GapMind for catabolism of small carbon sources

 

Aligments for a candidate for TRET1 in Klebsiella michiganensis M5al

Align Facilitated trehalose transporter Tret1; AmTRET1 (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter

Query= SwissProt::A9ZSY2
         (502 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS24055 BWI76_RS24055 MFS
           transporter
          Length = 464

 Score =  223 bits (567), Expect = 1e-62
 Identities = 141/456 (30%), Positives = 243/456 (53%), Gaps = 20/456 (4%)

Query: 33  KRSPMRYTMQLLAALAVSMASLMIGYSSSYTSPALVSMRDNTTATFEVTMDMAMWIGSIM 92
           K+     TM        ++A L+ G      + AL  + +     F+++     W+ S M
Sbjct: 6   KQGRSNKTMTFFVCFLAALAGLLFGLDIGVIAGALPFIANE----FQISAHTQEWVVSSM 61

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

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

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

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

Query: 325 VGLVNFISTFVAAMIIDRLGRKMLLYISSILMCITLFTFGTFFYVKELMDVTAFGWIPLM 384
           VGL N ++TF+A  ++DR GRK  L +  I+M + +   G+  ++  +   TA  +  LM
Sbjct: 296 VGLTNVLATFIAIGLVDRWGRKPTLILGFIVMALGMGILGSMMHIG-IHSATAQYFAVLM 354

Query: 385 SLIVYVIGFSFGFGPIPWLMMGEILPVKIRGTAASVATAFNWSCTFVVTKTYEDLVLHIG 444
            L+++++GF+   GP+ W++  EI P+K R    + +TA NW    +V  T+  ++  +G
Sbjct: 355 -LLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNSLG 413

Query: 445 PYGTFWLFGTLVAVAFIFVIICVPETRGRSLEEIER 480
              TFW++G L  +     +  +PET+  SLE IER
Sbjct: 414 SANTFWVYGGLNILFIFLTLWLIPETKNVSLEHIER 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: 635
Number of extensions: 34
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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