GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natG in Mesorhizobium ciceri WSM1271

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate YP_004144834.1 Mesci_5724 polar amino acid ABC transporter inner membrane subunit

Query= TCDB::Q8YPM8
         (308 letters)



>NCBI__GCF_000185905.1:YP_004144834.1
          Length = 324

 Score =  130 bits (328), Expect = 3e-35
 Identities = 93/289 (32%), Positives = 146/289 (50%), Gaps = 44/289 (15%)

Query: 25  FLAAFVVAILLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAY----KPTDTYSLALW 80
           F  AFV+AI+   LN  L       GF  LK Q      E L+ +    K  +     +W
Sbjct: 60  FAIAFVIAIIFC-LNIVL------IGFVSLKVQIGVVWAELLVLFLAFFKSFNLSMPFIW 112

Query: 81  V--------GLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLL 132
                    G + ++ I+ V +I  +I+ ++A IA+LS N     I+  Y   FR  PLL
Sbjct: 113 ENLPYLITQGAVTTIYISAVSLIFASIIAMIAAIAKLSSNGFAYAIASFYTSFFRGLPLL 172

Query: 133 LQLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFI 192
           +Q+    + ++LGLP+      LG FI    +G+               L L   TGA++
Sbjct: 173 VQI----YLIYLGLPQ------LGIFINAVPSGV---------------LALSLCTGAYM 207

Query: 193 AEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLA 252
            EI R GIQS+ +GQWEA RS+G    L MR +I PQAL VIIPP+ + ++++ K+SSL 
Sbjct: 208 TEIFRAGIQSIDRGQWEASRSMGFGFGLTMRRIILPQALPVIIPPMGNTFISMLKDSSLV 267

Query: 253 IAIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNR 301
             +G  ++ F+A T    T + +E+++   + Y  +S+ + L+ +   R
Sbjct: 268 SILGVWELTFLARTLGQPTFQHMEMLITAAIIYWIMSICLELVQSRIER 316


Lambda     K      H
   0.328    0.143    0.430 

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: 253
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: 308
Length of database: 324
Length adjustment: 27
Effective length of query: 281
Effective length of database: 297
Effective search space:    83457
Effective search space used:    83457
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 (21.7 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