GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Desulfoscipio geothermicus DSM 3669

Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= TCDB::Q9HU30
         (231 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  136 bits (343), Expect = 3e-37
 Identities = 77/222 (34%), Positives = 123/222 (55%), Gaps = 8/222 (3%)

Query: 12  LLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLMI 71
           +  G  +TL++++ +V +G LLGL+G +++ S+   LRFL   Y    RG P  + + ++
Sbjct: 12  IFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFIV 71

Query: 72  YFGTVSGLNALG----DLFGKPDLA----LSPFAAGTLALGLCFGAYATEVFRGALLSIP 123
           YFG    L  L     D +G   +A    L  F A  +A  L  GAY  E+FR  + SI 
Sbjct: 72  YFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSIE 131

Query: 124 RGHREAGQALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKA 183
           RG  EA ++LG++ G+    ++LPQ ++  +P LGN ++ +LKDT+L+S+I   E+ R  
Sbjct: 132 RGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRNG 191

Query: 184 QVASNATKEPFTFYMTAAAIYLSLTVVIMVALHFLERRAGRG 225
           Q+    T E F  ++T   IYL +T  +   + +LERR   G
Sbjct: 192 QLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLERRYKTG 233


Lambda     K      H
   0.327    0.143    0.431 

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: 109
Number of extensions: 5
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: 231
Length of database: 234
Length adjustment: 23
Effective length of query: 208
Effective length of database: 211
Effective search space:    43888
Effective search space used:    43888
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 46 (22.3 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