GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Methanospirillum stamsii Pt1

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized)
to candidate WP_109939664.1 DLD82_RS03180 ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_16275
         (244 letters)



>NCBI__GCF_003173335.1:WP_109939664.1
          Length = 230

 Score =  148 bits (373), Expect = 1e-40
 Identities = 97/225 (43%), Positives = 130/225 (57%), Gaps = 11/225 (4%)

Query: 1   MISIKNVNKWY----GDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKG 56
           +I+  +V K Y    GD   L     EV +GE I + GPSGSGKSTL+  +  L+    G
Sbjct: 7   VIAFHDVTKIYPLDSGDVTALNHVDVEVVRGEFIAIMGPSGSGKSTLLNMMGCLDIPTSG 66

Query: 57  DVVVDGTSIADPKTD-LPKLRSRV-GMVFQHFELFPHLTITENLTIAQIKVLGRSKEEAT 114
           DV + G +I     D L +LR  V G +FQ F L   L   EN+    I   G +    T
Sbjct: 67  DVFISGQNIKTMNDDQLTELRRDVLGFIFQQFNLILLLDALENVQYPLILKTGETG--CT 124

Query: 115 KKGLQLLERVGLSAHA-HKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVN 173
           K+ +++LE VGL+ H  H  PGQLSGGQQQRVAIARAL  DP ++L DEPT  LD +   
Sbjct: 125 KRCMEVLEAVGLAPHLWHHRPGQLSGGQQQRVAIARALVNDPEILLCDEPTGNLDTKTGM 184

Query: 174 EVLDVMVQLANE-GMTMMCVTHEMGFARKVADRVIFMDQGKIIED 217
            ++D++ QL  E G T++ VTH+   A + ADR I ++ GKI E+
Sbjct: 185 AIMDLLTQLCREQGKTIVMVTHDPRIA-EYADRTILIEDGKIKEE 228


Lambda     K      H
   0.321    0.136    0.394 

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: 149
Number of extensions: 7
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: 244
Length of database: 230
Length adjustment: 23
Effective length of query: 221
Effective length of database: 207
Effective search space:    45747
Effective search space used:    45747
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 24 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