Align Arabinose/xylose transporter, AraE (characterized)
to candidate BWI76_RS17580 BWI76_RS17580 MFS transporter
Query= TCDB::C4B4V9 (479 letters) >FitnessBrowser__Koxy:BWI76_RS17580 Length = 479 Score = 254 bits (648), Expect = 6e-72 Identities = 164/464 (35%), Positives = 253/464 (54%), Gaps = 16/464 (3%) Query: 16 VMMTETVQQTKKIPRPYIYFFGSFGGILFGYDIGVMTGALPFLQSDWNIQHEAAIIGWIT 75 ++M +QQ K++ + I +FGG+LFGYD GV+ GA L+ + G + Sbjct: 3 LIMNLNLQQRKRLHQ--ITLVATFGGLLFGYDTGVINGAFSSLKQYMALTPTTE--GLVM 58 Query: 76 SSLMLGAVFGGVLAGQLSDKLGRRKMILFSALVFMIFSLGCAVAPDGGWVFLAIVRVFLG 135 S L++GA G V G+ +D GRRK +LF + +F I +L A+APD L I R LG Sbjct: 59 SVLLIGAALGSVFGGKFADFFGRRKYLLFLSFIFFIGALMSALAPD--ITVLLISRFILG 116 Query: 136 LGVGAASALVPAYMSEMAPAKIRGRLSGLNQTMIVSGMLASYIVAYFLRNL--HETTAWR 193 VG AS P ++SE+AP ++RG+L+GLN+ IV G LA++ + + L H WR Sbjct: 117 YAVGGASVTAPTFISEVAPTEMRGKLTGLNEVAIVIGQLAAFAINAIIGILWGHLPDVWR 176 Query: 194 LMLGLAAIPALVLFLGVLRLPESPRFLIKNGRIEEARTVLSYIRDNDAIDSELKNIQET- 252 ML + IPA+ LF+G+LR PESPR+LI R EEA +L IR + E +I Sbjct: 177 YMLMVQTIPAICLFIGMLRSPESPRWLISKNRHEEALEILKQIRPLERATKEFNDITTLI 236 Query: 253 -AELENAIQAKTRLATLFSGRYRY-LVAAGVGVAAFQQFQGANAIFYYIPLIVEKASGTE 310 AE + + ++ T+ + + L+ GV AA QQ G N I YY I+ A +E Sbjct: 237 KAEADKKLHSQNAFITILQTPWIFKLLLVGVIWAALQQTTGVNVIMYYGTEILSSAGFSE 296 Query: 311 ASNALMWPIIQGVILVLGSLLFMVI--ADKFNRRTLLTVGGTVMGLSFLFPTFIHMT-IP 367 ++ L+ ++ GV V G +LF V+ D+F R+T++ G +M L + T + Sbjct: 297 RTS-LICNVLNGVFSV-GGMLFGVLFLVDRFKRKTIIIYGFALMATLHLIIAGVDYTLVG 354 Query: 368 DANPMMIVVFLSIYVAFYSFTWAPLTWVIVGEIFPLAIRGRASGLASSFNWIGSFSVGLL 427 D I + +++V T +TWV++ E+FPL RG + G++ F W+ + V L Sbjct: 355 DIKATAIWLLGAMFVGVMQGTMGFITWVVLAELFPLKFRGLSMGISVFFMWVMNAIVSYL 414 Query: 428 FPIMTAQMTQDAVFAIFGIICILGVLFVRFLVPETRGRTLEEIE 471 FP++ A++ VF IF I L ++FV +PET ++LE++E Sbjct: 415 FPLLQAKLGLGPVFLIFAAINYLAIVFVITALPETSNKSLEQLE 458 Lambda K H 0.328 0.142 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: 684 Number of extensions: 44 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: 479 Length of database: 479 Length adjustment: 34 Effective length of query: 445 Effective length of database: 445 Effective search space: 198025 Effective search space used: 198025 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 (21.8 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