GapMind for catabolism of small carbon sources

 

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

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate WP_011974043.1 MAEO_RS06850 ABC transporter ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>NCBI__GCF_000017185.1:WP_011974043.1
          Length = 238

 Score =  160 bits (406), Expect = 2e-44
 Identities = 95/223 (42%), Positives = 134/223 (60%), Gaps = 9/223 (4%)

Query: 1   MIELKNVNKYYGTHH----VLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSG 56
           +IE KN+ K YG       VL+ INL +KEGE + I+GPSG GKST +  +  L+  + G
Sbjct: 17  LIEAKNIWKIYGGGEAKTVVLRGINLKIKEGEFVAIMGPSGCGKSTLLNILGLLDVPNKG 76

Query: 57  EVVVNN---LVLNHKNKIEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAE 113
            V +      + +  ++    RK    +FQ FNL   +T L+N+ L P+ L +K+K    
Sbjct: 77  MVYIKGKKTTMFSENDRAVFRRKISGFIFQQFNLINTLTALENVEL-PLVLDEKNKNYRI 135

Query: 114 ETAFKYLKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQE 173
           + A K LK++ L  + N YP  LSGGQQQRVAIAR+L      I  DEPT  LD +  +E
Sbjct: 136 KKAKKLLKIINLGHRENYYPNQLSGGQQQRVAIARALSNNPKIIFADEPTGNLDSKNSRE 195

Query: 174 VLDVMKEISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVE 216
           V+D++KE++ +   T+++VTHE  FAK  A RII M+DG IVE
Sbjct: 196 VMDILKELNEKEGITVIMVTHEPEFAK-YASRIINMKDGEIVE 237


Lambda     K      H
   0.317    0.133    0.372 

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: 172
Number of extensions: 8
Number of successful extensions: 4
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: 238
Length adjustment: 23
Effective length of query: 219
Effective length of database: 215
Effective search space:    47085
Effective search space used:    47085
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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