Align D-xylose-proton symporter (characterized)
to candidate 350322 BT0794 D-xylose-proton symporter (D-xylose transporter) (NCBI ptt file)
Query= CharProtDB::CH_109760 (491 letters) >FitnessBrowser__Btheta:350322 Length = 484 Score = 448 bits (1152), Expect = e-130 Identities = 240/489 (49%), Positives = 330/489 (67%), Gaps = 37/489 (7%) Query: 9 YIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGC 68 Y++SIT VA LGGLLFGYDTAVISG + L F++ + + + G +SALIGC Sbjct: 12 YLYSITSVAILGGLLFGYDTAVISGAEKGLEAFFLSASDFQYNKV--MHGITSSSALIGC 69 Query: 69 IIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPE 128 ++GGAL G ++R GRR+SL++AAVLFF+S +GS +PE+ F N + + +A Sbjct: 70 VLGGALSGVFASRLGRRNSLRLAAVLFFLSALGSYYPEVLFFEYGKPN-MDLLIA----- 123 Query: 129 FVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARS 188 F +YR++GGIGVGLAS + PMYIAE+AP++IRG LVS NQFAIIFG L+VY VNY I Sbjct: 124 FNLYRVLGGIGVGLASAVCPMYIAEIAPSNIRGTLVSCNQFAIIFGMLVVYFVNYLIMGD 183 Query: 189 G-------DAS-----------WLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSR 230 DA+ W +GWRYMF SE PA F +LL+ VP++PR+L+ Sbjct: 184 HQNPIILKDAAGVLSVSAESDMWTVQEGWRYMFGSEAFPAAFFGLLLFFVPKTPRYLVLV 243 Query: 231 GKQEQAEGILRKIMGNTLATQAVQEIKHSLDHGRKTGGRLLMFGVGVIVIGVMLSIFQQF 290 ++E+A IL KI G A + + +IK + + +L +GV VIVIG++LS+FQQ Sbjct: 244 QQEEKAYTILEKINGKKKAQEILNDIKATAQEKTE---KLFTYGVTVIVIGILLSVFQQA 300 Query: 291 VGINVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGAL 350 +GIN VLYYAP +F+ GA ++QT+I+G++N+ FT++AI TVD+FGRKPL IIG++ Sbjct: 301 IGINAVLYYAPRIFENAGAEGG-GMMQTVIMGIVNIIFTLVAIFTVDRFGRKPLLIIGSI 359 Query: 351 GMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAI 410 GMA+G F++ G++ +LS++ Y A F MSWGP+CWVL+SEIFPN IRGKA+AI Sbjct: 360 GMAVGAFAVAMCDSMAIKGVLPVLSIIVYAAFFMMSWGPICWVLISEIFPNTIRGKAVAI 419 Query: 411 AVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKT 470 AVA QW+ NY VS TFP + F F+Y +YG + V AA+F+W++VPETKGKT Sbjct: 420 AVAFQWIFNYIVSSTFPAL-------YDFSPMFAYSLYGIICVAAAIFVWRWVPETKGKT 472 Query: 471 LEELEALWE 479 LE++ LW+ Sbjct: 473 LEDMSKLWK 481 Lambda K H 0.326 0.140 0.433 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: 679 Number of extensions: 34 Number of successful extensions: 8 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: 491 Length of database: 484 Length adjustment: 34 Effective length of query: 457 Effective length of database: 450 Effective search space: 205650 Effective search space used: 205650 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: 52 (24.6 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