GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Mesorhizobium ciceri WSM1271

Align Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate YP_004141922.1 Mesci_2738 ABC transporter

Query= TCDB::Q9HU32
         (257 letters)



>NCBI__GCF_000185905.1:YP_004141922.1
          Length = 252

 Score =  244 bits (622), Expect = 2e-69
 Identities = 127/250 (50%), Positives = 175/250 (70%), Gaps = 11/250 (4%)

Query: 5   TPALEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHQGQI 64
           T  ++ R ++K +G L VLK I+L+    +V+ + G SGSGKST +RC+N LE    G +
Sbjct: 9   TGMIDFRGVNKWFGSLNVLKDITLSVEPREVVVVCGPSGSGKSTLIRCVNGLEAIKNGDL 68

Query: 65  LVSGEELRLKKSKNGDLVAADSQQINRLRSELGFVFQNFNLWPHMSILDNVIEAPRRVLG 124
           +V G+ L       GD     +  + +LR+E+GFVFQ+FNL+PH + L+NV  AP  V  
Sbjct: 69  VVDGQRL-------GD----PATNMTQLRTEIGFVFQSFNLYPHKTALENVTLAPIHVRK 117

Query: 125 KSKAEAIEIAEGLLAKVGIADKRHSYPAQLSGGQQQRAAIARTLAMQPKVILFDEPTSAL 184
             +AEA +    LLAKVG+ADK ++YPAQLSGGQQQR AIAR L M+PK++LFDEPTSAL
Sbjct: 118 IPRAEAEKAGRELLAKVGLADKVNAYPAQLSGGQQQRVAIARCLGMRPKIMLFDEPTSAL 177

Query: 185 DPEMVQEVLNVIRALAEEGRTMLLVTHEMSFARQVSSEVVFLHQGLVEEQGTPQQVFENP 244
           DPEM+ EVL+V+ A+AEEG TM++VTHEM FAR+V+  VVF+  G + E GTP + F +P
Sbjct: 178 DPEMISEVLDVMVAVAEEGMTMMVVTHEMGFARKVAQRVVFMDAGAIVESGTPDEFFSHP 237

Query: 245 QSARCKQFMS 254
           ++ R + F+S
Sbjct: 238 KTDRSRAFLS 247


Lambda     K      H
   0.317    0.133    0.367 

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: 167
Number of extensions: 3
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: 257
Length of database: 252
Length adjustment: 24
Effective length of query: 233
Effective length of database: 228
Effective search space:    53124
Effective search space used:    53124
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 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