GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Lactobacillus silagei IWT126

Align histidine transport ATP-binding protein hisP (characterized)
to candidate WP_054655718.1 CES79_RS03450 amino acid ABC transporter ATP-binding protein

Query= CharProtDB::CH_003210
         (257 letters)



>NCBI__GCF_002217945.1:WP_054655718.1
          Length = 247

 Score =  240 bits (613), Expect = 2e-68
 Identities = 123/249 (49%), Positives = 180/249 (72%), Gaps = 14/249 (5%)

Query: 5   KLNVIDLHKRYGEHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGSIVV 64
           K+ V +L K +G+++VLKG++++ +  +V+ +IG SGSGKSTFLR +N LE P+ GSIV+
Sbjct: 6   KVKVSNLVKNFGDNKVLKGINMEVHDNEVVVVIGPSGSGKSTFLRNLNRLEAPTSGSIVI 65

Query: 65  NGQTINLVRDKDGQLKVAD-KNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGL 123
           +             + +AD K  +  +R  + MVFQHFNL+S+++V ENVM AP+++   
Sbjct: 66  D------------DMDIADPKTDINKVRENIGMVFQHFNLFSNLSVSENVMLAPVELKKK 113

Query: 124 SKQEARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPTSAL 183
           +K+EA ++A   L  VG++ +        LSGGQQQRV+IARALAM P V+LFDEPTSAL
Sbjct: 114 TKEEATKQAHDLLNMVGLESKFNATVQ-SLSGGQQQRVAIARALAMNPNVMLFDEPTSAL 172

Query: 184 DPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQLFGNP 243
           DPE+VG+VL +M+QLA++G TM+VVTHEMGFA+ V+  V+F+  G I+E+G P+++F +P
Sbjct: 173 DPEMVGDVLAVMKQLAKQGMTMIVVTHEMGFAKEVADRVVFVDDGNIQEQGTPDEMFNHP 232

Query: 244 QSPRLQRFL 252
           Q+P LQ FL
Sbjct: 233 QNPHLQDFL 241


Lambda     K      H
   0.318    0.134    0.375 

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: 190
Number of extensions: 4
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: 257
Length of database: 247
Length adjustment: 24
Effective length of query: 233
Effective length of database: 223
Effective search space:    51959
Effective search space used:    51959
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: 46 (22.3 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