Align m-Inositol ABC transporter, ATPase component (itaA) (characterized)
to candidate PfGW456L13_7 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_21385 (521 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_7 Length = 521 Score = 257 bits (657), Expect = 6e-73 Identities = 162/491 (32%), Positives = 254/491 (51%), Gaps = 15/491 (3%) Query: 17 PNAIPVDEPY-LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAG 75 PN P+ +P L++ ++K +PG +A + L + PG + AL+GENGAGKSTLMKII G Sbjct: 2 PNHAPIPDPVPRLQLRRITKRYPGCLANDAIDLTIAPGEIHALLGENGAGKSTLMKIIYG 61 Query: 76 IYQPDAGELRLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGFHM 135 + D+GE+ +G+ V+ P A GI M+ Q +L +S+A+NI + G Sbjct: 62 VTHADSGEVIWQGQRVSLRNPAQARGLGIGMVFQHFSLFETLSVAQNIALAMGAAAG--- 118 Query: 136 IDHREMHRCTAQLLERLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAI 195 +++ ++ R + L+PE V +LSI ERQ VEI + + D +LI+DEPTS + Sbjct: 119 -TPKQLEPKIREVSRRYGMTLEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVL 177 Query: 196 TDKEVAHLFSIIADLKAQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDS 255 T +E LF + L A+G I++I+HK+ EV ++ V R G G Sbjct: 178 TPQEADDLFVTLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQ 237 Query: 256 LISMMVGRELSQLFPVREKPIGDLLMSVRDLRLDGV------FKGVSFDLHAGEILGIAG 309 L +MVG + + GD + VR L + ++ GEI+GIAG Sbjct: 238 LARLMVGEAAELIADYPKVTGGDACLDVRGLSWHNPDPFGCSLANIDLEVRRGEIVGIAG 297 Query: 310 LMGSGRTNVAEAIFG---ITPSDGGEICLDGQPVRISDPHMAIEKGFALLTEDRKLSGLF 366 + G+G+ + + G + + I +PV P + G A + +R G Sbjct: 298 VAGNGQDELLALLSGEALLPRNASATIRFGKEPVAHLRPDARRQLGLAFVPAERLGHGAV 357 Query: 367 PCLSVLENMEMAVLPH-YAGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQ 425 P LS+ +N + H NG IQ+ + AL E++ ++ VKTP + +LSGGN Q Sbjct: 358 PELSLADNALLTAFQHGLVSNGLIQRGKVEALAEEIIRRFGVKTPDSQAPARSLSGGNLQ 417 Query: 426 KALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMS 485 K +L R ++ PR+L+ PT G+DVGA A I+R + L G A+++IS +L E+ +S Sbjct: 418 KFILGREILQQPRLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQIS 477 Query: 486 DRVMVMHEGDL 496 DR+ + G L Sbjct: 478 DRLGALCGGRL 488 Score = 87.4 bits (215), Expect = 1e-21 Identities = 60/222 (27%), Positives = 113/222 (50%), Gaps = 9/222 (4%) Query: 295 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEICLDGQPVRISDPHMAIEKGFA 354 + + GEI + G G+G++ + + I+G+T +D GE+ GQ V + +P A G Sbjct: 32 IDLTIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEVIWQGQRVSLRNPAQARGLGIG 91 Query: 355 LLTEDRKLSGLFPCLSVLENMEMAVLPHYAGNGFIQQKALRALCEDMCKKLRVKTPSLEQ 414 ++ + LF LSV +N+ +A+ G K L ++ ++ + T E+ Sbjct: 92 MVFQH---FSLFETLSVAQNIALAM-----GAAAGTPKQLEPKIREVSRRYGM-TLEPER 142 Query: 415 CIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMI 474 + +LS G +Q+ + R LM + R+LILDEPT + +++ + LA+EG +++ I Sbjct: 143 LVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADDLFVTLRRLAAEGCSILFI 202 Query: 475 SSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 516 S +L EV + V+ G + G +E + +++ +L G Sbjct: 203 SHKLGEVRALCHSATVLRGGRVAGHCVPAECSDQQLARLMVG 244 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: 579 Number of extensions: 29 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 521 Length of database: 521 Length adjustment: 35 Effective length of query: 486 Effective length of database: 486 Effective search space: 236196 Effective search space used: 236196 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