GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Escherichia coli BW25113

Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate 16922 b2841 arabinose transporter (NCBI)

Query= SwissProt::P0AEP1
         (464 letters)



>FitnessBrowser__Keio:16922
          Length = 472

 Score =  595 bits (1534), Expect = e-174
 Identities = 296/456 (64%), Positives = 364/456 (79%), Gaps = 3/456 (0%)

Query: 9   RSNKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVG 68
           R  + M  FV   AA+AGLLFGLDIGVIAGALPFI D F +TS  QEWVVSSMM GAA+G
Sbjct: 16  RDTRRMNMFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLTSRLQEWVVSSMMLGAAIG 75

Query: 69  AVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPL 128
           A+ +GWLSF+LGRK SLM GAILFV GS+ SA A +VE+LI +RV+LG+AVG+ASYTAPL
Sbjct: 76  ALFNGWLSFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARVVLGIAVGIASYTAPL 135

Query: 129 YLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYTGAWRWMLGVIIIPAILLLIGV 188
           YLSE+A E +RG MISMYQLM+T+GI+ A+LSDTAFSY+G WR MLGV+ +PA+LL+I V
Sbjct: 136 YLSEMASENVRGKMISMYQLMVTLGIVLAFLSDTAFSYSGNWRAMLGVLALPAVLLIILV 195

Query: 189 FFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGWALFKENSNF 248
            FLP+SPRW A K R ++AE VL  LRDTS +A+ EL+EIRESL++KQ GWALFK N N 
Sbjct: 196 VFLPNSPRWLAEKGRHIEAEEVLRMLRDTSEKAREELNEIRESLKLKQGGWALFKINRNV 255

Query: 249 RRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLATFIAI 308
           RRAVFLG+LLQ MQQFTGMN+IMYYAP+IF++AG+T T +QM  T++VGLT + ATFIA+
Sbjct: 256 RRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIATLVVGLTFMFATFIAV 315

Query: 309 GLVDRWGRKPTLTLGFLVMAAGMGVLG---TMMHIGIHSPSAQYFAIAMLLMFIVGFAMS 365
             VD+ GRKP L +GF VMA G  VLG        G  S    + ++ M +M I G+AMS
Sbjct: 316 FTVDKAGRKPALKIGFSVMALGTLVLGYCLMQFDNGTASSGLSWLSVGMTMMCIAGYAMS 375

Query: 366 AGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAALN 425
           A P++W+LCSEIQPLK RDFGITCST TNW++NMI+GATFLT+L+++G A TFW+Y ALN
Sbjct: 376 AAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLDSIGAAGTFWLYTALN 435

Query: 426 VLFILLTLWLVPETKHVSLEHIERNLMKGRKLREIG 461
           + F+ +T WL+PETK+V+LEHIER LM G KLR IG
Sbjct: 436 IAFVGITFWLIPETKNVTLEHIERKLMAGEKLRNIG 471


Lambda     K      H
   0.327    0.140    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: 779
Number of extensions: 37
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: 464
Length of database: 472
Length adjustment: 33
Effective length of query: 431
Effective length of database: 439
Effective search space:   189209
Effective search space used:   189209
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: 51 (24.3 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:

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