GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Sulfurimonas denitrificans DSM 1251

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

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>NCBI__GCF_000012965.1:WP_011373501.1
          Length = 261

 Score =  112 bits (279), Expect = 1e-29
 Identities = 79/255 (30%), Positives = 141/255 (55%), Gaps = 16/255 (6%)

Query: 4   LEVQDLHKRYGSHEV--LKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKIL 61
           LEV++    Y   +V  +K +S+  A  ++ ++IG SG GK+T LR  N +   +     
Sbjct: 13  LEVKNFEFTYAKADVPSVKKLSMPVAKHNITALIGPSGCGKTTLLRSFNRMHDLYP---- 68

Query: 62  LNNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGM 121
            NN+    +  KD  +  +  + L ++R ++ M+FQ    +  M+  +N+    + + G+
Sbjct: 69  -NNKYSGEITFKDRNILTSK-EDLIKLRIQIGMIFQKPTAFP-MSIFDNVAYG-LKLQGI 124

Query: 122 -SKTEAREKAEHYLNKVGVAHRKDAYPGH----MSGGEQQRVAIARALAMEPEVMLFDEP 176
            ++TE   + E  L    + +       H    +SGG+QQR+ IARA+A+EPEV+LFDEP
Sbjct: 125 KNRTELSGRVEKALKDAAIWNEVKDRLKHDANGLSGGQQQRLCIARAVAVEPEVLLFDEP 184

Query: 177 TSALDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREV 236
           TSALDP   G + +++  L +E  ++++VTH M  A  VS+   F++ G + E G   E+
Sbjct: 185 TSALDPISTGGIEELIVEL-RERVSIIIVTHNMQQAARVSDYTGFMYLGELIELGKTEEI 243

Query: 237 LVNPQSERLQQFLSG 251
            V P+ +  +++++G
Sbjct: 244 FVTPKEKLTEEYITG 258


Lambda     K      H
   0.317    0.131    0.366 

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: 152
Number of extensions: 6
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: 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 ( 7.3 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 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