Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate Pf6N2E2_523 Inositol transport system ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_523 Length = 517 Score = 952 bits (2462), Expect = 0.0 Identities = 486/518 (93%), Positives = 503/518 (97%), Gaps = 1/518 (0%) Query: 1 MFASATASSIPLVGVQPNAIPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMG 60 MFASATASS P + +P+ IP DEPYLLE++NVSKGFPGVVALSDVQLRVRPGSVLALMG Sbjct: 1 MFASATASSAPAMTFRPDVIP-DEPYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMG 59 Query: 61 ENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIA 120 ENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIA Sbjct: 60 ENGAGKSTLMKIIAGIYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIA 119 Query: 121 ENIWIGREQLNGFHMIDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVS 180 ENIWIGREQLNG HM+DH EMHRCTA+LLERLRI LDPEEQVGNLSIAERQMVEIAKAVS Sbjct: 120 ENIWIGREQLNGLHMVDHGEMHRCTARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVS 179 Query: 181 YDSDILIMDEPTSAITDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDG 240 YDSDILIMDEPTSAIT+ EVAHLFSIIADLK+QGKGIIYITHKMNEVF+IADEVAVFRDG Sbjct: 180 YDSDILIMDEPTSAITETEVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDG 239 Query: 241 AYIGLQRADSMDGDSLISMMVGRELSQLFPVREKPIGDLLMSVRDLRLDGVFKGVSFDLH 300 AYIGLQRADSMDGDSLISMMVGRELSQLFPVRE+PIGDL++SVRDL LDG+FKGVSFDLH Sbjct: 240 AYIGLQRADSMDGDSLISMMVGRELSQLFPVREQPIGDLVLSVRDLSLDGIFKGVSFDLH 299 Query: 301 AGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDR 360 AGEILGIAGLMGSGRTNVAEAIFG+TPS GGEI LDGQPVRISDPHMAIEKGFALLTEDR Sbjct: 300 AGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEILLDGQPVRISDPHMAIEKGFALLTEDR 359 Query: 361 KLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLS 420 KLSGLFPCLSVLENMEMAVLPHY GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLS Sbjct: 360 KLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLS 419 Query: 421 GGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPE 480 GGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPE Sbjct: 420 GGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPE 479 Query: 481 VLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMS 518 VLGMSDRVMVMHEGDLMGTL+R EATQERVMQLASG+S Sbjct: 480 VLGMSDRVMVMHEGDLMGTLNRGEATQERVMQLASGLS 517 Lambda K H 0.321 0.137 0.391 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: 1012 Number of extensions: 21 Number of successful extensions: 6 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: 521 Length of database: 517 Length adjustment: 35 Effective length of query: 486 Effective length of database: 482 Effective search space: 234252 Effective search space used: 234252 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 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