GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Sulfurimonas denitrificans DSM 1251

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

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>NCBI__GCF_000012965.1:WP_011373501.1
          Length = 261

 Score =  119 bits (297), Expect = 8e-32
 Identities = 86/259 (33%), Positives = 134/259 (51%), Gaps = 29/259 (11%)

Query: 16  LEIRDLHKQYGPLEV--LKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIL 73
           LE+++    Y   +V  +K + + + + N+  LIG SG GKTTLLR  N + +     + 
Sbjct: 13  LEVKNFEFTYAKADVPSVKKLSMPVAKHNITALIGPSGCGKTTLLRSFNRMHD-----LY 67

Query: 74  LDGESIGYHEVNGKRVRHSEKVIAQHRAMTGMAFQQFNLFPHLTALQNVTLGLL------ 127
            + +  G      + +  S++ + + R   GM FQ+   FP ++   NV  GL       
Sbjct: 68  PNNKYSGEITFKDRNILTSKEDLIKLRIQIGMIFQKPTAFP-MSIFDNVAYGLKLQGIKN 126

Query: 128 ------KVKKLHKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSL 181
                 +V+K  KD A+     W E   + +R  H    LSGGQQQR+ IARA+A+ P +
Sbjct: 127 RTELSGRVEKALKDAAI-----WNE---VKDRLKHDANGLSGGQQQRLCIARAVAVEPEV 178

Query: 182 MLFDEVTSALDPELVGEVLSVIKGLAEDGMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQ 241
           +LFDE TSALDP   G +  +I  L E  +++++VTH M+ A  VSD   FM  G + E 
Sbjct: 179 LLFDEPTSALDPISTGGIEELIVELRE-RVSIIIVTHNMQQAARVSDYTGFMYLGELIEL 237

Query: 242 GPPKELFERPQSPRLAEFL 260
           G  +E+F  P+     E++
Sbjct: 238 GKTEEIFVTPKEKLTEEYI 256


Lambda     K      H
   0.319    0.135    0.379 

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: 132
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: 265
Length of database: 261
Length adjustment: 25
Effective length of query: 240
Effective length of database: 236
Effective search space:    56640
Effective search space used:    56640
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 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