GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Desulfovibrio vulgaris Miyazaki F

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate 8502445 DvMF_3151 ABC transporter related (RefSeq)

Query= TCDB::P0AAG3
         (241 letters)



>FitnessBrowser__Miya:8502445
          Length = 242

 Score =  295 bits (754), Expect = 7e-85
 Identities = 143/240 (59%), Positives = 185/240 (77%)

Query: 1   MITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITV 60
           MI   +V KWYG F VL   + +V+KGEV+V+CGPSGSGKS+ I+ +N LEP+Q+G+I +
Sbjct: 3   MIEFHDVHKWYGEFHVLKGITQKVEKGEVLVICGPSGSGKSSFIRCLNRLEPIQKGQILL 62

Query: 61  DGIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALKL 120
           +G  ++DK  D+ +LR+ VG+VFQ F L+PHLS++ N+TLA  KV K  KA A   A++L
Sbjct: 63  EGKSIHDKGVDVNELRTEVGIVFQQFNLYPHLSVLHNVTLAPTKVRKMPKAKAESIAMEL 122

Query: 121 LERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVMV 180
           LERVG+   A K+P +LSGGQQQRVAIARAL M P  MLFDEPTSALDPEMINEVL+ M 
Sbjct: 123 LERVGIHDQARKYPVELSGGQQQRVAIARALAMQPKVMLFDEPTSALDPEMINEVLNAMK 182

Query: 181 ELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDFLAKIL 240
           +LA  GMTM+ VTHEMGFAR+VA+RV+FMD GK++E++P D FF  PK +R + FL +IL
Sbjct: 183 DLARAGMTMLCVTHEMGFAREVADRVVFMDGGKVIEEAPPDVFFSSPKHERTQAFLREIL 242


Lambda     K      H
   0.320    0.135    0.383 

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: 204
Number of extensions: 8
Number of successful extensions: 1
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: 241
Length of database: 242
Length adjustment: 23
Effective length of query: 218
Effective length of database: 219
Effective search space:    47742
Effective search space used:    47742
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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