GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Dyella japonica UNC79MFTsu3.2

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3133
          Length = 273

 Score =  127 bits (319), Expect = 4e-34
 Identities = 81/236 (34%), Positives = 126/236 (53%), Gaps = 14/236 (5%)

Query: 153 PPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRA 212
           P   T ANY  +        GM R   N+L V+   T++ +     A YA A + F GR 
Sbjct: 48  PTHATLANYHELF----ERAGMGRYLLNSLGVSSAITLLSLAFNLMAGYAFAKLRFSGRE 103

Query: 213 LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAH--TGFGMPLAIYLLRNYMV 270
            L  +++G LV+P Q+A++PL  L   +G+   Y    +    T FG    I+L+R Y  
Sbjct: 104 RLFQVLLGGLVIPAQVAMLPLFLLLKYLGLVNSYAAVVVPAMATIFG----IFLVRQYAR 159

Query: 271 GLPRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFLIDATG 330
           G+P D++E A++DGA + +IF +IVLPL  P + + AIF FL  WND +     LI  TG
Sbjct: 160 GIPDDLMEAARIDGAGELRIFVQIVLPLLKPIMVTLAIFTFLTAWNDFMWP---LIALTG 216

Query: 331 QT-TVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSVK 385
           Q    +   +  L      + E++   + V++   L++F ++QR+ ++GLL GSVK
Sbjct: 217 QEHYTLPIALASLSREHVQDSELMMAGSVVTVLPVLVLFLALQRYYLQGLLLGSVK 272


Lambda     K      H
   0.323    0.138    0.419 

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: 254
Number of extensions: 12
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: 385
Length of database: 273
Length adjustment: 28
Effective length of query: 357
Effective length of database: 245
Effective search space:    87465
Effective search space used:    87465
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 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