GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK1 in Magnetospirillum magneticum AMB-1

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_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein

Query= TCDB::Q9X103
         (369 letters)



>NCBI__GCF_000009985.1:WP_011385004.1
          Length = 379

 Score =  219 bits (557), Expect = 1e-61
 Identities = 135/331 (40%), Positives = 187/331 (56%), Gaps = 11/331 (3%)

Query: 21  AVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDGKVVNDVEPKDRDI 80
           AV++ +L +   EF  LLG SGCGKTT LRM+AG E  T G+I IDG+ V +V P +R +
Sbjct: 37  AVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILIDGQDVTEVPPYERPV 96

Query: 81  AMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIENLLDRKPRQLSGG 140
            M+FQ+YAL+PHM+V +N+AFGLK     K  I  +V  A +++ +     RKP QLSGG
Sbjct: 97  NMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELVQMGRFSGRKPHQLSGG 156

Query: 141 QRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQATIIYVTHDQVEA 200
           QRQRVA+ R + + PKV L DEPL+ LD KLR   + EL  +  R+  T + VTHDQ EA
Sbjct: 157 QRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQDRVGITFVMVTHDQGEA 216

Query: 201 MTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNARVVRGEGGLWIQA 260
           MTM+ +I VM  G I+Q+G+P +IY  P   FVA FIG+   N     V  GEG L I  
Sbjct: 217 MTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGA--ANMFQGSVRGGEGALAIAC 274

Query: 261 SGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIY---DKLFALAPSPENTITGVVDVVEPL 317
              +++      +  A      +   +RPE +    DK      S  N   GVV  +  L
Sbjct: 275 P--ELEHDLSVTEAGAVAAGTPVTVMVRPEKVMIARDK----PASGLNWAEGVVSDIAYL 328

Query: 318 GSETILHVKVGDDLIVASVNPRTQAKEEQKI 348
           G  +I HV++     + ++       EE ++
Sbjct: 329 GDVSIYHVRLASGRKIQALRTNLHHGEESRL 359


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: 291
Number of extensions: 14
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: 379
Length adjustment: 30
Effective length of query: 339
Effective length of database: 349
Effective search space:   118311
Effective search space used:   118311
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: 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