Align Galactose-proton symporter; Galactose transporter (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter
Query= SwissProt::P0AEP1 (464 letters) >FitnessBrowser__Koxy:BWI76_RS24055 Length = 464 Score = 865 bits (2236), Expect = 0.0 Identities = 433/464 (93%), Positives = 452/464 (97%) Query: 1 MPDAKKQGRSNKAMTFFVCFLAALAGLLFGLDIGVIAGALPFIADEFQITSHTQEWVVSS 60 MPD KKQGRSNK MTFFVCFLAALAGLLFGLDIGVIAGALPFIA+EFQI++HTQEWVVSS Sbjct: 1 MPDNKKQGRSNKTMTFFVCFLAALAGLLFGLDIGVIAGALPFIANEFQISAHTQEWVVSS 60 Query: 61 MMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLILSRVLLGLAVG 120 MMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVL++SRVLLGLAVG Sbjct: 61 MMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPNVEVLLISRVLLGLAVG 120 Query: 121 VASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYTGAWRWMLGVIIIP 180 VASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSY+GAWRWMLGVIIIP Sbjct: 121 VASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSYSGAWRWMLGVIIIP 180 Query: 181 AILLLIGVFFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLQVKQSGWA 240 A+LLLIGV FLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESL+VKQSGW+ Sbjct: 181 AVLLLIGVVFLPDSPRWFAAKRRFVDAERVLLRLRDTSAEAKRELDEIRESLKVKQSGWS 240 Query: 241 LFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTEQMWGTVIVGLTN 300 LFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGY NTTEQMWGTVIVGLTN Sbjct: 241 LFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTTEQMWGTVIVGLTN 300 Query: 301 VLATFIAIGLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSPSAQYFAIAMLLMFIV 360 VLATFIAIGLVDRWGRKPTL LGF+VMA GMG+LG+MMHIGIHS +AQYFA+ MLLMFIV Sbjct: 301 VLATFIAIGLVDRWGRKPTLILGFIVMALGMGILGSMMHIGIHSATAQYFAVLMLLMFIV 360 Query: 361 GFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNTLGNANTFWV 420 GFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLN+LG+ANTFWV Sbjct: 361 GFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVGATFLTMLNSLGSANTFWV 420 Query: 421 YAALNVLFILLTLWLVPETKHVSLEHIERNLMKGRKLREIGAHD 464 Y LN+LFI LTLWL+PETK+VSLEHIERNLMKGRKLREIGA D Sbjct: 421 YGGLNILFIFLTLWLIPETKNVSLEHIERNLMKGRKLREIGARD 464 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: 1025 Number of extensions: 28 Number of successful extensions: 1 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: 464 Length adjustment: 33 Effective length of query: 431 Effective length of database: 431 Effective search space: 185761 Effective search space used: 185761 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 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