Align Inositol transport system permease protein (characterized)
to candidate H281DRAFT_04148 H281DRAFT_04148 monosaccharide ABC transporter membrane protein, CUT2 family
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Burk376:H281DRAFT_04148 Length = 335 Score = 231 bits (589), Expect = 2e-65 Identities = 135/308 (43%), Positives = 188/308 (61%), Gaps = 18/308 (5%) Query: 33 IGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLAL 92 IGL+ + SFL + + ++ QVSI ++A+G+T VI+T GIDLS GSV+AL Sbjct: 41 IGLLVVCIVMVFASDSFLSGAN-IENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMAL 99 Query: 93 SAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIAT 152 + +AA L + + +A+G+ VGL GA NG +A G+PP I T Sbjct: 100 AGTLAAGLM------------VAGMNALAALAVGVAVGLGFGAANGFFVAFAGMPPIIVT 147 Query: 153 LGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAM-----PVIIFLVVAVIFHIALRYTK 207 L M ARGLA YT G P+ L D + G G + PV+I V+ VI + L Sbjct: 148 LATMGIARGLALIYTGGYPIDGLPDWVSFFGSGKILGIQAPVVIMAVIYVIAWVLLERMP 207 Query: 208 YGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYE 267 +G+Y YAIGGN QA R SG+ V R +IVY+IAGL + A +V +AR +GQ G+ +E Sbjct: 208 FGRYVYAIGGNEQATRLSGVRVARVKLIVYTIAGLTSSFAAIVLTARLMSGQPNAGVGFE 267 Query: 268 LDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAV 327 LDAIAA V+GGTS++GG G I GT+IGAL+LGV+ +G VGV+ Y+Q++IKG II++A+ Sbjct: 268 LDAIAAVVMGGTSISGGRGSIIGTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIILLAI 327 Query: 328 VIDQYRNK 335 I + R K Sbjct: 328 YISRDRRK 335 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: 282 Number of extensions: 10 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: 335 Length adjustment: 28 Effective length of query: 312 Effective length of database: 307 Effective search space: 95784 Effective search space used: 95784 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