GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1749 in Escherichia coli BW25113

Align TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 15605 b1484 D-ala-D-ala transporter subunit (NCBI)

Query= TCDB::Q9X271
         (324 letters)



>FitnessBrowser__Keio:15605
          Length = 328

 Score =  266 bits (681), Expect = 4e-76
 Identities = 135/314 (42%), Positives = 197/314 (62%), Gaps = 1/314 (0%)

Query: 4   LLNVNNLKVEFHRVEGIVKAVDGISYKLNKGESLGIVGESGSGKSVSVLSLLRLINRNGR 63
           +L++  L + F    G V A++ +S ++N+GE +G+VGESGSGKSV+ + ++RL+     
Sbjct: 5   VLDIQQLHLSFPGFNGDVHALNNVSLQINRGEIVGLVGESGSGKSVTAMLIMRLLPTGSY 64

Query: 64  IVD-GEAIFLGKDLLKLNKEELRNIRGKDISIIFQNPMTSLNPIIRVGIQVMEPIIWHRL 122
            V  G+   LG+D+L   +++LR  RG  +++IFQ PMT+LNP  R+G+Q+M+ I  H+ 
Sbjct: 65  CVHRGQISLLGEDVLNAREKQLRQWRGARVAMIFQEPMTALNPTRRIGLQMMDVIRHHQP 124

Query: 123 MKNEEARERAIELLERVGIPESPKRFLNYPFQFSGGMRQRVMIAMALACHPKLLIADEPT 182
           +   EAR +AI+LLE + IP++ +    YPF+ SGGMRQRVMIA+A +C P+L+IADEPT
Sbjct: 125 ISRREARAKAIDLLEEMQIPDAVEVMSRYPFELSGGMRQRVMIALAFSCEPQLIIADEPT 184

Query: 183 TALDVTIQAQIMELLQELKEEYGMSVIFITHDLSVATNFCDRIITMYAGKIVEEAPVEEI 242
           TALDVT+Q Q++ LL+      G +V+FI+HD++V +  CD +  MYAG ++E     ++
Sbjct: 185 TALDVTVQLQVLRLLKHKARASGTAVLFISHDMAVVSQLCDSVYVMYAGSVIESGVTADV 244

Query: 243 LKTPLHPYTKGLLNSTLEIGSRGKKLVPIPGNPPNPTKHPSGCKFHPRCSFAMEICQREE 302
           +  P HPYT GLL    E G   + L  IPG  PN T  P GC F  RC  A   C+   
Sbjct: 245 IHHPRHPYTIGLLQCAPEHGVPRQLLPAIPGTVPNLTHLPDGCAFRDRCYAAGAQCENVP 304

Query: 303 PPLVNISENHRVAC 316
                   N R AC
Sbjct: 305 ALTACGDNNQRCAC 318


Lambda     K      H
   0.320    0.139    0.401 

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: 259
Number of extensions: 14
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: 324
Length of database: 328
Length adjustment: 28
Effective length of query: 296
Effective length of database: 300
Effective search space:    88800
Effective search space used:    88800
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: 48 (23.1 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