GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03050 in Paraburkholderia phymatum STM815

Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate WP_012404721.1 BPHY_RS27410 amino acid ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_03050
         (229 letters)



>NCBI__GCF_000020045.1:WP_012404721.1
          Length = 219

 Score =  119 bits (298), Expect = 5e-32
 Identities = 73/212 (34%), Positives = 119/212 (56%), Gaps = 12/212 (5%)

Query: 8   VILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPDLVLILL 67
           V+L GA +TL+ AL+S  L +++G I   + +S    +A +   Y +++RG P LV I +
Sbjct: 13  VLLLGAMVTLKFALASAVLGLLVGFIVAIMGISGQPIIAGIARAYVSLMRGTPLLVQIFV 72

Query: 68  IFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEA 127
           ++YG  DL             I L+P  AGI  L    GAYLSE+ RGA + I +GQ  A
Sbjct: 73  VYYGLPDL------------GISLDPTSAGILALTANAGAYLSESMRGAILGISQGQWGA 120

Query: 128 GAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADA 187
             + G++  Q    V+ PQ +R+A+P   N  + L K T+L+SV+ + +M+  A++   +
Sbjct: 121 AHSLGLTHMQTLRYVICPQALRMAVPSLGNTLISLIKDTSLVSVITVTEMLRAAQEVIAS 180

Query: 188 TREPFTFFLAVAAMYLVITSVSLLALRHLEKR 219
           T +P   +LA AA+Y ++++      RH+E R
Sbjct: 181 TFQPLPLYLAAAAIYWLLSTGMSWVQRHVEVR 212


Lambda     K      H
   0.329    0.144    0.421 

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: 153
Number of extensions: 14
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: 219
Length adjustment: 22
Effective length of query: 207
Effective length of database: 197
Effective search space:    40779
Effective search space used:    40779
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