GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Magnetospirillum magneticum AMB-1

Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein

Query= SwissProt::Q9YGA6
         (372 letters)



>NCBI__GCF_000009985.1:WP_011385004.1
          Length = 379

 Score =  236 bits (601), Expect = 1e-66
 Identities = 146/344 (42%), Positives = 198/344 (57%), Gaps = 23/344 (6%)

Query: 4   VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63
           +R   + K FG+ TAV  + L +  GEF  LLG SGCGKTT LRM+AG E P+ G+I I 
Sbjct: 23  IRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILID 82

Query: 64  DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123
            + V +      VPP +R + M+FQSYAL+PHM+V DNIAF LK   + +  I  +V   
Sbjct: 83  GQDVTE------VPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAA 136

Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183
            EL+ +     RKP +LSGGQRQRVAL R + ++P+V L+DEPL+ LD KLR   + EL 
Sbjct: 137 LELVQMGRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELV 196

Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243
            +Q ++G+T + VTHDQ EAMTM  RI VMN G ++QVGSP ++Y+ P   FVA FIG+ 
Sbjct: 197 NIQDRVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGAA 256

Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFE---VLGELGYV--GREVIFGIRPEDLYDAM 298
            M          G V  GE  L +   + E    + E G V  G  V   +RPE +   M
Sbjct: 257 NM--------FQGSVRGGEGALAIACPELEHDLSVTEAGAVAAGTPVTVMVRPEKV---M 305

Query: 299 FAQVR-VPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRS 341
            A+ +   G N    VV  +  LG   I H+R+     + + R+
Sbjct: 306 IARDKPASGLNWAEGVVSDIAYLGDVSIYHVRLASGRKIQALRT 349


Lambda     K      H
   0.323    0.142    0.406 

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: 314
Number of extensions: 10
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: 372
Length of database: 379
Length adjustment: 30
Effective length of query: 342
Effective length of database: 349
Effective search space:   119358
Effective search space used:   119358
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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