GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Rhodobacter viridis JA737

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate WP_110806878.1 C8J30_RS16140 ABC transporter permease subunit

Query= reanno::Smeli:SMc02120
         (384 letters)



>NCBI__GCF_003217355.1:WP_110806878.1
          Length = 235

 Score =  103 bits (257), Expect = 5e-27
 Identities = 73/236 (30%), Positives = 115/236 (48%), Gaps = 21/236 (8%)

Query: 159 PGGWFGLTYVETPLWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEV 218
           P GW         L  G+ VTL L+   + V L LG ++A    S  PV++ +   +  V
Sbjct: 9   PQGW------GDELLAGVWVTLRLAAATLPVGLLLGFVVAAASLSRRPVLRAMGWGYTTV 62

Query: 219 IRGVPLITVLFMA--------SVMLPLFLPQ--GVTFDKFLRALIGVSLFASAYMAEVVR 268
           +RG+P I  LF+         + +L  F PQ   V F  F   +I ++L  +A+ AEV+R
Sbjct: 63  MRGMPEILTLFIVYNGLGLGLNRLLDHFAPQIGAVDFPPFAAGVIALALVFAAFAAEVLR 122

Query: 269 GGLQAIPKGQYEGADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGM 328
           G  QA+P+GQ     ++G++  Q    I LPQ  +  +PG+ N ++ L KDT+LVS+I +
Sbjct: 123 GAFQAVPEGQVLAGLAIGMTGRQVFWRIKLPQLWRFALPGMGNLWLNLLKDTALVSVIAL 182

Query: 329 FDLLGIVRLNFSDTNWATAVTPLTGLIFAGFVFWLFCFGMSRYSGFMERLLDRSQR 384
            DL+   ++    T       P T  + A  ++W  C G       +E   +R  R
Sbjct: 183 DDLMRATKVAVGVTK-----QPFTFYLAACLIYWGLCLGSELVLTRLEARANRGVR 233


Lambda     K      H
   0.329    0.144    0.454 

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: 265
Number of extensions: 15
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: 384
Length of database: 235
Length adjustment: 27
Effective length of query: 357
Effective length of database: 208
Effective search space:    74256
Effective search space used:    74256
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: 48 (23.1 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