GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Desulfovibrio vulgaris Miyazaki F

Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate 8500594 DvMF_1342 ABC transporter related (RefSeq)

Query= TCDB::P48243
         (242 letters)



>FitnessBrowser__Miya:8500594
          Length = 243

 Score =  286 bits (733), Expect = 2e-82
 Identities = 151/243 (62%), Positives = 181/243 (74%), Gaps = 3/243 (1%)

Query: 1   MIKMTGVQKYF---GDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGT 57
           MI  T V K+F      HAL  + L +  G+VVV++GPSGSGKST  R +NRLE  +EG 
Sbjct: 1   MINATNVHKFFYTPDKLHALRGVSLSVAPGEVVVIIGPSGSGKSTFLRCLNRLEYADEGA 60

Query: 58  IEIDGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLA 117
           I I+G+ + +    +  +RA+VGMVFQSFNLFPHLT+ +N+TLA   VRK  K+EAEK  
Sbjct: 61  IRIEGRDILDPDCEINEVRAEVGMVFQSFNLFPHLTVLENLTLAQTTVRKRGKAEAEKKG 120

Query: 118 MSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLD 177
           M LL +VGIA + + YP QLSGGQQQRVAIARALAM+PK MLFDEPTSALDPEMV EVLD
Sbjct: 121 MELLRKVGIAEKHNVYPDQLSGGQQQRVAIARALAMDPKAMLFDEPTSALDPEMVGEVLD 180

Query: 178 VMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFLG 237
           VM +LA+EGMTMV VTHEMGFAR+ ADRV+FM  G I+E   PD FFT P+ DR K FL 
Sbjct: 181 VMKNLAREGMTMVVVTHEMGFAREVADRVVFMDQGSILEVGSPDKFFTAPEHDRTKLFLS 240

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


Lambda     K      H
   0.319    0.135    0.379 

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: 196
Number of extensions: 5
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: 242
Length of database: 243
Length adjustment: 23
Effective length of query: 219
Effective length of database: 220
Effective search space:    48180
Effective search space used:    48180
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