GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM0028 in Escherichia coli BW25113

Align TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized)
to candidate 1936449 b1246 oligopeptide transporter ATP-binding component (NCBI)

Query= TCDB::Q9WXN5
         (330 letters)



>FitnessBrowser__Keio:1936449
          Length = 337

 Score =  202 bits (515), Expect = 7e-57
 Identities = 119/329 (36%), Positives = 188/329 (57%), Gaps = 13/329 (3%)

Query: 3   EILLKAENVRAYYKLEKVSVKAVDGLSFEILEDEVIGVVGESGCGKTTLSNVIFMNMVKP 62
           + LL  +++R  +      V AV+ L+F +   E +G+VGESG GK+  +  +       
Sbjct: 17  DALLNVKDLRVTFSTPDGDVTAVNDLNFSLRAGETLGIVGESGSGKSQTAFALM-----G 71

Query: 63  LTLVDGKIFLRVNGEFVELSSMTRDEVKRKFWGKEITIIPQAAMNALMPTIRMEKYVRHL 122
           L   +G+I         E+ ++   E+  K   ++I++I Q  M +L P +R+ + +  +
Sbjct: 72  LLAANGRIGGSATFNGREILNLPEHELN-KLRAEQISMIFQDPMTSLNPYMRVGEQLMEV 130

Query: 123 AESH-GIDEEELLDKARRRFEEVGLDPLW--IKRYPFELSGGMRQRAVIAIATILNPSLL 179
              H  + + E  +++ R  + V +      +K YP E SGGMRQR +IA+A +  P LL
Sbjct: 131 LMLHKNMSKAEAFEESVRMLDAVKMPEARKRMKMYPHEFSGGMRQRVMIAMALLCRPKLL 190

Query: 180 IADEPTSALDVVNQKVLLKVLMQMKRQGIVKSIIFITHDIATVRQIADRMIIMYAGKIVE 239
           IADEPT+ALDV  Q  ++ +L ++KR+    +II ITHD+  V  I D++++MYAG+ +E
Sbjct: 191 IADEPTTALDVTVQAQIMTLLNELKRE-FNTAIIMITHDLVVVAGICDKVLVMYAGRTME 249

Query: 240 FAPVESLLEKPLHPYTQGLFNSVLTPEPEVKKRGITTIPGAPPNLINPPSGCRFHPRCPH 299
           +     +  +P+HPY+ GL N+V  P  + +   + TIPG PPNL+  P GC F PRCPH
Sbjct: 250 YGNARDVFYQPVHPYSIGLLNAV--PRLDAEGETMLTIPGNPPNLLRLPKGCPFQPRCPH 307

Query: 300 AMDVCKEKEPPLTEIEPGRRVACWLYMEE 328
           AM++C    PPL E  PGR  AC+  +EE
Sbjct: 308 AMEIC-SSAPPLEEFTPGRLRACFKPVEE 335


Lambda     K      H
   0.321    0.138    0.405 

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: 289
Number of extensions: 13
Number of successful extensions: 5
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: 330
Length of database: 337
Length adjustment: 28
Effective length of query: 302
Effective length of database: 309
Effective search space:    93318
Effective search space used:    93318
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