Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate WP_084932255.1 HA51_RS04135 sugar porter family MFS transporter
Query= TCDB::Q8NTX0 (491 letters) >NCBI__GCF_002095475.1:WP_084932255.1 Length = 474 Score = 432 bits (1112), Expect = e-126 Identities = 224/452 (49%), Positives = 308/452 (68%), Gaps = 4/452 (0%) Query: 22 EGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFGAAA 81 + +++ + + ++ATFGGLLFGYD GVINGAL M + LGL + + G++TS+LL GA Sbjct: 4 QAEHKRYMRKIIVIATFGGLLFGYDVGVINGALPYMAKSLGLNSLSTGLITSALLMGAVF 63 Query: 82 GAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGASTVVP 141 GA+ G++SD GRRK I+ LA+ FFV T+ C AP M+V R +LG AVGGAS VP Sbjct: 64 GAILGGKLSDLVGRRKNILFLALLFFVSTLGCSIAPDIQTMMVCRFVLGFAVGGASVTVP 123 Query: 142 VYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAIPAI 201 YLAE+AP + RG + NELMIV G L AF+ NA++G G ++ VWRYMLA+A IPA+ Sbjct: 124 TYLAEMAPAQSRGRMVTWNELMIVGGVLIAFISNAVLGITLGENEHVWRYMLALAMIPAV 183 Query: 202 ALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSEKSM 261 LFFGML VPESPRWLV++GR EA++VLE IR A E+ +++H E + + + Sbjct: 184 CLFFGMLTVPESPRWLVKQGREAEAKSVLERIRDEHTAGIELYNIKHAISHEQQLGK--V 241 Query: 262 GLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVAPGV 321 RE L+ W+ RI+L+GI + V Q TG+NSIMY+G +L +AG +AALI N A G+ Sbjct: 242 KFRE-LNIPWIRRIMLIGIAVAVFSQTTGVNSIMYFGTEILRDAGLETSAALIGNTAFGL 300 Query: 322 IAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAFPVGDPLRPYVILTLVVV 381 I+V+ F +W++DR RR ++ G + TT+ ++I IA+ + G+P PYV+LTL V+ Sbjct: 301 ISVLSTFAGIWLLDRAGRRPMMLVGLAGTTVILLVIAIAT-SMLAGNPAMPYVVLTLTVI 359 Query: 382 FVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFFPTIMEAVGLTGT 441 F+ MQ + WV LSE+FPL +RG +GISV FLWI N F+GL FP ++E GL+GT Sbjct: 360 FLAFMQGAIGPVLWVTLSEIFPLRIRGAGMGISVAFLWITNFFIGLTFPMMLEGFGLSGT 419 Query: 442 FFMFAGIGVVALIFIYTQVPETRGRTLEEIDE 473 FF FA IGVV I + PET+G++LEEI+E Sbjct: 420 FFAFAAIGVVGFIIMKMFFPETKGKSLEEIEE 451 Lambda K H 0.327 0.142 0.420 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: 639 Number of extensions: 35 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: 491 Length of database: 474 Length adjustment: 34 Effective length of query: 457 Effective length of database: 440 Effective search space: 201080 Effective search space used: 201080 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 24 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