GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03050 in Paenisporosarcina indica PN2

Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate WP_139311101.1 GY23_RS08105 ABC transporter permease subunit

Query= reanno::pseudo1_N1B4:Pf1N1B4_3432
         (229 letters)



>NCBI__GCF_001939075.1:WP_139311101.1
          Length = 233

 Score =  113 bits (283), Expect = 3e-30
 Identities = 73/213 (34%), Positives = 111/213 (52%), Gaps = 13/213 (6%)

Query: 9   ILDG-VWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILL 67
           +L+G V  TL L L + VL + L ++    R+S I+ L W+   Y + IRG P LV + +
Sbjct: 27  LLEGAVVYTLPLTLITFVLGLTLAILTALARISTIKPLQWIARFYVSAIRGTPLLVQLFI 86

Query: 68  IFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEA 127
           +FYG    L  V         I ++P  A +       GAY SE  R A ++IPKGQ EA
Sbjct: 87  LFYG----LGSVG--------IVIDPFPAAVIGFSLNVGAYASEVIRAAILSIPKGQWEA 134

Query: 128 GMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADA 187
               GMS  Q   RV++PQ  R++IP  +N ++ L K T+L S + + +M  +A++ A  
Sbjct: 135 AQMIGMSYSQTLRRVILPQATRVSIPPLSNTFIGLVKDTSLASAILVTEMFRRAQEIAAF 194

Query: 188 TREPFTFFLAVAAMYLVITSVSLLALRHLEKRY 220
             E    +  VA +Y +I  +  L    LE+R+
Sbjct: 195 NYEVLLLYTEVAILYWIICFLLSLVQGRLERRF 227


Lambda     K      H
   0.329    0.144    0.428 

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: 144
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: 229
Length of database: 233
Length adjustment: 23
Effective length of query: 206
Effective length of database: 210
Effective search space:    43260
Effective search space used:    43260
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 Sep 24 2021. 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