GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TRET1 in Escherichia coli BW25113

Align Facilitated trehalose transporter Tret1; AmTRET1 (characterized)
to candidate 17022 b2943 D-galactose transporter (NCBI)

Query= SwissProt::A9ZSY2
         (502 letters)



>FitnessBrowser__Keio:17022
          Length = 464

 Score =  223 bits (567), Expect = 1e-62
 Identities = 139/456 (30%), Positives = 240/456 (52%), Gaps = 20/456 (4%)

Query: 33  KRSPMRYTMQLLAALAVSMASLMIGYSSSYTSPALVSMRDNTTATFEVTMDMAMWIGSIM 92
           K+      M        ++A L+ G      + AL  + D     F++T     W+ S M
Sbjct: 6   KQGRSNKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADE----FQITSHTQEWVVSSM 61

Query: 93  PLSALIGGIIGGPCIEYIGRRNTILSTALPFLAGWLFIALATNVAMILVGRSICGFCVGV 152
              A +G +  G     +GR+ +++  A+ F+AG LF A A NV ++++ R + G  VGV
Sbjct: 62  MFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGV 121

Query: 153 ASLSLPVYLGESIQPEVRGSLGLLPTVFGNSGILMCF---TAGMYL-AWRNLALLGACI- 207
           AS + P+YL E    ++RGS+  +  +    GIL  +   TA  Y  AWR   +LG  I 
Sbjct: 122 ASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYTGAWR--WMLGVIII 179

Query: 208 -PIIFLILMFLIPETPRWYISKGKIKEARKSLQWLRGKTADISEELDSIQKMHIESERIA 266
             I+ LI +F +P++PRW+ +K +  +A + L  LR  +A+   ELD I+    ES ++ 
Sbjct: 180 PAILLLIGVFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIR----ESLQVK 235

Query: 267 TEGALIELFRKNHIKPVFISLGLMFFQQFSGINAVIFYTVQIFKDSG--STVDENLSTII 324
             G  +     N  + VF+ + L   QQF+G+N +++Y  +IF+ +G  +T ++   T+I
Sbjct: 236 QSGWALFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVI 295

Query: 325 VGLVNFISTFVAAMIIDRLGRKMLLYISSILMCITLFTFGTFFYVKELMDVTAFGWIPLM 384
           VGL N ++TF+A  ++DR GRK  L +  ++M   +   GT  ++   +   +  +  + 
Sbjct: 296 VGLTNVLATFIAIGLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIG--IHSPSAQYFAIA 353

Query: 385 SLIVYVIGFSFGFGPIPWLMMGEILPVKIRGTAASVATAFNWSCTFVVTKTYEDLVLHIG 444
            L+++++GF+   GP+ W++  EI P+K R    + +TA NW    +V  T+  ++  +G
Sbjct: 354 MLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLG 413

Query: 445 PYGTFWLFGTLVAVAFIFVIICVPETRGRSLEEIER 480
              TFW++  L  +  +  +  VPET+  SLE IER
Sbjct: 414 NANTFWVYAALNVLFILLTLWLVPETKHVSLEHIER 449


Lambda     K      H
   0.327    0.141    0.425 

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: 629
Number of extensions: 36
Number of successful extensions: 6
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: 502
Length of database: 464
Length adjustment: 34
Effective length of query: 468
Effective length of database: 430
Effective search space:   201240
Effective search space used:   201240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 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