GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltK in Desulfovibrio vulgaris Miyazaki F

Align PP1069, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate 8500098 DvMF_0861 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q88NY4
         (223 letters)



>FitnessBrowser__Miya:8500098
          Length = 263

 Score =  114 bits (285), Expect = 2e-30
 Identities = 70/211 (33%), Positives = 113/211 (53%), Gaps = 8/211 (3%)

Query: 12  LPALWEGMVMTLKLMVMGVIGGIVLGTILALMRLSSSKLLSNLAGAYVNYFRSIPLLLVI 71
           L  L +G+ +T K+ V+ ++  I +G I  L RLS ++L++ +A  YV   R IPLL+ +
Sbjct: 56  LQFLPDGIAVTFKVTVLSILCSIPIGLITGLGRLSRNRLINLVASTYVEVVRGIPLLVQL 115

Query: 72  TWFYLAVPFVLRWITGEDTPVGAFTSCVVAFMMFEAAYFCEIVRAGVQSISKGQMGAAQA 131
            + Y A+        G    V    + ++A  +   AY  E+ RAG+ SISKGQ  AA++
Sbjct: 116 FYIYYAL--------GRFLKVPDLLAAIIALSVCYGAYMGEVFRAGIDSISKGQTEAARS 167

Query: 132 LGMNYAQTMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLVDFLNSARSNGDIIGR 191
           LG N A+TM ++ILPQA+R + P +  + I + +DTSLV  + + D L   R        
Sbjct: 168 LGFNRAETMFMVILPQAWRTILPPVGNEFIAMLKDTSLVSIIAVADILRRGREFASESFL 227

Query: 192 SHEFLIFAGVVYFLISFSASWLVKRLQKRIS 222
             E      ++Y LI+   S  V  ++ R++
Sbjct: 228 YFETYTMVALIYLLITLFLSKGVSIMESRLN 258


Lambda     K      H
   0.330    0.141    0.417 

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: 123
Number of extensions: 5
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: 223
Length of database: 263
Length adjustment: 23
Effective length of query: 200
Effective length of database: 240
Effective search space:    48000
Effective search space used:    48000
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 (21.9 bits)
S2: 46 (22.3 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