GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Escherichia coli BW25113

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__Keio:14400
          Length = 348

 Score =  233 bits (594), Expect = 6e-66
 Identities = 131/319 (41%), Positives = 191/319 (59%), Gaps = 11/319 (3%)

Query: 4   LEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63
           +E+RN+ KR+G    +  I++ +  G+ + LLG SGCGK+T+L ++AGL +PS G I I 
Sbjct: 7   VELRNVTKRFGSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFID 66

Query: 64  ERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQI 123
              V     + RDI MVFQSYAL+P++S+  N+G+GL+M  VP+AE    V++   ++ +
Sbjct: 67  GEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMVDL 126

Query: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183
           E   DR   Q+SGGQ+QRVA+ RAL+  P+V LFDEPLSNLDA LR  MR +++ L +  
Sbjct: 127 EGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQKQF 186

Query: 184 RTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNILD 243
             T +YVTHDQ EA  ++  + VM  G I Q+ +P ++Y +PA+ ++A F+G    N+  
Sbjct: 187 DITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGD--ANLFP 244

Query: 244 AEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLA-AGSEAQRLTASVEV 302
           A  +   + I G    LP P  F G    G    VG+RPEA+ L+  G E+QR    +  
Sbjct: 245 ATFSDGYVDIYGYH--LPRPLHF-GTQGEG---MVGVRPEAITLSDRGEESQRCV--IRH 296

Query: 303 VELTGPELVTTATVGSQRI 321
           V   GP+   T     Q I
Sbjct: 297 VAYMGPQYEVTVEWHGQEI 315


Lambda     K      H
   0.320    0.136    0.385 

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: 280
Number of extensions: 11
Number of successful extensions: 2
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: 360
Length of database: 348
Length adjustment: 29
Effective length of query: 331
Effective length of database: 319
Effective search space:   105589
Effective search space used:   105589
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