GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Marinobacter adhaerens HP15

Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate GFF2976 HP15_2920 amino acid ABC transporter, ATP-binding protein

Query= TCDB::P48243
         (242 letters)



>FitnessBrowser__Marino:GFF2976
          Length = 248

 Score =  309 bits (791), Expect = 4e-89
 Identities = 154/245 (62%), Positives = 192/245 (78%), Gaps = 3/245 (1%)

Query: 1   MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60
           ++KM G+ KYFG  H L DIDL + +G+VVV++G SGSGKSTL R +N LE  E GT+E+
Sbjct: 4   IVKMKGMNKYFGKLHVLKDIDLTVEQGEVVVIIGASGSGKSTLIRCVNGLEEYESGTLEV 63

Query: 61  DGKVL-PEEG--KGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLA 117
           DG+ L P+ G  K LA +R +VGMVFQ FNLFPHLT+K N+ LAP KV++  ++ A   A
Sbjct: 64  DGQQLAPKSGNPKALAEIRKEVGMVFQQFNLFPHLTVKRNIMLAPKKVKETPETVANATA 123

Query: 118 MSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLD 177
             LL RVGI NQADKYP+QLSGGQQQRVAIARALAM P++MLFDEPTSALDPEM+ EVLD
Sbjct: 124 ERLLNRVGIGNQADKYPSQLSGGQQQRVAIARALAMEPRLMLFDEPTSALDPEMIGEVLD 183

Query: 178 VMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFLG 237
           VM  LAKEGMTM+ VTHEMGFAR+ ADRV+++ +G IVE  +PD  F NP+++R + FL 
Sbjct: 184 VMRELAKEGMTMMVVTHEMGFAREVADRVIYIHEGAIVEQGKPDDVFDNPQNERTQAFLS 243

Query: 238 KILAH 242
           ++LAH
Sbjct: 244 RVLAH 248


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: 219
Number of extensions: 6
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: 242
Length of database: 248
Length adjustment: 24
Effective length of query: 218
Effective length of database: 224
Effective search space:    48832
Effective search space used:    48832
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