GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Herbaspirillum seropedicae SmR1

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 HSERO_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__HerbieS:HSERO_RS01355
          Length = 381

 Score =  301 bits (772), Expect = 2e-86
 Identities = 177/374 (47%), Positives = 241/374 (64%), Gaps = 17/374 (4%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M ++ L    K Y +A    + N +LDI + EF VF+GPSGCGKST LR IAGLED+T G
Sbjct: 1   MASITLRAAQKAYGDAPPV-IRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSG 59

Query: 61  NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120
           +L+I  K +ND     R +AMVFQ+YAL+PHM+VYENM+FGL L K  K +I ++V EAA
Sbjct: 60  DLFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAA 119

Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180
            IL L E L+RKP +LSGGQRQRVA+GRAIVR   VFL DEPLSNLDA LR   R EIA+
Sbjct: 120 RILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIAR 179

Query: 181 IHRRI-GATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPAN 239
           +HR+   A+ +YVTHDQ EAMTLADRIV++ A  +  + GSI    Q+GTP ELY+ P N
Sbjct: 180 LHRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIA---QVGTPMELYHHPRN 236

Query: 240 KFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKIL-EEKGYL--GKKVTLGIR 296
           +FVAGFIGSP MNF    V     V ++G+ + L   +E +L   +G L  G+ VT+G+R
Sbjct: 237 RFVAGFIGSPRMNFLPAQVAG---VQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVR 293

Query: 297 PEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSH-SPGEK 355
           PE +        +     +  ++++ E LG ++ +++   + +      A D+  + GE+
Sbjct: 294 PEHMEIG-----SQGQYGIHREVVLVERLGEQTYVHLDEPAGQPLVAKAAGDARITRGER 348

Query: 356 VQLTFNIAKGHFFD 369
           V++    A  + FD
Sbjct: 349 VRVAIAPACAYLFD 362


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: 353
Number of extensions: 20
Number of successful extensions: 4
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: 377
Length of database: 381
Length adjustment: 30
Effective length of query: 347
Effective length of database: 351
Effective search space:   121797
Effective search space used:   121797
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: 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