GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Sulfurimonas denitrificans DSM 1251

Align ABC transporter for L-Lysine, ATPase component (characterized)
to candidate WP_011373501.1 SUDEN_RS09795 phosphate ABC transporter ATP-binding protein PstB

Query= reanno::pseudo5_N2C3_1:AO356_05515
         (254 letters)



>NCBI__GCF_000012965.1:WP_011373501.1
          Length = 261

 Score =  112 bits (281), Expect = 6e-30
 Identities = 82/258 (31%), Positives = 141/258 (54%), Gaps = 22/258 (8%)

Query: 4   LTIEGLHKSYGEHEV--LKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQ--PND-- 57
           L ++    +Y + +V  +K +S+     ++ +LIG SG GK+T LR  N +    PN+  
Sbjct: 13  LEVKNFEFTYAKADVPSVKKLSMPVAKHNITALIGPSGCGKTTLLRSFNRMHDLYPNNKY 72

Query: 58  -GAMTLDGQPVQMIKDRHGMHVADADELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRR 116
            G +T         KDR+ +     ++L ++R ++ M+FQ    +  M++ +N+    + 
Sbjct: 73  SGEITF--------KDRNIL--TSKEDLIKLRIQIGMIFQKPTAFP-MSIFDNVAYGLKL 121

Query: 117 VLGVSKQEADDRARRYLDKVGLPARVAEQYPAF---LSGGQQQRVAIARALAMEPEVMLF 173
               ++ E   R  + L    +   V ++       LSGGQQQR+ IARA+A+EPEV+LF
Sbjct: 122 QGIKNRTELSGRVEKALKDAAIWNEVKDRLKHDANGLSGGQQQRLCIARAVAVEPEVLLF 181

Query: 174 DEPTSALDPELVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSNQVLFLHQGLVEEEGAP 233
           DEPTSALDP   G + ++I  L E   ++I+VTH M  A +VS+   F++ G + E G  
Sbjct: 182 DEPTSALDPISTGGIEELIVELRER-VSIIIVTHNMQQAARVSDYTGFMYLGELIELGKT 240

Query: 234 EDVLGNPKSERLKQFLSG 251
           E++   PK +  +++++G
Sbjct: 241 EEIFVTPKEKLTEEYITG 258


Lambda     K      H
   0.319    0.135    0.380 

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: 139
Number of extensions: 5
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: 254
Length of database: 261
Length adjustment: 24
Effective length of query: 230
Effective length of database: 237
Effective search space:    54510
Effective search space used:    54510
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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