GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5402 in Pantoea rwandensis LMG 26275

Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate WP_084938021.1 HA51_RS24860 amino acid ABC transporter substrate-binding protein

Query= reanno::pseudo6_N2E2:Pf6N2E2_5402
         (343 letters)



>NCBI__GCF_002095475.1:WP_084938021.1
          Length = 341

 Score =  470 bits (1209), Expect = e-137
 Identities = 227/342 (66%), Positives = 278/342 (81%), Gaps = 3/342 (0%)

Query: 2   KLLKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGI 61
           K++ STL  + AA++L V+  A AG TLDA++KKGFVQCG+SDGLPGFS  D++GK  GI
Sbjct: 3   KMMLSTL--VAAASLLAVAQQAHAGTTLDAIKKKGFVQCGISDGLPGFSYADASGKFTGI 60

Query: 62  DADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFP 121
           D D CRA AAAVFGDA+KVK++ L AKERFTALQSGE+D+LSRN+T TSSRD GMG  F 
Sbjct: 61  DVDVCRAAAAAVFGDASKVKYTPLTAKERFTALQSGEVDILSRNTTWTSSRDGGMGFLFA 120

Query: 122 GFITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDT 181
           G + YYDGIGFL + K G+KSAKELDGAT+CIQAGT TELNV+DYF+AN ++YTP+TFD 
Sbjct: 121 G-VNYYDGIGFLTHKKAGLKSAKELDGATVCIQAGTDTELNVADYFKANKMQYTPVTFDR 179

Query: 182 SDESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWL 241
           SDESAK+L+SGRCD L+SD+SQL+A R KL  P D++VLPE ISKEPLGPVVR GDD+W 
Sbjct: 180 SDESAKALDSGRCDTLSSDQSQLYALRVKLGKPDDFIVLPEVISKEPLGPVVRRGDDDWF 239

Query: 242 AIVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLGADGEYGKDLKLPKDWVVQIV 301
            IV+W+ +A+LNAEE G+ SKNV+  A     PD+A +LGA+G++GKDLKL   W   I+
Sbjct: 240 TIVKWSLFAMLNAEEMGINSKNVDQMAAKPTTPDMAHLLGAEGDFGKDLKLDNKWAYNII 299

Query: 302 KQVGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343
           KQVGNY E+F+RN+GK + L+I RG NALWN GGIQYAPPVR
Sbjct: 300 KQVGNYQEVFDRNVGKDSALKIARGQNALWNQGGIQYAPPVR 341


Lambda     K      H
   0.315    0.133    0.383 

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: 451
Number of extensions: 17
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: 343
Length of database: 341
Length adjustment: 29
Effective length of query: 314
Effective length of database: 312
Effective search space:    97968
Effective search space used:    97968
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. 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