GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Shewanella amazonensis SB2B

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 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Query= TCDB::Q8DT25
         (377 letters)



>FitnessBrowser__SB2B:6936480
          Length = 341

 Score =  177 bits (448), Expect = 5e-49
 Identities = 113/340 (33%), Positives = 182/340 (53%), Gaps = 35/340 (10%)

Query: 1   MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60
           M+TL +  ++  Y   +   +   NL +   E    +GPSGCGK+T LR IAGL+DI+ G
Sbjct: 1   MSTLSIQGLHSDYRGEQ--VLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAG 58

Query: 61  NLYIDDKLMND----ASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRV 116
           ++ I+ K ++      +P+ R I M+FQ+YAL+PH++V +N+ FG+  R+  K   + R+
Sbjct: 59  SIAINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGV--RQLDKQSRSVRL 116

Query: 117 HEAAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRA 176
            E   ++ L    +R P +LSGGQ+QRV++ RA+  +  + L+DEP SN+DA++R A+  
Sbjct: 117 EEMLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALML 176

Query: 177 EIAKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNE 236
           EI  I +    + ++VTH + EA   AD + +  A          GRI Q G P+ LY  
Sbjct: 177 EIRAILKARNVSAVFVTHSKDEAFAFADTLALFEA----------GRIVQHGIPETLYQS 226

Query: 237 PANKFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIR 296
           P   +VA F+G  A N+ +V +E  +L++  G +  LPQ  +   E   +L       +R
Sbjct: 227 PNTPYVADFLG--ASNYLDVRLEAGQLISTLG-AFPLPQDFKAASETGRWL-------LR 276

Query: 297 PEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFG 336
           PE +  +         A    +IL    LG+     V+ G
Sbjct: 277 PEQLLIE-------ARADGAGEILERRFLGNGCHYLVRLG 309


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: 265
Number of extensions: 12
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: 341
Length adjustment: 29
Effective length of query: 348
Effective length of database: 312
Effective search space:   108576
Effective search space used:   108576
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: 49 (23.5 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