Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate H281DRAFT_02714 H281DRAFT_02714 monosaccharide ABC transporter membrane protein, CUT2 family
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >FitnessBrowser__Burk376:H281DRAFT_02714 Length = 331 Score = 223 bits (568), Expect = 5e-63 Identities = 128/321 (39%), Positives = 188/321 (58%), Gaps = 24/321 (7%) Query: 23 ELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGI 82 EL++ VL+ +GL+ +F + + + L+ + S+I L++IG+ VIIT GI Sbjct: 27 ELNVLSVLLLVGLLISVFS------PYFLTTNNLMGVFRSFSLIALMSIGMMLVIITGGI 80 Query: 83 DLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGAINGSIIA 142 DLS GSV+ LS+++ A + Q A A + AGL VG+ GA NG +I Sbjct: 81 DLSVGSVMGLSSLVTALVFQHGYNAPAA------------IGAGLAVGIAVGAFNGFMIT 128 Query: 143 VTGIPPFIATLGMMVSARGLARYYTEGQPVSM-LSDSYTAIGHGAM-----PVIIFLVVA 196 +PPFIATLG + RGL T+G PV+ + DS+T IG G + PV+I L + Sbjct: 129 WIQLPPFIATLGTLSIGRGLMYIITKGVPVTPDVPDSFTFIGQGYIGFVPFPVVILLAMT 188 Query: 197 VIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAA 256 +F + +R T++G+Y YA GGN AAR SG+ R VY ++GL+A +AGV+A +R Sbjct: 189 AVFSVVMRQTRFGRYVYATGGNEVAARLSGVRTARVKFTVYVLSGLIASMAGVIAFSRFV 248 Query: 257 TGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQD 316 + + G ELD IAAA IGG SL+GG G + G +IGA + G++ +G + +D Y Q Sbjct: 249 SAEPASGFGAELDVIAAAAIGGASLSGGAGSVEGAIIGAALAGIITNGVVLLNIDTYAQQ 308 Query: 317 IIKGLIIVIAVVIDQYRNKRK 337 I G +I+IAV ID +R +RK Sbjct: 309 AITGCVILIAVSIDIWRVRRK 329 Lambda K H 0.326 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: 260 Number of extensions: 12 Number of successful extensions: 3 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: 331 Length adjustment: 28 Effective length of query: 312 Effective length of database: 303 Effective search space: 94536 Effective search space used: 94536 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: 49 (23.5 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