GapMind for catabolism of small carbon sources

 

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

Align Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized)
to candidate 5208462 Shew_0974 spermidine/putrescine ABC transporter ATPase subunit (RefSeq)

Query= TCDB::Q72L52
         (376 letters)



>FitnessBrowser__PV4:5208462
          Length = 378

 Score =  243 bits (620), Expect = 6e-69
 Identities = 136/329 (41%), Positives = 203/329 (61%), Gaps = 8/329 (2%)

Query: 4   VRLEHVWKRFGKVVAVKDFNLETEDGEFVVFVGPSGCGKTTTLRMIAGLEEISEGNIYIG 63
           +++E V K F  V AV D +L    GE    +G SG GK+T LRM+AG E+ +EG IY+ 
Sbjct: 21  LKIERVSKLFDDVRAVDDVSLNINRGEIFALLGGSGSGKSTLLRMLAGFEKPTEGRIYLD 80

Query: 64  DRLVNDVPPKDRDIAMVFQNYALYPHMNVYENMAFGLRLRRYPKDEIDRRVKEAARILKI 123
            + + D+PP +R I M+FQ+YAL+PHM V +N+AFGL+  + PK EI++RVKE  +++ +
Sbjct: 81  GQDITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKMPKAEIEQRVKEMLKLVHM 140

Query: 124 EHLLNRKPRELSGGQRQRVAMGRAIVREPKVFLMDEPLSNLDAKLRVEMRAEIAKLQRRL 183
           E    RKP +LSGGQRQRVA+ R++ + PK+ L+DEP+  LD KLR +M+ E+  +   +
Sbjct: 141 EPYAKRKPNQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVDILEAV 200

Query: 184 GVTTIYVTHDQVEAMTLGHRIVVMKDGEIQQVDTPLNLYDFPANRFVAGFIGSPSMNFVR 243
           GVT + VTHDQ EAMT+  RI +M DG I Q  +P+++Y+ PANR VA FIGS ++    
Sbjct: 201 GVTCVMVTHDQEEAMTMAERIAIMNDGWIAQTGSPMDIYESPANRMVAEFIGSVNL---F 257

Query: 244 AGVEVQGEKVYLVAPGFRIRANAVLGSALKPYAG-KEVWLGVRPEHLGLKGYTTIPEE-E 301
            G  V+ E  ++V     I     +G  +       +VW+ +RPE   +      PE+  
Sbjct: 258 EGDIVEDEVDHVVINVANIPQPFYVGYGVSTSVDTTQVWVAIRPEKTHIS--REQPEDAR 315

Query: 302 NVLRGEVEVVEPLGAETEIHVAV-NGTLL 329
           N   G+VE +  LG  +  ++ + NG L+
Sbjct: 316 NWCAGKVEDIAYLGGISVYYIRLCNGQLI 344


Lambda     K      H
   0.320    0.139    0.400 

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: 345
Number of extensions: 16
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: 376
Length of database: 378
Length adjustment: 30
Effective length of query: 346
Effective length of database: 348
Effective search space:   120408
Effective search space used:   120408
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