GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Shewanella loihica PV-4

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)

Query= reanno::BFirm:BPHYT_RS16095
         (369 letters)



>FitnessBrowser__PV4:5208462
          Length = 378

 Score =  228 bits (581), Expect = 2e-64
 Identities = 126/309 (40%), Positives = 183/309 (59%), Gaps = 4/309 (1%)

Query: 6   LRNIRKAYDENEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDLTIDGM 65
           +  + K +D+   + D++L+I  GE    +G SG GKSTL+RM+AG E  + G + +DG 
Sbjct: 23  IERVSKLFDDVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYLDGQ 82

Query: 66  RVNDVAPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKILHIDH 125
            + D+ P +R I M+FQSYAL+PHMT+  N+AFGLK     K EI+  V+   K++H++ 
Sbjct: 83  DITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEMLKLVHMEP 142

Query: 126 LLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLHDELKT 185
              RKP QLSGGQRQRVA+ R++ ++PK+ L DEP+  LD  LR +M+LE   + + +  
Sbjct: 143 YAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVDILEAVGV 202

Query: 186 TMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMNFMEGV 245
           T + VTHDQ EAMT+A++I +++ G + Q GSP  +Y +PANR VA FIGS  +N  EG 
Sbjct: 203 TCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIGS--VNLFEGD 260

Query: 246 VQSVTHDGVTVRY-ETGETQRVAVEPAAVKQGDKVTVGIRPEHLHVGMAEDGISARTMAV 304
           +     D V +      +   V    +      +V V IRPE  H+   E    AR    
Sbjct: 261 IVEDEVDHVVINVANIPQPFYVGYGVSTSVDTTQVWVAIRPEKTHIS-REQPEDARNWCA 319

Query: 305 ESLGDAAYL 313
             + D AYL
Sbjct: 320 GKVEDIAYL 328


Lambda     K      H
   0.320    0.135    0.384 

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: 329
Number of extensions: 9
Number of successful extensions: 1
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: 378
Length adjustment: 30
Effective length of query: 339
Effective length of database: 348
Effective search space:   117972
Effective search space used:   117972
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