Align Inositol transport system permease protein (characterized)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 171 bits (434), Expect = 5e-47 Identities = 115/346 (33%), Positives = 180/346 (52%), Gaps = 29/346 (8%) Query: 1 MNAIT-DNKPATVPTKS---RRRLPTELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQRL 56 MNA T PA P+ + R +L T L + VL G+ +F + +++ Sbjct: 563 MNAPTAPAAPAATPSSASVWRSQLGTYLGLLAVLAGMVALFSSLS------EYFWSAETF 616 Query: 57 VLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTD 116 + + ++ + ++A+G+T V+I GIDLS GSV+AL+A +A+ A+ Sbjct: 617 ITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAA---------AILQWGWT 667 Query: 117 LPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTE------GQ 170 +P A+ L GL+ G I G+I +P FI +LGM+ + RG A T+ G Sbjct: 668 VPA--AAALALATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRTQYVGD 725 Query: 171 PVSMLSDSYTAIGHGAMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVK 230 +S LS + G + ++ +V+ V+ + L T +G+ IG N +A R +G++ + Sbjct: 726 AISWLSAPF--FGGISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGVDPR 783 Query: 231 RHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITG 290 +IV+++ GLLAGLAG++ SAR G EL IAA VIGGTSL GG G + Sbjct: 784 PIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGSVVN 843 Query: 291 TVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKR 336 T G LI+ V+ +G VG + II G +IV AV++D R +R Sbjct: 844 TAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIVDTLRQRR 889 Lambda K H 0.325 0.140 0.394 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: 544 Number of extensions: 20 Number of successful extensions: 2 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: 340 Length of database: 892 Length adjustment: 36 Effective length of query: 304 Effective length of database: 856 Effective search space: 260224 Effective search space used: 260224 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: 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