GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Azospirillum brasilense Sp245

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate AZOBR_RS18180 AZOBR_RS18180 sugar ABC transporter

Query= reanno::Smeli:SMc03063
         (380 letters)



>FitnessBrowser__azobra:AZOBR_RS18180
          Length = 273

 Score =  119 bits (297), Expect = 1e-31
 Identities = 72/235 (30%), Positives = 124/235 (52%), Gaps = 8/235 (3%)

Query: 146 PPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLA 205
           P    +  YA   +   + +  +NSL VAV +TV+ IL++   AYAL+ + F G+ +L  
Sbjct: 46  PTLSQIGTYAAAFTETSLRQWLINSLIVAVGTTVLSILLSVLPAYALSRLTFNGKLLLGF 105

Query: 206 VVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAG 265
            +    ++P  M ++PL  ++  +         T +G+ LA+T F +P+  ++L+  + G
Sbjct: 106 ALFMTQMLPEAMLVVPLYDIFTKLSLL-----NTLLGLILANTAFTVPVVTWILKGAIDG 160

Query: 266 LPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDK 325
           +P EI E+ARVDG S   I + +++PL  P LA+ A+  F   WN+ + A  F+   DD 
Sbjct: 161 VPSEIEEAARVDGCSRLGIVLAVVVPLIAPTLAAAAVIAFFHGWNEYVFAQTFI--SDDA 218

Query: 326 L-VLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379
           L   +  L + +G        + A  FI  +  ++ +  +QRY+V G+  G VKG
Sbjct: 219 LRTASVGLASFVGELSTPVHTVMAVGFIYTLPAVVFYLFVQRYVVAGMTTGGVKG 273


Lambda     K      H
   0.324    0.139    0.418 

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: 222
Number of extensions: 10
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: 380
Length of database: 273
Length adjustment: 28
Effective length of query: 352
Effective length of database: 245
Effective search space:    86240
Effective search space used:    86240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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