GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisQ in Desulfoscipio geothermicus DSM 3669

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

Query= reanno::pseudo6_N2E2:Pf6N2E2_2959
         (242 letters)



>NCBI__GCF_900115975.1:WP_092487756.1
          Length = 234

 Score =  143 bits (361), Expect = 3e-39
 Identities = 79/223 (35%), Positives = 123/223 (55%), Gaps = 8/223 (3%)

Query: 22  LLMQGTWMTIKLSALSLLLSVLLGLLGASAKLSSVKLLRIPAQLYTTLIRGVPDLVLMLL 81
           L+ QG  +T++++ +S+ +  LLGL+G  ++LS  K+LR  A  Y    RG P LV + +
Sbjct: 11  LIFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFI 70

Query: 82  IFYSLQTWLTSLTDFMEWEY--------IEIDPFGAGVITLGFIYGAYFTETFRGAILSV 133
           +++ +   L  L  FM   Y          +  F A VI      GAY  E FR  + S+
Sbjct: 71  VYFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSI 130

Query: 134 PRGQVEAATAYGLKRGQRFRFVVFPQMMRFALPGIGNNWMVMLKATALVSIIGLADLVKA 193
            RGQ+EAA + G+  GQ  R+V+ PQ  +  +P +GN ++ MLK T+L+S+IG A+L + 
Sbjct: 131 ERGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRN 190

Query: 194 AQDAGKSTYQLFYFLVLAALIYLLITSASNFILRWLERRYAAG 236
            Q     TY+ F   +    IYL++T   + I+ +LERRY  G
Sbjct: 191 GQLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLERRYKTG 233


Lambda     K      H
   0.329    0.142    0.418 

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: 143
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: 242
Length of database: 234
Length adjustment: 23
Effective length of query: 219
Effective length of database: 211
Effective search space:    46209
Effective search space used:    46209
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.

Links

Downloads

Related tools

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