Align Arabinose/xylose transporter, AraE (characterized)
to candidate BWI76_RS03110 BWI76_RS03110 MFS transporter
Query= TCDB::C4B4V9 (479 letters) >FitnessBrowser__Koxy:BWI76_RS03110 Length = 499 Score = 271 bits (694), Expect = 3e-77 Identities = 160/448 (35%), Positives = 254/448 (56%), Gaps = 15/448 (3%) Query: 33 IYFFGSFGGILFGYDIGVMTGALPFLQSDWNIQHEAAIIGWITSSLMLGAVFGGVLAGQL 92 + + GG+LFGYD GV++GAL F+ ++ ++ G +TSSL+ GA FG +L+G L Sbjct: 28 VALIATLGGLLFGYDTGVISGALLFMGTELHLTPFTT--GLVTSSLLFGAAFGALLSGNL 85 Query: 93 SDKLGRRKMILFSALVFMIFSLGCAVAPDGGWVFLAIVRVFLGLGVGAASALVPAYMSEM 152 ++ GR+K+IL+ A++F I ++G ++APD W+ R+ LG+ VG A+A VP Y++E+ Sbjct: 86 ANAAGRKKIILWLAVLFAIGAIGTSMAPDVNWMIF--FRLILGVAVGGAAATVPVYIAEI 143 Query: 153 APAKIRGRLSGLNQTMIVSGMLASYIV-AYFLRNLHETTAWRLMLGLAAIPALVLFLGVL 211 APA RG+L L + MIVSG L +YI A F + WR ML +A +PA++L+ G++ Sbjct: 144 APANKRGQLVTLQELMIVSGQLLAYISNATFHEVWGGESTWRWMLAVATLPAVLLWFGMM 203 Query: 212 RLPESPRFLIKNGRIEEARTVLSYIRDNDAIDSELKNIQETAELENAIQAKTRLATLFSG 271 +P+SPR+ GR+ EAR VL R D ++ EL I ET + + + K R + + + Sbjct: 204 FMPDSPRWYAMKGRLAEARRVLERTRHKDDVEWELLEITETLDEQRNL-GKPRFSEIMTP 262 Query: 272 RYRYLVAAGVGVAAFQQFQGANAIFYYIPLIVEKASGTEASNALMWPIIQGVILVLGSLL 331 L G+G+A QQ G N I YY P ++ T+ + AL I GV+ VL + + Sbjct: 263 WLFKLFMIGIGIAVIQQLTGVNTIMYYAPTVLTSVGMTDNA-ALFATIANGVVSVLMTFV 321 Query: 332 FMVIADKFNRRTLLTVGGT--------VMGLSFLFPTFIHMTIPDANPMMIVVFLSIYVA 383 + + K RR + +G + +S+L P ++ M++ + ++++ Sbjct: 322 GIWMLGKIGRRPMTMIGQFGCTACLVFIGAVSYLLPETVNGQPDALRAYMVLAGMLLFLS 381 Query: 384 FYSFTWAPLTWVIVGEIFPLAIRGRASGLASSFNWIGSFSVGLLFPIMTAQMTQDAVFAI 443 F +P+TW+++ EIFP +RG G A WI +F + L FPI+ A + F I Sbjct: 382 FQQGALSPVTWLLMSEIFPTRLRGIFMGGAVFSMWIANFLISLFFPILLAWLGLSGTFFI 441 Query: 444 FGIICILGVLFVRFLVPETRGRTLEEIE 471 F I + G +FV VPETR R+LE+IE Sbjct: 442 FAGIGVFGAIFVIKCVPETRHRSLEQIE 469 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: 762 Number of extensions: 50 Number of successful extensions: 7 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: 499 Length adjustment: 34 Effective length of query: 445 Effective length of database: 465 Effective search space: 206925 Effective search space used: 206925 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: 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