GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Lacinutrix algicola AKS293

Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate WP_055437631.1 ASC41_RS15790 ABC transporter ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>NCBI__GCF_001418085.1:WP_055437631.1
          Length = 220

 Score =  131 bits (329), Expect = 2e-35
 Identities = 76/216 (35%), Positives = 121/216 (56%), Gaps = 11/216 (5%)

Query: 9   ENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEIT---DGKIYI 65
           EN+ K Y++  V +K  N+ ++  E V ++G SG GKTT L+++  L+ I+   D  + I
Sbjct: 5   ENIHKYYDDLHV-LKGVNVHIKKGEVVSIVGSSGAGKTTLLQILGTLDTISKTDDSSLII 63

Query: 66  DGKVVNDVEPK------DRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVRE 119
           +GK ++ +  K      +  I  +FQ + L P  T  EN+     ++K PK E  +R +E
Sbjct: 64  NGKNISSLSEKQLAKFRNEHIGFIFQFHQLLPEFTAIENVCIPAFIKKTPKAEATKRAKE 123

Query: 120 AAKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSEL 179
               LG+ +  + KP +LSGG++QRVAV RA++ NP +   DEP  NLD++    + S  
Sbjct: 124 LLDFLGLSHRYNHKPNELSGGEQQRVAVARALINNPSLIFADEPSGNLDSESAENLHSLF 183

Query: 180 KKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEI 215
            KL      T + VTH++ E   +AD+ +VM DG I
Sbjct: 184 FKLRDEFGQTFVIVTHNE-ELADLADRKLVMVDGVI 218


Lambda     K      H
   0.319    0.138    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: 154
Number of extensions: 8
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: 369
Length of database: 220
Length adjustment: 26
Effective length of query: 343
Effective length of database: 194
Effective search space:    66542
Effective search space used:    66542
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: 47 (22.7 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