein HisP (TC 3.A.1.3.1)
          Length = 254

 Score =  360 bits (925), Expect = e-104
 Identities = 183/253 (72%), Positives = 212/253 (83%), Gaps = 1/253 (0%)

Query: 11  KLAVQDIHKRYGDNEVLKGVSLNANKGDVISIIGASGSGKSTFLRCINFLERPNAGQIVV 70
           KL ++ +HK YGD++VLKGVSL A  GDVIS+IGASGSGKSTFLRCINFLE+PN G + +
Sbjct: 3   KLTIEGLHKSYGDHQVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMSL 62

Query: 71  DGEMVKTKTDRAGNLEVADHKQLQRIRTKLAMVFQHFNLWAHMNVLENIVEAPIHVLGLK 130
           DG+ ++   DR G + VAD  +LQRIRT+LAMVFQHFNLW+HM VLENI  AP  VLG  
Sbjct: 63  DGQTIRMIHDRHG-MRVADADELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLGCS 121

Query: 131 RKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTSALD 190
           ++EAEDRAR YL+KVGLA R+  QYP+ LSGGQQQRVAIARALAM P+VMLFDEPTSALD
Sbjct: 122 KQEAEDRARRYLDKVGLAARVADQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALD 181

Query: 191 PELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEEGLPAEVLSAPR 250
           PELVGEVLKV+Q LAEEGRTMI+VTHEM FAR VS+ V+FLHQG  EEEG P +VL  P+
Sbjct: 182 PELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSSQVLFLHQGLVEEEGAPEDVLGNPK 241

Query: 251 SERLKQFLSGSLK 263
           SERLKQFLSG+LK
Sbjct: 242 SERLKQFLSGNLK 254


Lambda     K      H
   0.318    0.133    0.374 

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: 245
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: 263
Length of database: 254
Length adjustment: 24
Effective length of query: 239
Effective length of database: 230
Effective search space:    54970
Effective search space used:    54970
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