GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21106 in Shewanella amazonensis SB2B

Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Query= reanno::Smeli:SM_b21106
         (365 letters)



>FitnessBrowser__SB2B:6936480
          Length = 341

 Score =  192 bits (488), Expect = 1e-53
 Identities = 108/299 (36%), Positives = 178/299 (59%), Gaps = 12/299 (4%)

Query: 1   MAPVTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAI 60
           M+ ++++ L   Y   +V+ G++L +   E  AL+GPSGCGK+T LR IAGL+++S G+I
Sbjct: 1   MSTLSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSI 60

Query: 61  EIGGRKVND----LPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAE 116
            I G+ V+     + P  R+I M+FQ YAL+PH+TVA+N+ F ++   + +  +  R+ E
Sbjct: 61  AINGKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILFGVRQLDKQSRSV--RLEE 118

Query: 117 AAAILDLAHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEI 176
             +++ L  L +R P +LSGGQ+QRV++ RA+  +PD+ L DEP SN+DA++R  +  EI
Sbjct: 119 MLSLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEI 178

Query: 177 KKLHARMQATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGS 236
           + +      + ++VTH + EA   +D + +   G I Q G PE +++ P T +VA F+G+
Sbjct: 179 RAILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLGA 238

Query: 237 PPMNMEEAVLTDGKLAFASGATLPLPPRFRSLVREGQKVTFGLRPDDVYPSGHGLHAGD 295
              N  +  L  G+L    GA  PLP  F++    G+ +   LRP+ +        AG+
Sbjct: 239 --SNYLDVRLEAGQLISTLGA-FPLPQDFKAASETGRWL---LRPEQLLIEARADGAGE 291


Lambda     K      H
   0.320    0.137    0.397 

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: 10
Number of successful extensions: 3
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: 365
Length of database: 341
Length adjustment: 29
Effective length of query: 336
Effective length of database: 312
Effective search space:   104832
Effective search space used:   104832
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: 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