GapMind for catabolism of small carbon sources

 

Aligments for a candidate for frt1 in Escherichia coli BW25113

Align Fructose:H+ symporter, Frt1 (characterized)
to candidate 16922 b2841 arabinose transporter (NCBI)

Query= TCDB::Q8NJ22
         (566 letters)



>lcl|FitnessBrowser__Keio:16922 b2841 arabinose transporter (NCBI)
          Length = 472

 Score =  184 bits (468), Expect = 5e-51
 Identities = 141/455 (30%), Positives = 224/455 (49%), Gaps = 25/455 (5%)

Query: 91  MVIMLGFFASFAGILSGVDQSTISGASYGMKASLKLTSDEDSLISSLMPLGAVGGSILLT 150
           M + +   A+ AG+L G+D   I+GA   +     LTS     + S M LGA  G++   
Sbjct: 21  MNMFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLTSRLQEWVVSSMMLGAAIGALFNG 80

Query: 151 PLSEYFGRKVALVISCIFYTIGGILCAAAQDVHTMYAGRFLIGVGVGIEGGGVGVYIAES 210
            LS   GRK +L+   I + +G I  A A  V  + A R ++G+ VGI      +Y++E 
Sbjct: 81  WLSFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARVVLGIAVGIASYTAPLYLSEM 140

Query: 211 VPSTVRGSLVSLYQFNIALGELVGYVIGVIFFDVKGGWRYMLGSSLVFSTILFVGLFFLP 270
               VRG ++S+YQ  + LG ++ ++     F   G WR MLG   + + +L + + FLP
Sbjct: 141 ASENVRGKMISMYQLMVTLGIVLAFLSDTA-FSYSGNWRAMLGVLALPAVLLIILVVFLP 199

Query: 271 ESPRWLIHKGYDVEAYKVWRRLRDTSDLGNKREFLEMKHAAEQDRQLKEQESRFKSMFDL 330
            SPRWL  KG  +EA +V R LRDTS+            A E+  +++E     +  + L
Sbjct: 200 NSPRWLAEKGRHIEAEEVLRMLRDTSE-----------KAREELNEIRESLKLKQGGWAL 248

Query: 331 ILIPRN-RRALLYSIMMVSLGQLTGINAIMYYMSTLMGQIGF-SPKQAVAMSMVGGAALL 388
             I RN RRA+   +++ ++ Q TG+N IMYY   +    GF + +Q +  ++V G   +
Sbjct: 249 FKINRNVRRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIATLVVGLTFM 308

Query: 389 IGTIPAILYMDKFGRRPWSMTIIGFSV-GLVLVGVGYQIDLNTNLAAAEGVYLTGQILYN 447
             T  A+  +DK GR+P     IGFSV  L  + +GY +    N  A+ G+      +  
Sbjct: 309 FATFIAVFTVDKAGRKP--ALKIGFSVMALGTLVLGYCLMQFDNGTASSGLSWLSVGMTM 366

Query: 448 IFFGTY----ATLTWVVPSESFSLATRSIGMTICSAFLYLWAFTVTYNFNKMKDAFTYTG 503
           +    Y    A + W++ SE   L  R  G+T  +   ++    +   F  + D+    G
Sbjct: 367 MCIAGYAMSAAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLDSIGAAG 426

Query: 504 LTLGFYGGIAIV-IGIPYQLLFMPETKDKTLEEID 537
            T   Y  + I  +GI + L+  PETK+ TLE I+
Sbjct: 427 -TFWLYTALNIAFVGITFWLI--PETKNVTLEHIE 458


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: 538
Number of extensions: 32
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: 566
Length of database: 472
Length adjustment: 35
Effective length of query: 531
Effective length of database: 437
Effective search space:   232047
Effective search space used:   232047
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.

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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 paper from 2022 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