Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate WP_068000560.1 PsAD2_RS00560 ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >NCBI__GCF_001623255.1:WP_068000560.1 Length = 332 Score = 193 bits (491), Expect = 5e-54 Identities = 118/318 (37%), Positives = 183/318 (57%), Gaps = 24/318 (7%) Query: 26 IFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLS 85 I L L+ + L F +F + + + ++ QV+I +LA+G+T VI+ GIDLS Sbjct: 27 IGLALLALILFFSIF------TEHFLTANNITNILTQVTINLILAVGMTFVILIGGIDLS 80 Query: 86 SGSVLALSAMIAA---SLAQTSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGAINGSIIA 142 GSV+A +++IA +LA F V + VIA VG++ GAING+I A Sbjct: 81 VGSVMAFASVIAGKAITLAGLGPFEAIV----------LAVIAATAVGVVCGAINGTITA 130 Query: 143 VTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHG---AMPVIIFLVVAVIF 199 +P FI TLGM+ ARG A + Q + ++ G +PV+ + +A++F Sbjct: 131 RWSLPSFIITLGMLNIARGAALQASNAQTIYSFPLAFEDFGSAMFYGVPVVFMVALALVF 190 Query: 200 --HIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAAT 257 L +T +G+ Y IG N +A R +G +V R+ + ++I GL AG+A VV AR Sbjct: 191 IAWFILNFTVFGRLLYGIGNNEEAVRLAGHSVYRYKIAAFTICGLTAGIAAVVYMARLNI 250 Query: 258 GQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDI 317 G+ +EL+AIAA +IGGTSL GG G + GT+IGA I+GV+A+G +G+ +++ + Sbjct: 251 SSPIAGIGFELNAIAAVIIGGTSLNGGRGSVIGTLIGAFIIGVLANGLILIGLSDFMRQM 310 Query: 318 IKGLIIVIAVVIDQYRNK 335 I G++I+IAV++D YR K Sbjct: 311 ITGVVIIIAVILDYYRAK 328 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: 292 Number of extensions: 14 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: 332 Length adjustment: 28 Effective length of query: 312 Effective length of database: 304 Effective search space: 94848 Effective search space used: 94848 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 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