GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Pf6N2E2_5402 in Sinorhizobium meliloti 1021

Align ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized)
to candidate SMc02118 SMc02118 general L-amino acid-binding periplasmic ABC transporter protein

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



>lcl|FitnessBrowser__Smeli:SMc02118 SMc02118 general L-amino
           acid-binding periplasmic ABC transporter protein
          Length = 341

 Score =  396 bits (1018), Expect = e-115
 Identities = 191/343 (55%), Positives = 251/343 (73%), Gaps = 4/343 (1%)

Query: 3   LLKSTLAVMTAAAVLGVSGFAQAGATLDAVQKKGFVQCGVSDGLPGFSVPDSTGKIVGID 62
           + +  L  +  AAV+G+   A + ATLD V+ KGFVQCGV+ GL GF+ PD++G   G D
Sbjct: 1   MARRILTALVGAAVVGIGTHAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFD 60

Query: 63  ADFCRAVAAAVFGDATKVKFSQLNAKERFTALQSGEIDMLSRNSTMTSSRDAGMGLKFPG 122
            D+C+A+AAA+FGD +KVK++ L+AKERF ALQSGE+D+L+RN+T + +RD  +G  F  
Sbjct: 61  VDYCKAIAAAIFGDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRP 120

Query: 123 FITYYDGIGFLANNKLGVKSAKELDGATICIQAGTTTELNVSDYFRANGLKYTPITFDTS 182
            + YYDG GF+   +L VKSA EL GA +C+Q GTTTELN++DYF+AN L+Y P+ F+  
Sbjct: 121 -VNYYDGQGFMVRKELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKL 179

Query: 183 DESAKSLESGRCDVLTSDKSQLFAQRSKLASPKDYVVLPETISKEPLGPVVRNGDDEWLA 242
           +E   + ++GRCDV T+D+S L++ R  L+ P D++VLPE ISKEPL P VR GDD+W  
Sbjct: 180 EEVNAAYDAGRCDVYTTDQSGLYSLRLTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFD 239

Query: 243 IVRWTGYALLNAEEAGVTSKNVEAEAKSTKNPDVARMLG--ADGEYGKDLKLPKDWVVQI 300
           IV W  YAL+ AEE GVT  N+E   KST NPDV R LG  AD + G DL L  +W V I
Sbjct: 240 IVSWVHYALVQAEEFGVTQANLEEMKKST-NPDVQRFLGVEADSKIGTDLGLTNEWAVNI 298

Query: 301 VKQVGNYGEMFERNLGKGTPLEIDRGLNALWNAGGIQYAPPVR 343
           VK VGNYGE+F+RN+G G+PL+I+RGLNALWN GG+QYAPPVR
Sbjct: 299 VKAVGNYGEVFDRNIGAGSPLKIERGLNALWNKGGLQYAPPVR 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: 398
Number of extensions: 16
Number of successful extensions: 3
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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