Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate 17022 b2943 D-galactose transporter (NCBI)
Query= SwissProt::P0AE24 (472 letters) >FitnessBrowser__Keio:17022 Length = 464 Score = 595 bits (1534), Expect = e-174 Identities = 296/456 (64%), Positives = 364/456 (79%), Gaps = 3/456 (0%) Query: 16 RDTRRMNMFVSVAAAVAGLLFGLDIGVIAGALPFITDHFVLTSRLQEWVVSSMMLGAAIG 75 R + M FV AA+AGLLFGLDIGVIAGALPFI D F +TS QEWVVSSMM GAA+G Sbjct: 9 RSNKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVG 68 Query: 76 ALFNGWLSFRLGRKYSLMAGAILFVLGSIGSAFATSVEMLIAARVVLGIAVGIASYTAPL 135 A+ +GWLSF+LGRK SLM GAILFV GS+ SA A +VE+LI +RV+LG+AVG+ASYTAPL Sbjct: 69 AVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPL 128 Query: 136 YLSEMASENVRGKMISMYQLMVTLGIVLAFLSDTAFSYSGNWRAMLGVLALPAVLLIILV 195 YLSE+A E +RG MISMYQLM+T+GI+ A+LSDTAFSY+G WR MLGV+ +PA+LL+I V Sbjct: 129 YLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYTGAWRWMLGVIIIPAILLLIGV 188 Query: 196 VFLPNSPRWLAEKGRHIEAEEVLRMLRDTSEKAREELNEIRESLKLKQGGWALFKINRNV 255 FLP+SPRW A K R ++AE VL LRDTS +A+ EL+EIRESL++KQ GWALFK N N Sbjct: 189 FFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGWALFKENSNF 248 Query: 256 RRAVFLGMLLQAMQQFTGMNIIMYYAPRIFKMAGFTTTEQQMIATLVVGLTFMFATFIAV 315 RRAVFLG+LLQ MQQFTGMN+IMYYAP+IF++AG+T T +QM T++VGLT + ATFIA+ Sbjct: 249 RRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLATFIAI 308 Query: 316 FTVDKAGRKPALKIGFSVMALGTLVLGYCLMQFDNGTASSGLSWLSVGMTMMCIAGYAMS 375 VD+ GRKP L +GF VMA G VLG G S + ++ M +M I G+AMS Sbjct: 309 GLVDRWGRKPTLTLGFLVMAAGMGVLG---TMMHIGIHSPSAQYFAIAMLLMFIVGFAMS 365 Query: 376 AAPVVWILCSEIQPLKCRDFGITCSTTTNWVSNMIIGATFLTLLDSIGAAGTFWLYTALN 435 A P++W+LCSEIQPLK RDFGITCST TNW++NMI+GATFLT+L+++G A TFW+Y ALN Sbjct: 366 AGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAALN 425 Query: 436 IAFVGITFWLIPETKNVTLEHIERKLMAGEKLRNIG 471 + F+ +T WL+PETK+V+LEHIER LM G KLR IG Sbjct: 426 VLFILLTLWLVPETKHVSLEHIERNLMKGRKLREIG 461 Lambda K H 0.327 0.138 0.409 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: 746 Number of extensions: 36 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: 472 Length of database: 464 Length adjustment: 33 Effective length of query: 439 Effective length of database: 431 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.
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:
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