Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate WP_012112843.1 XAUT_RS04125 MFS transporter
Query= SwissProt::P0AEP1 (464 letters) >NCBI__GCF_000017645.1:WP_012112843.1 Length = 456 Score = 319 bits (818), Expect = 1e-91 Identities = 179/455 (39%), Positives = 275/455 (60%), Gaps = 13/455 (2%) Query: 14 MTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSSMMFGAAVGAVGSG 73 M + + +A +AG LFG D GVIAGAL + + I + + +++ FGA +GA+ G Sbjct: 1 MMYLIAAIAGIAGALFGFDEGVIAGALAPLRRDLGIDPVAEGMMTAAVPFGAFLGAIVGG 60 Query: 74 WLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVGVASYTAPLYLSEI 133 L+ LGR++ L+ A+LFV G+L SA A + L +R+++GL VGVA+ APLY+SE Sbjct: 61 RLALALGRRRLLLAAAVLFVVGALLSAFAFGLWTLTFARLIIGLGVGVAAMMAPLYISEC 120 Query: 134 APEKIRGSMISMYQLMITIGILGAYLSDTAFSYTGAWRWMLGVIIIPAILLLIGVFFLPD 193 AP RG ++S+YQL IT+GILGAY+ +++ +WRWM V +PAI L +G+F L D Sbjct: 121 APAAQRGMLVSIYQLAITLGILGAYV--VGYAFHESWRWMFAVGAVPAIALFVGIFGLSD 178 Query: 194 SPRWFAAKRRFVDAERVLLRLRDTSAE---AKRELDEIRESLQVKQSGWALFKE--NSNF 248 +PRW A + R +A L R+R+ S K E EI ++ A + Sbjct: 179 TPRWLAVRGREAEARAALARVREKSESDPAVKAEFAEILTGATQDENRKARLSDLLTPRV 238 Query: 249 RRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTNVLATFIAI 308 R A+ + + L ++QQ +G+N ++YYAP +FEL+G+++TT Q+ T +G+ NVL T + + Sbjct: 239 RPALIVAMGLFLLQQLSGINAVIYYAPTVFELSGFSSTTTQILATAGIGVVNVLMTLVGM 298 Query: 309 GLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAM--LLMFIVGFAMSA 366 L+DR GR+ L +GF AG V +++ IG + S +A+ L+++I FA++ Sbjct: 299 ALIDRLGRRLLLLIGF----AGTAVALSVIAIGAATGSEMMGKLALGGLVLYIASFAIAI 354 Query: 367 GPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWVYAALNV 426 GPL WV+ SE+ PL R G++ ++ NW N +V +F ++ G A F +YA + V Sbjct: 355 GPLPWVMMSEVFPLDVRALGMSIASLVNWGFNFLVVFSFPVLVAEFGLAGVFGLYAVVCV 414 Query: 427 LFILLTLWLVPETKHVSLEHIERNLMKGRKLREIG 461 + + T WLVPET VSLE IER+L GR LR++G Sbjct: 415 VGLAFTQWLVPETSGVSLEEIERHLDSGRPLRDLG 449 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: 664 Number of extensions: 31 Number of successful extensions: 4 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: 456 Length adjustment: 33 Effective length of query: 431 Effective length of database: 423 Effective search space: 182313 Effective search space used: 182313 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 24 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