GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34240 in Azospirillum brasilense Sp245

Align Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale)
to candidate AZOBR_RS27940 AZOBR_RS27940 ABC transporter permease

Query= uniprot:B2T9V8
         (351 letters)



>FitnessBrowser__azobra:AZOBR_RS27940
          Length = 329

 Score =  140 bits (352), Expect = 6e-38
 Identities = 93/303 (30%), Positives = 155/303 (51%), Gaps = 6/303 (1%)

Query: 46  ALALLIVIGAFISPSFLTKANLISVLGASAALALVVLAESLIVLTGKFDLSLESTVGIAP 105
           ALA LIV+G  ++P FL+  N+ +VL  +A + ++ +  + ++  G  DLS+ S    A 
Sbjct: 22  ALAALIVLGTIVNPVFLSPGNIGNVLTRTAFIGIIAVGATFVITAGGIDLSVGSLAAFAS 81

Query: 106 AVGAMLVMPAASAGFGMQWPAAA-GLLAIVVVGAVIGFINGFLVVRLRLNAFIVTLAMLI 164
            V  ++VM A     G   P    G+L  + +G V G +NG LV + R+ AFIVTL  + 
Sbjct: 82  GV-MIVVMNALVGSMGAGLPVILIGVLVALGLGLVAGLVNGLLVTKGRMEAFIVTLGTMG 140

Query: 165 VLRGMLVGATKGGTLF---DMPTSFFALATTIVLGLPLSVWLAAAAFAIAAFMLRYHRLG 221
           + R ++     GGTL    ++ T +  +    V G+   +   A    I A ++   R G
Sbjct: 141 IFRSLVTYIADGGTLSLNSEIRTIYRPVYYGGVFGISYPILAFAVVALIGALIMYRTRFG 200

Query: 222 RALYAIGGNPEAARAAGIRVERITWGVFVLGSILASVGGLIVTGYVGAINANQGNGMIFT 281
           R   AIG + + AR + I V+R+    FVL  I  ++  +I    +G+ +A  G      
Sbjct: 201 RYCAAIGSSEDVARYSAINVDRVKLLAFVLQGICVAIAVVIYVPRLGSASATTGLLWELE 260

Query: 282 VFAAAVIGGISLDGGKGTMFGALTGVLLLGVVQNLLTLAQVPSFWIQ-AIYGAIILGSLM 340
             AA +IGG  L GG G ++G + G ++L ++ N+L L    S ++   I G II+ +++
Sbjct: 261 AIAAVIIGGTMLKGGYGRIWGTVVGAVMLTLIDNILNLTGAISVYLNGTIQGVIIIVAVL 320

Query: 341 VAR 343
           + R
Sbjct: 321 LQR 323


Lambda     K      H
   0.326    0.140    0.397 

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: 318
Number of extensions: 20
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: 351
Length of database: 329
Length adjustment: 28
Effective length of query: 323
Effective length of database: 301
Effective search space:    97223
Effective search space used:    97223
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 (21.6 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 (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