GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztD in Methanococcus aeolicus Nankai-3

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein

Query= TCDB::Q52666
         (263 letters)



>NCBI__GCF_000017185.1:WP_011974043.1
          Length = 238

 Score =  143 bits (360), Expect = 4e-39
 Identities = 89/204 (43%), Positives = 123/204 (60%), Gaps = 5/204 (2%)

Query: 37  VLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVDGIELTSDLKNIDKV 96
           VLR INL +  GE + I GPSG GKST++  +  L+    G + + G + T   +N   V
Sbjct: 36  VLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKGMVYIKGKKTTMFSENDRAV 95

Query: 97  --RSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEETAMYYLEKVKIPEQAQKY 154
             R   G +FQ FNL   LT LEN+ L P+ + +  K    + A   L+ + +  +   Y
Sbjct: 96  FRRKISGFIFQQFNLINTLTALENVEL-PLVLDEKNKNYRIKKAKKLLKIINLGHRENYY 154

Query: 155 PGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEVLDTMIQLAE-EGMTMLCV 213
           P QLSGGQQQRVAIAR+L   PKI+  DEPT  LD +  +EV+D + +L E EG+T++ V
Sbjct: 155 PNQLSGGQQQRVAIARALSNNPKIIFADEPTGNLDSKNSREVMDILKELNEKEGITVIMV 214

Query: 214 THEMGFAQAVANRVIFMADGQIVE 237
           THE  FA+  A+R+I M DG+IVE
Sbjct: 215 THEPEFAK-YASRIINMKDGEIVE 237


Lambda     K      H
   0.320    0.134    0.391 

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: 164
Number of extensions: 6
Number of successful extensions: 5
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: 263
Length of database: 238
Length adjustment: 24
Effective length of query: 239
Effective length of database: 214
Effective search space:    51146
Effective search space used:    51146
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 Apr 09 2024. 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