GapMind for catabolism of small carbon sources

 

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

Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>NCBI__GCF_000009985.1:WP_011382978.1
          Length = 553

 Score =  140 bits (352), Expect = 1e-37
 Identities = 83/233 (35%), Positives = 134/233 (57%), Gaps = 13/233 (5%)

Query: 4   LKLDNIYKRYPNAKH--YSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGN 61
           ++   + K YP  K     V+ F+L +H  EFI  +G SGCGKST L M AGL D++EG 
Sbjct: 293 VEFSRVKKIYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGG 352

Query: 62  LYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA- 120
           + +D + +++A P   D A+VFQ  +L+P ++  +N+A G+  R Y      +R+   + 
Sbjct: 353 VILDGREVSEAGP---DRAVVFQAPSLFPWLTALQNVALGVD-RVYPHASPAERLDIVSY 408

Query: 121 --EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEI 178
             E +GL + +++K +D+S G RQRV + RA     K+ L+DEP   LD+  R  ++  +
Sbjct: 409 YLERVGLGDSMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVL 468

Query: 179 AKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQ 231
            ++  R   T I VTHD  EA+ LAD++V+M+  PN      IG++  +  P+
Sbjct: 469 MEVWTRTRVTAICVTHDVDEAILLADKVVMMTNGPN----ARIGKVLNVDIPR 517



 Score =  120 bits (302), Expect = 7e-32
 Identities = 78/215 (36%), Positives = 122/215 (56%), Gaps = 7/215 (3%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M  L+L  + K Y  +    + + +L+I D EFI  +G SG GK+T + ++AGL     G
Sbjct: 1   MPILELKGVAKSYGASS--VLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAG 58

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLK--LRKYKKDDINKRVHE 118
            + +  K + D    DR +  VFQ+Y+L P ++V  N+A  +   +    K +   RV +
Sbjct: 59  EVLLRGKPV-DGPGADRGV--VFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAK 115

Query: 119 AAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEI 178
              ++GL+   ER+P++LSGG RQRVA+ RA+     + L+DEPLS LDA  R  ++ EI
Sbjct: 116 YIGMVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEI 175

Query: 179 AKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATP 213
             I  +   T I +T+D  EA+ LADRI+ ++  P
Sbjct: 176 EAIWEQEKKTVILITNDVDEALLLADRIIPLNPGP 210


Lambda     K      H
   0.318    0.135    0.379 

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: 466
Number of extensions: 24
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 377
Length of database: 553
Length adjustment: 33
Effective length of query: 344
Effective length of database: 520
Effective search space:   178880
Effective search space used:   178880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 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