GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Pseudomonas fluorescens FW300-N2E2

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate Pf6N2E2_2962 Histidine ABC transporter, ATP-binding protein HisP (TC 3.A.1.3.1)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2962
          Length = 254

 Score =  345 bits (884), Expect = e-100
 Identities = 172/255 (67%), Positives = 213/255 (83%), Gaps = 2/255 (0%)

Query: 1   MYKLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKI 60
           MYKL ++ LHK YG HEVLKGVSLKA  GDVIS+IG+SGSGKSTFLRCIN LEQP+ G +
Sbjct: 1   MYKLTIEGLHKSYGEHEVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAM 60

Query: 61  LLNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLG 120
            L+ + ++++ ++ G +  AD  +LQR+R+RL+MVFQHFNLWSHMT +ENI  AP  VLG
Sbjct: 61  SLDGQPIQMIKDRHG-MHVADADELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLG 119

Query: 121 MSKTEAREKAEHYLNKVGVAHR-KDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSA 179
           +SK EA ++A  YL+KVG+  R  + YP  +SGG+QQRVAIARALAMEPEVMLFDEPTSA
Sbjct: 120 VSKQEADDRARRYLDKVGLPARVAEQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSA 179

Query: 180 LDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVN 239
           LDPELVG+VLKV+Q LA+EGRTM++VTHEM FAR+VSNQ++FLH+G+VEE G P +VL N
Sbjct: 180 LDPELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSNQVLFLHQGLVEEEGRPEDVLGN 239

Query: 240 PQSERLQQFLSGSLK 254
           P SERL+QFLSG+LK
Sbjct: 240 PTSERLKQFLSGNLK 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: 238
Number of extensions: 7
Number of successful extensions: 3
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 (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