GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK in Methanosarcina acetivorans C2A

Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein

Query= reanno::Smeli:SMc03065
         (362 letters)



>NCBI__GCF_000007345.1:WP_011020381.1
          Length = 353

 Score =  180 bits (457), Expect = 5e-50
 Identities = 103/289 (35%), Positives = 168/289 (58%), Gaps = 10/289 (3%)

Query: 1   MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60
           M+ L ++DI    G+ + + GIDL  ++G++V  +GPSG GKS LL  I G      G +
Sbjct: 1   MSFLEVRDIYLDVGSFE-LKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQGSV 59

Query: 61  FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120
           F++G  +    P KR I++V+Q   L+PHM +++N+A+ +R   + K++I+  V   A +
Sbjct: 60  FLEGRDITFFSPDKRQISIVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIAGV 119

Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180
           L +   L R P  LSGG++QR ++ R++   PK+ L DEP S LDA  R   R E+ K +
Sbjct: 120 LGIRELLHRKPDTLSGGEKQRASLARSLVARPKLLLLDEPFSALDARTREKLR-EMLKKA 178

Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240
                TT+++VTHD  +   LA+R+VV+  G + QVG P  ++ RP+  FVA F+G+   
Sbjct: 179 IADYSTTVLHVTHDFEDVWALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGT--- 235

Query: 241 NVIPATITA-TGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDL 288
           NV+  T+ A  G+ T +   G +  + D     +E G+  +  +RPE++
Sbjct: 236 NVLKGTVKALEGKLTVIDAEGMEIYSAD----PAEPGENVTVSIRPEEI 280


Lambda     K      H
   0.320    0.137    0.387 

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: 246
Number of extensions: 11
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: 362
Length of database: 353
Length adjustment: 29
Effective length of query: 333
Effective length of database: 324
Effective search space:   107892
Effective search space used:   107892
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.

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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