Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate AZOBR_RS31205 AZOBR_RS31205 sugar ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >FitnessBrowser__azobra:AZOBR_RS31205 Length = 354 Score = 157 bits (397), Expect = 4e-43 Identities = 117/327 (35%), Positives = 173/327 (52%), Gaps = 27/327 (8%) Query: 12 APAKSRRRLPTELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAI 71 AP SR LP ++ VL+ L+F F I L S L+ ++ + + + LLAI Sbjct: 5 APGPSRN-LPQYGALAAVLLANWLLFPDFFSIRLQDGRLFGS--LIDVLNRGAPVALLAI 61 Query: 72 GVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVW--IPVIAG-LG 128 G+T VI T G+DLS G+V+A+S +AA+L Q W PV+A L Sbjct: 62 GMTMVIATRGVDLSVGAVMAISGAVAATLTQAG---------------WGLTPVLAASLA 106 Query: 129 VGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGA-- 186 GLL G NG ++AV I P +ATL +MV+ RG+A+ TEGQ V+ S T IG G+ Sbjct: 107 AGLLCGLWNGLLVAVLRIQPIVATLILMVAGRGIAQLVTEGQIVTFTSPGLTFIGSGSFL 166 Query: 187 ---MPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLL 243 MPV+I V+ + + +R T G A+G + ++ +G+N LV VY GL Sbjct: 167 TVPMPVVITAVLLGVTALLVRMTALGLMIEAVGVSRLSSAGAGVNTPVVLVAVYVWCGLC 226 Query: 244 AGLAGVVASARAATGQA-GMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMA 302 A +AG+V +A A G+ ELDAI A V+GGTSL GG + +V+GAL + M Sbjct: 227 AAVAGLVVAADIRGADANNAGLWLELDAILAVVVGGTSLLGGRFGLLLSVVGALTIQAMN 286 Query: 303 SGFTFVGVDAYIQDIIKGLIIVIAVVI 329 +G G I+K ++++ +++ Sbjct: 287 TGILLSGFKPEFNLIVKAGVLMVVLLL 313 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: 250 Number of extensions: 15 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: 340 Length of database: 354 Length adjustment: 29 Effective length of query: 311 Effective length of database: 325 Effective search space: 101075 Effective search space used: 101075 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