GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artP in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for L-Arginine, putative ATPase component (characterized)
to candidate H281DRAFT_00221 H281DRAFT_00221 amino acid ABC transporter ATP-binding protein, PAAT family

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



>lcl|FitnessBrowser__Burk376:H281DRAFT_00221 H281DRAFT_00221 amino
           acid ABC transporter ATP-binding protein, PAAT family
          Length = 259

 Score =  422 bits (1084), Expect = e-123
 Identities = 213/253 (84%), Positives = 231/253 (91%)

Query: 11  KLAVQDIHKRYGDNEVLKGVSLNANKGDVISIIGASGSGKSTFLRCINFLERPNAGQIVV 70
           KL V ++HK+YGDNEVLKGV+L AN GDVIS+IG+SGSGKST LRCINFLE+PNAG+I V
Sbjct: 7   KLFVDELHKQYGDNEVLKGVTLKANAGDVISVIGSSGSGKSTMLRCINFLEQPNAGRIFV 66

Query: 71  DGEMVKTKTDRAGNLEVADHKQLQRIRTKLAMVFQHFNLWAHMNVLENIVEAPIHVLGLK 130
           DGE V+T+  + G L V+D KQLQR+RTKL+MVFQHFNLW+HMNVLENIVEAP++VLGLK
Sbjct: 67  DGEEVRTQIAKNGALRVSDPKQLQRVRTKLSMVFQHFNLWSHMNVLENIVEAPVNVLGLK 126

Query: 131 RKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTSALD 190
           RKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAM+PDVMLFDEPTSALD
Sbjct: 127 RKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMHPDVMLFDEPTSALD 186

Query: 191 PELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEEGLPAEVLSAPR 250
           PELVGEVLKVMQ LAEEGRTMIVVTHEM FARNVSNHVMFLHQGR EEEG P EV    R
Sbjct: 187 PELVGEVLKVMQTLAEEGRTMIVVTHEMAFARNVSNHVMFLHQGRVEEEGHPDEVFRNTR 246

Query: 251 SERLKQFLSGSLK 263
           SERLKQFLSGSLK
Sbjct: 247 SERLKQFLSGSLK 259


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: 289
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: 263
Length of database: 259
Length adjustment: 25
Effective length of query: 238
Effective length of database: 234
Effective search space:    55692
Effective search space used:    55692
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.

Links

Downloads

Related tools

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 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