GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Escherichia coli BW25113

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 17601 b3540 dipeptide transporter (NCBI)

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__Keio:17601
          Length = 334

 Score =  311 bits (796), Expect = 2e-89
 Identities = 149/319 (46%), Positives = 230/319 (72%), Gaps = 8/319 (2%)

Query: 11  KPLLQTVDLKKYFPQGK------RILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64
           +PLLQ +DLKK++P  K      R++KA+DG+S  ++ G+TL +VGESGCGKSTLGR + 
Sbjct: 10  QPLLQAIDLKKHYPVKKGMFAPERLVKALDGVSFNLERGKTLAVVGESGCGKSTLGRLLT 69

Query: 65  KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124
            +  P GG+++++G+D+   + +  K  R+K+QI+FQ+P GSLNP+  VG+I+E+PL+I+
Sbjct: 70  MIEMPTGGELYYQGQDLLKHDPQAQKLRRQKIQIVFQNPYGSLNPRKKVGQILEEPLLIN 129

Query: 125 KIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184
              +K++RR++   ++  VG+  E  + +PH FSGGQ+QRI IAR L L+P  ++ DEPV
Sbjct: 130 TSLSKEQRREKALSMMAKVGLKTEHYDRYPHMFSGGQRQRIAIARGLMLDPDVVIADEPV 189

Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244
           SALDVS++AQ+++L+ ++QQ++G+SY+FI+H+L+VVEHI+ +V VMYLG+ VE G  D+I
Sbjct: 190 SALDVSVRAQVLNLMMDLQQELGLSYVFISHDLSVVEHIADEVMVMYLGRCVEKGTKDQI 249

Query: 245 FLNPIHPYTRALLKSVPKIPWDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFE 304
           F NP HPYT+ALL + P++  D +++R   L GELPSP++ P GC F  RC  +   C +
Sbjct: 250 FNNPRHPYTQALLSATPRLNPDDRRERI-KLSGELPSPLNPPPGCAFNARCRRRFGPCTQ 308

Query: 305 KEPELTEVEKNHFVSCHLV 323
            +P+L +      V+C  V
Sbjct: 309 LQPQLKDY-GGQLVACFAV 326


Lambda     K      H
   0.321    0.142    0.417 

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: 384
Number of extensions: 19
Number of successful extensions: 3
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: 328
Length of database: 334
Length adjustment: 28
Effective length of query: 300
Effective length of database: 306
Effective search space:    91800
Effective search space used:    91800
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