GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03045 in Desulfoscipio geothermicus DSM 3669

Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_03045
         (232 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  132 bits (331), Expect = 8e-36
 Identities = 76/229 (33%), Positives = 127/229 (55%), Gaps = 11/229 (4%)

Query: 6   NVIWEALP-LYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRG 64
           +V+ E LP L F G   TL++  +S+  G L  L  GL R+S++ ++   A  Y    RG
Sbjct: 2   DVVIENLPVLIFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRG 61

Query: 65  TPMLVQLFLIYYGLAQFEAVRESFL------WPWLSSATF----CACLAFAINTSAYTAE 114
           TP+LVQ+F++Y+G+ +     +SF+       P   S        A +A ++N+ AY AE
Sbjct: 62  TPLLVQIFIVYFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAE 121

Query: 115 IIAGSLRATPNGEIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASI 174
           I    +++   G++EAA+++GM+  +  + ++LP A +R +P   NE I ML+ TSL S+
Sbjct: 122 IFRAGVQSIERGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSV 181

Query: 175 VTLIDITGAARTVNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRW 223
           +   ++T   + + A+ Y  F  ++T G  YL MTF L R+    E R+
Sbjct: 182 IGFAELTRNGQLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLERRY 230


Lambda     K      H
   0.329    0.139    0.427 

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: 114
Number of extensions: 3
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: 232
Length of database: 234
Length adjustment: 23
Effective length of query: 209
Effective length of database: 211
Effective search space:    44099
Effective search space used:    44099
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 (21.8 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