GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Phaeobacter inhibens BS107

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate GFF1916 PGA1_c19480 ABC transporter, inner-membrane protein

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



>FitnessBrowser__Phaeo:GFF1916
          Length = 297

 Score =  146 bits (369), Expect = 6e-40
 Identities = 82/224 (36%), Positives = 127/224 (56%), Gaps = 9/224 (4%)

Query: 158 LSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQM 217
           L   GI   F NS+ + +PS V+ I   A   Y L +  F G  +  A+++    VP Q 
Sbjct: 81  LQCEGIKVGFWNSMRILLPSLVVSITAGALCGYILTFWTFRGAEIFFAILLFGAFVPYQA 140

Query: 218 SLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVD 277
            + P++++++  G +      T  GI L HT FGLP+   + RNY + LP EI ++ARVD
Sbjct: 141 LIFPMIRIFSATGLY-----GTLPGIVLVHTIFGLPIMTLIFRNYYSTLPSEIFKAARVD 195

Query: 278 GASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLG 337
           GA  F +F  ++LP+S P +   AI Q    WND L+ ++F   G + + +T +L N++ 
Sbjct: 196 GAGFFSVFWYVLLPISTPIIVVAAILQVTGIWNDYLLGLIF--GGRENMPMTVQLNNIVN 253

Query: 338 S-RGG-NWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379
           S RGG  + +  A+  +T +VPL V+F   R+ VRG+ AG+VKG
Sbjct: 254 SVRGGKEYNVNMAATLLTALVPLTVYFVSGRWFVRGIAAGAVKG 297


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: 283
Number of extensions: 15
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: 297
Length adjustment: 28
Effective length of query: 352
Effective length of database: 269
Effective search space:    94688
Effective search space used:    94688
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: 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