GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Hafnia paralvei ATCC 29927

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_064573369.1 M988_RS06580 histidine ABC transporter ATP-binding protein HisP

Query= TCDB::Q52666
         (263 letters)



>NCBI__GCF_001655005.1:WP_064573369.1
          Length = 257

 Score =  235 bits (599), Expect = 8e-67
 Identities = 128/251 (50%), Positives = 171/251 (68%), Gaps = 12/251 (4%)

Query: 23  IQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVD 82
           + + +++K YG   VL+ ++LT   G+ I I G SGSGKST +RCIN LE+   G I ++
Sbjct: 6   LNVIELHKRYGDHEVLKGVSLTAKAGDVISIIGSSGSGKSTFLRCINFLEKPSEGTIAIN 65

Query: 83  GIEL-----------TSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPK 131
           G ++             D K +  +R+ + MVFQHFNL+ H+T+LEN+  API V  + K
Sbjct: 66  GTDIGLVRDTDGQLKVGDKKQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSK 125

Query: 132 REAEETAMYYLEKVKIPEQAQ-KYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDP 190
            EA E A+ YL+KV I E+A+ KYP  LSGGQQQRV+IAR+L M+P+++LFDEPTSALDP
Sbjct: 126 AEAHERAIRYLDKVGIDERARGKYPINLSGGQQQRVSIARALAMEPEVLLFDEPTSALDP 185

Query: 191 EMIKEVLDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQS 250
           E++ EVL  M +LAEEG TM+ VTHEMGFA+ V+N VIF+  G I EQ  P   F NP+S
Sbjct: 186 ELVGEVLRIMQKLAEEGKTMVVVTHEMGFARHVSNHVIFLHQGIIEEQGPPELVFGNPKS 245

Query: 251 ERTKQFLSQIL 261
            R +QFLS  L
Sbjct: 246 VRLQQFLSGAL 256


Lambda     K      H
   0.320    0.134    0.391 

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: 193
Number of extensions: 10
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: 263
Length of database: 257
Length adjustment: 24
Effective length of query: 239
Effective length of database: 233
Effective search space:    55687
Effective search space used:    55687
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 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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