GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Methanosarcina acetivorans C2A

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein

Query= reanno::Smeli:SM_b21106
         (365 letters)



>NCBI__GCF_000007345.1:WP_011020381.1
          Length = 353

 Score =  186 bits (473), Expect = 6e-52
 Identities = 102/304 (33%), Positives = 169/304 (55%), Gaps = 10/304 (3%)

Query: 21  GIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIGGRKVNDLPPRARNISMV 80
           GIDL  +  +++AL+GPSG GKS  L  I G      G++ + GR +    P  R IS+V
Sbjct: 20  GIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQGSVFLEGRDITFFSPDKRQISIV 79

Query: 81  FQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDLAHLLERRPSQLSGGQRQ 140
           +Q   L+PHM + EN+ ++L+   +  ++I+  V + A +L +  LL R+P  LSGG++Q
Sbjct: 80  YQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIAGVLGIRELLHRKPDTLSGGEKQ 139

Query: 141 RVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARMQATMIYVTHDQVEAMTL 200
           R ++ R++V +P + L DEP S LDA+ R ++R  +KK  A    T+++VTHD  +   L
Sbjct: 140 RASLARSLVARPKLLLLDEPFSALDARTREKLREMLKKAIADYSTTVLHVTHDFEDVWAL 199

Query: 201 SDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEEAVLTDGKLAFASGATLP 260
           ++R+V++R G + QVG PE VFRRP+  FVA F+G+  +      L +GKL       + 
Sbjct: 200 ANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGTNVLKGTVKAL-EGKLTVIDAEGME 258

Query: 261 LPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHA-------GDADAVHEIELPVTITEPLG 313
           +          G+ VT  +RP+++  +G  + +       G    + + E  V +   +G
Sbjct: 259 I--YSADPAEPGENVTVSIRPEEIILAGGTVESSARNTLKGRVSGIFKKEHLVVVEVKMG 316

Query: 314 NETL 317
           N  +
Sbjct: 317 NSEI 320


Lambda     K      H
   0.320    0.137    0.397 

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: 318
Number of extensions: 14
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: 365
Length of database: 353
Length adjustment: 29
Effective length of query: 336
Effective length of database: 324
Effective search space:   108864
Effective search space used:   108864
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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