GapMind for catabolism of small carbon sources

 

Aligments 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 8500594 DvMF_1342 ABC transporter related (RefSeq)

Query= TCDB::P0AAG3
         (241 letters)



>lcl|FitnessBrowser__Miya:8500594 DvMF_1342 ABC transporter related
           (RefSeq)
          Length = 243

 Score =  266 bits (681), Expect = 2e-76
 Identities = 140/243 (57%), Positives = 175/243 (72%), Gaps = 3/243 (1%)

Query: 1   MITLKNVSKWY---GHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGE 57
           MI   NV K++        L   S  V  GEVVV+ GPSGSGKST ++ +N LE   +G 
Sbjct: 1   MINATNVHKFFYTPDKLHALRGVSLSVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADEGA 60

Query: 58  ITVDGIVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKA 117
           I ++G  + D   ++ ++R+ VGMVFQ F LFPHL+++ENLTLAQ  V KR KA A +K 
Sbjct: 61  IRIEGRDILDPDCEINEVRAEVGMVFQSFNLFPHLTVLENLTLAQTTVRKRGKAEAEKKG 120

Query: 118 LKLLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLD 177
           ++LL +VG++   N +P QLSGGQQQRVAIARAL MDP AMLFDEPTSALDPEM+ EVLD
Sbjct: 121 MELLRKVGIAEKHNVYPDQLSGGQQQRVAIARALAMDPKAMLFDEPTSALDPEMVGEVLD 180

Query: 178 VMVELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDFLA 237
           VM  LA EGMTM+VVTHEMGFAR+VA+RV+FMD+G I+E    D FF  P+ DR K FL+
Sbjct: 181 VMKNLAREGMTMVVVTHEMGFAREVADRVVFMDQGSILEVGSPDKFFTAPEHDRTKLFLS 240

Query: 238 KIL 240
           +IL
Sbjct: 241 QIL 243


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: 174
Number of extensions: 6
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: 243
Length adjustment: 23
Effective length of query: 218
Effective length of database: 220
Effective search space:    47960
Effective search space used:    47960
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.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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