Align D-xylose transporter; D-xylose-proton symporter (characterized)
to candidate AO356_27270 AO356_27270 MFS transporter
Query= SwissProt::O52733 (457 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27270 Length = 472 Score = 302 bits (774), Expect = 1e-86 Identities = 161/443 (36%), Positives = 258/443 (58%), Gaps = 12/443 (2%) Query: 9 VYFFGALGGLLFGYDTGVISGAILFIQKQMNLGSWQQGWVVSAVLLGAILGAAIIGPSSD 68 + + GGLLFG+DTGVI+GA+L+++ + L + +G V SA+L+GA++GA G SD Sbjct: 31 ITWIATFGGLLFGFDTGVINGALLYMKDDLGLTPFTEGLVASALLIGAMMGALFSGRLSD 90 Query: 69 RFGRRKLLLLSAIIFFVGALGSAFSPEFWTLIISRIILGMAVGAASALIPTYLAELAPSD 128 GRR+++L A++FF+GAL A +P ++ +R LG+AVG AS ++P YLAE+APS Sbjct: 91 LKGRRRIILFLAVVFFLGALACALAPTLNVMVAARFTLGLAVGGASVVVPAYLAEMAPSS 150 Query: 129 KRGTVSSLFQLMVMTGILLAYITNYSFSGFYTG----WRWMLGFAAIPAALLFLGGLILP 184 RG + + +LM++TG LA+ TN + ++ WRWML A +PA L+LG L +P Sbjct: 151 IRGRIITRNELMIVTGQFLAFTTNATLGNLFSDLDGVWRWMLALATLPAVALWLGMLYMP 210 Query: 185 ESPRFLVKSGHLDEARHVLDTMNKHDQVAVNKE--INDIQESAKIVSGGWSELFGKMVRP 242 ESPR+L G E VL + + E I I GGW +L K R Sbjct: 211 ESPRWLATKGRFREGLEVLKLVREEYYAKAEMEAITQQISNERFIKKGGWRDLSQKGARR 270 Query: 243 SLIIGIGLAIFQQVMGCNTVLYYAPTIFTDVGFGVSAALLAHIGIGIFNVIVTAIAVAIM 302 +IGIG+A+ Q+ G N+++Y+ I T+ G +AL+A++ G+ ++ T + +A++ Sbjct: 271 IFLIGIGIAVTSQLTGVNSIMYFGTQILTEAGLEQRSALIANVVNGVISIGATFVGIALL 330 Query: 303 DKIDRKKIVNIGAVGMGISLFVMSIGMKFSGGSQTAAIISVIALTVYIAFFSATWGPVMW 362 D++ R+ ++ +G G +SL ++ + F S T A++ + A+ +++A GP W Sbjct: 331 DRVGRRPMMLLGFTGTTLSLLLIGLVSVFVDPSVTRAMLILGAMAMFLASMQGLIGPAFW 390 Query: 363 VMIGEVFPLNIRGLGNSFASVINWTANMIVSLTFPSLLDFFGTGS---LFIGYGILCFAS 419 V++ E+FP+ IRG A W N+++ + FPSL+ G G +F+G G+L S Sbjct: 391 VLLAEIFPMRIRGGCMGMAIAAFWLTNVMIGMFFPSLVATIGIGQTFFVFVGAGLL---S 447 Query: 420 IWFVQKKVFETRNRSLEDIEATL 442 + FV V ETR +LE+IE L Sbjct: 448 LTFVAVWVPETRGSTLEEIEQRL 470 Lambda K H 0.327 0.141 0.424 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: 577 Number of extensions: 33 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: 457 Length of database: 472 Length adjustment: 33 Effective length of query: 424 Effective length of database: 439 Effective search space: 186136 Effective search space used: 186136 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