GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aapP in Pseudomonas stutzeri RCH2

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate GFF139 Psest_0139 ABC-type histidine transport system, ATPase component

Query= reanno::Smeli:SMc02121
         (258 letters)



>lcl|FitnessBrowser__psRCH2:GFF139 Psest_0139 ABC-type histidine
           transport system, ATPase component
          Length = 257

 Score =  243 bits (621), Expect = 2e-69
 Identities = 129/248 (52%), Positives = 170/248 (68%), Gaps = 11/248 (4%)

Query: 18  AIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIVV 77
           A+EI N++K YGD  VL+ I+L    G+ I + G SGSGKST +RCIN LE   +G+I+V
Sbjct: 7   ALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHEGEILV 66

Query: 78  DGIEL-----------TNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMP 126
            G +L             D K+++ +R E+G VFQ+FNL+PH+TIL+N   AP  V    
Sbjct: 67  AGEQLKLKRDKQGDLVAADGKQLNRIRSELGFVFQNFNLWPHMTILDNIIEAPRRVLGQS 126

Query: 127 KKEAEQVAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDP 186
           K EA +VA   L +V I ++   YP QLSGGQQQR AIAR+L M+PK++LFDEPTSALDP
Sbjct: 127 KAEATEVAEALLAKVGIADKRHVYPNQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDP 186

Query: 187 EMVKEVLDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQH 246
           EMV+EVL  +  LAEEG TM+ VTHEM FA+QV++ V+F+ QG + EQ +P + FDNPQ 
Sbjct: 187 EMVQEVLAVIRSLAEEGRTMLLVTHEMNFAKQVSSEVVFLHQGLVEEQGTPEQVFDNPQS 246

Query: 247 ERTKLFLS 254
            R K F+S
Sbjct: 247 ARCKQFMS 254


Lambda     K      H
   0.322    0.136    0.397 

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: 192
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: 258
Length of database: 257
Length adjustment: 24
Effective length of query: 234
Effective length of database: 233
Effective search space:    54522
Effective search space used:    54522
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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, the preprint on GapMind for carbon sources, 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