Align m-Inositol ABC transporter, permease component (iatP) (characterized)
to candidate GFF3462 PS417_17725 ribose ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_21390 (340 letters) >FitnessBrowser__WCS417:GFF3462 Length = 330 Score = 225 bits (573), Expect = 1e-63 Identities = 126/308 (40%), Positives = 189/308 (61%), Gaps = 18/308 (5%) Query: 33 IGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLAL 92 +GLV I+ +FL S L + QVSI ++A+G+T VI+T GIDLS G V+AL Sbjct: 36 VGLVVVTLVMILASDTFLTASN-LSNIARQVSINAIIAVGMTCVILTGGIDLSVGPVMAL 94 Query: 93 SAMIAASLAQTSDFARAVFPSLTDLPVWIPVIAGLGVGLLAGAINGSIIAVTGIPPFIAT 152 S + A L + LP + + AG+ +G+ G NG +A +PP I T Sbjct: 95 SGTLTAGLM------------VAGLPPGLAIGAGMLIGVAFGIGNGLFVAYLHMPPIIVT 142 Query: 153 LGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAM-----PVIIFLVVAVIFHIALRYTK 207 L M ARGL YT+G P+S L D + G ++ P++I L+ ++ ++ L++T+ Sbjct: 143 LATMGIARGLGLMYTDGYPISGLPDWFAFFGRESLFGIQVPILIMLLTYLVAYVLLQHTR 202 Query: 208 YGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAATGQAGMGMSYE 267 G+Y YAIGGN +A R SG+ R ++VY I+GL A +AG+V ++R +GQ G+S+E Sbjct: 203 IGRYIYAIGGNEEAVRLSGVRAARFKLLVYGISGLTAAIAGLVLTSRLMSGQPNAGVSFE 262 Query: 268 LDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVIAV 327 LDAIAA V+GG S+AGG G I GT++GA++LGV+ +G +GV Y+Q +IKG II++A+ Sbjct: 263 LDAIAAVVLGGASIAGGRGVIVGTLLGAMLLGVLNNGLNMLGVSPYVQSVIKGGIILLAI 322 Query: 328 VIDQYRNK 335 I + R+K Sbjct: 323 FISRQRHK 330 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: 286 Number of extensions: 14 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: 330 Length adjustment: 28 Effective length of query: 312 Effective length of database: 302 Effective search space: 94224 Effective search space used: 94224 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