GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Dyella japonica UNC79MFTsu3.2

Align histidine transport ATP-binding protein hisP (characterized)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein

Query= CharProtDB::CH_003210
         (257 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1085
          Length = 336

 Score =  172 bits (435), Expect = 1e-47
 Identities = 105/257 (40%), Positives = 150/257 (58%), Gaps = 18/257 (7%)

Query: 6   LNVIDLHKRYG----EHEVLKGVSLQANAGDVISIIGSSGSGKSTFLRCINFLEKPSEGS 61
           +  +D+HK Y     +   L+  SL    G+V  IIG SG+GKST +R IN LE+PS GS
Sbjct: 2   IRFVDVHKSYRVDGKDIPALQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGS 61

Query: 62  IVVNGQTINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVL 121
           I+++G  +  + D            LR  R R+ M+FQHFNL S  TV +N+   P+++ 
Sbjct: 62  ILIDGTEMTALGDA----------ALRAQRRRIGMIFQHFNLLSSQTVADNIA-FPLRLA 110

Query: 122 GLSKQ-EARERAVKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPEVLLFDEPT 180
           G +   + + R  + L +VG++  A  KYP  LSGGQ+QRV IARALA  P +LL DE T
Sbjct: 111 GETDAGKIKARVDELLRRVGLEAHAS-KYPAQLSGGQKQRVGIARALANRPSILLCDEAT 169

Query: 181 SALDPELVGEVLRIMQQLAEEGK-TMVVVTHEMGFARHVSTHVIFLHQGKIEEEGAPEQL 239
           SALDP+    VL ++ ++  E K T+V++THEM   R V   V  L  G+I E GA   +
Sbjct: 170 SALDPQTTASVLELLAEINRELKLTIVLITHEMDVVRRVCDRVAVLDAGRIVEHGAVADV 229

Query: 240 FGNPQSPRLQRFLKGSL 256
           F +P+ P  +RF+  +L
Sbjct: 230 FLHPRHPTTRRFVNEAL 246


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: 200
Number of extensions: 10
Number of successful extensions: 4
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: 336
Length adjustment: 26
Effective length of query: 231
Effective length of database: 310
Effective search space:    71610
Effective search space used:    71610
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: 48 (23.1 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:

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