GapMind for catabolism of small carbon sources

 

Aligments for a candidate for MFS-glucose in Klebsiella michiganensis M5al

Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate BWI76_RS23425 BWI76_RS23425 MFS transporter

Query= SwissProt::P0AEP1
         (464 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS23425 BWI76_RS23425 MFS
           transporter
          Length = 472

 Score =  593 bits (1528), Expect = e-174
 Identities = 295/456 (64%), Positives = 365/456 (80%), Gaps = 3/456 (0%)

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

Query: 69  AVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPL 128
           A+ +GWLSF+LGRK SLM+GA+LFVAGS+ SA A +VE+L+ +R++LG+AVG+ASYTAPL
Sbjct: 76  ALFNGWLSFRLGRKYSLMVGAVLFVAGSVGSAFAGSVEMLLAARIVLGVAVGIASYTAPL 135

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

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

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

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

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

Query: 426 VLFILLTLWLVPETKHVSLEHIERNLMKGRKLREIG 461
           V FI +T WL+PETK+V+LEHIER LM G KLR IG
Sbjct: 436 VAFIGVTFWLIPETKNVTLEHIERKLMSGEKLRNIG 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: 789
Number of extensions: 39
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.

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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