Align Minor myo-inositol transporter IolF (characterized)
to candidate Ga0059261_2621 Ga0059261_2621 Arabinose efflux permease
Query= SwissProt::P42417 (438 letters) >FitnessBrowser__Korea:Ga0059261_2621 Length = 416 Score = 335 bits (858), Expect = 2e-96 Identities = 180/422 (42%), Positives = 263/422 (62%), Gaps = 11/422 (2%) Query: 1 MGNTNGDSAFNKRTIAAALANYIDAGSIVAGSAGLSLWVSYLKLSDTQIGLLGALSANAI 60 M + + D K TI A LANYIDAGSIVAG+ L+LW L D+ +GL+ A NAI Sbjct: 1 MSSASADREDWKNTILAGLANYIDAGSIVAGAVALALWKKEYGLDDSLLGLIAAFGPNAI 60 Query: 61 SAAVGALLGGFLADKVGRKAVYTNSMLVYALGICLVLFGVNFPMLLSGYIIIGLSVGADI 120 +A +GAL+GG L D +GRK +Y ML YA G+ ++F +N M++ G+ ++GL+VGADI Sbjct: 61 AAGIGALIGGRLCDLLGRKKIYQYDMLFYAFGMLWLVFAMNAWMVIIGFFLVGLAVGADI 120 Query: 121 TASWTIIAENAPKKNRARHCGVAQVAWAAGAVVVLLLSVLAGDLGLLGNKIVFAHLLVIA 180 ASW++IAE AP K R +H GVAQ+ W G VVVL+++++ LGLLG +I+FAHL ++A Sbjct: 121 PASWSLIAEMAPDKKRGKHSGVAQLLWYLGPVVVLVMALVLDKLGLLGVRIIFAHLAILA 180 Query: 181 LITYILRIRLPESDAW-QTKNQPEEAQAEKPAVLNKTSYFDLLKPMYLKSILFLMGVYLV 239 + LR ++ ES W + + E AQ + + DL ++ S+ FL G YL Sbjct: 181 IALTFLRSKMQESQRWVEAQKSGETAQ--------RGRWQDLFTRQHIGSMAFLAGTYLF 232 Query: 240 WNLAAGVMGFFMPYIYQQVGGVSANMANLLQMGLFIFTGLGVALIFMPFADKY-RKTVFG 298 WNL AG GFF PYI VG + ++ +Q F+ + IFM AD+ ++ +FG Sbjct: 233 WNLWAGTNGFFFPYILSTVGSQTQVVSVAVQTLSFLLGMASIFFIFMKLADRVNQRLLFG 292 Query: 299 IAAFMAVIGWTLFLLPVEGLPILLLFIVVIGINNGAGQQANYQLWASEIFPTQYRASAQG 358 I+A VIG L + LP+ ++ + ++ + G G Q+ +QLW+SE+FPT RA+AQG Sbjct: 293 ISAVTQVIGMALLAIFPLTLPVAIIHVFLMSVGGGFGAQSFFQLWSSEMFPTALRATAQG 352 Query: 359 LMFFLVRISIGIWSLFVPMIITNFGIGTMAAILLGCVTASMIIGLLFAPNTSGKSLEQIQ 418 +MF +VRI +G++S FVP ++ G T+A IL+G + S +IG ++AP GKSLEQ+ Sbjct: 353 VMFAIVRIVLGVFSFFVPALVAT-GFHTLAWILVGFLAISGVIGFVWAPRNEGKSLEQLD 411 Query: 419 EE 420 E Sbjct: 412 AE 413 Lambda K H 0.325 0.140 0.413 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: 527 Number of extensions: 20 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: 438 Length of database: 416 Length adjustment: 32 Effective length of query: 406 Effective length of database: 384 Effective search space: 155904 Effective search space used: 155904 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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