GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frt1 in Klebsiella michiganensis M5al

Align Fructose:H+ symporter, Frt1 (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter

Query= TCDB::Q8NJ22
         (566 letters)



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

 Score =  190 bits (483), Expect = 9e-53
 Identities = 141/460 (30%), Positives = 237/460 (51%), Gaps = 29/460 (6%)

Query: 86  SNKTYMVIMLGFFASFAGILSGVDQSTISGASYGMKASLKLTSDEDSLISSLMPLGAVGG 145
           SNKT M   + F A+ AG+L G+D   I+GA   +    ++++     + S M  GA  G
Sbjct: 10  SNKT-MTFFVCFLAALAGLLFGLDIGVIAGALPFIANEFQISAHTQEWVVSSMMFGAAVG 68

Query: 146 SILLTPLSEYFGRKVALVISCIFYTIGGILCAAAQDVHTMYAGRFLIGVGVGIEGGGVGV 205
           ++    LS   GRK +L+I  I +  G +  AAA +V  +   R L+G+ VG+      +
Sbjct: 69  AVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISRVLLGLAVGVASYTAPL 128

Query: 206 YIAESVPSTVRGSLVSLYQFNIALGELVGYVIGVIFFDVKGGWRYMLGSSLVFSTILFVG 265
           Y++E  P  +RGS++S+YQ  I +G ++G  +    F   G WR+MLG  ++ + +L +G
Sbjct: 129 YLSEIAPEKIRGSMISMYQLMITIG-ILGAYLSDTAFSYSGAWRWMLGVIIIPAVLLLIG 187

Query: 266 LFFLPESPRWLIHKGYDVEAYKVWRRLRDTS-----DLGNKREFLEMKHAAEQDRQLKEQ 320
           + FLP+SPRW   K   V+A +V  RLRDTS     +L   RE L++K   +    L ++
Sbjct: 188 VVFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLKVK---QSGWSLFKE 244

Query: 321 ESRFKSMFDLILIPRNRRALLYSIMMVSLGQLTGINAIMYYMSTLMGQIGF-SPKQAVAM 379
            S F            RRA+   +++  + Q TG+N IMYY   +    G+ +  + +  
Sbjct: 245 NSNF------------RRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTTEQMWG 292

Query: 380 SMVGGAALLIGTIPAILYMDKFGRRPWSMTIIGFSVGLVLVGV-GYQIDLNTNLAAAEGV 438
           +++ G   ++ T  AI  +D++GR+P    I+GF V  + +G+ G  + +  + A A+  
Sbjct: 293 TVIVGLTNVLATFIAIGLVDRWGRKP--TLILGFIVMALGMGILGSMMHIGIHSATAQYF 350

Query: 439 YLTGQILYNIFFGTYA-TLTWVVPSESFSLATRSIGMTICSAFLYLWAFTVTYNFNKMKD 497
            +   +++ + F   A  L WV+ SE   L  R  G+T  +A  ++    V   F  M +
Sbjct: 351 AVLMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLN 410

Query: 498 AFTYTGLTLGFYGGIAIVIGIPYQLLFMPETKDKTLEEID 537
           +   +  T   YGG+ I+  I   L  +PETK+ +LE I+
Sbjct: 411 SLG-SANTFWVYGGLNILF-IFLTLWLIPETKNVSLEHIE 448


Lambda     K      H
   0.323    0.139    0.404 

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: 612
Number of extensions: 33
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: 566
Length of database: 464
Length adjustment: 35
Effective length of query: 531
Effective length of database: 429
Effective search space:   227799
Effective search space used:   227799
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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