Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate Pf1N1B4_1243 ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1243 Length = 521 Score = 254 bits (650), Expect = 4e-72 Identities = 159/474 (33%), Positives = 251/474 (52%), Gaps = 12/474 (2%) Query: 4 LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63 L + ++SK +PG A D +DL + GE+HALLGENGAGKSTL+KI+ AD+G + + Sbjct: 14 LQLRRISKRYPGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMIWQ 73 Query: 64 GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWS--RLRADA 121 GQ + R+ P + + LGI ++Q F+LF LSVA+N+ L +G + +L Sbjct: 74 GQRVTMRN-PAQARGLGIGMVFQHFSLFETLSVAQNIALA-----MGAAAGTPKQLEPKI 127 Query: 122 QALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 + + G+ L P+ V L++ E+Q VEI + + + RL+I+DEPT+ L+ +E D L Sbjct: 128 REVSQRYGMALEPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFV 187 Query: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 + L A S++++SH+LGEV+A+C TV+R GR A + +LMVG Sbjct: 188 TLRRLAAEGCSILFISHKLGEVRALCHSATVLRGGRVAGHCVPAQCSDRQLAQLMVGEAA 247 Query: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301 E + L V G++ P L+ + F R GEIVG+AG+ G G+ +L Sbjct: 248 ELITDYPKVMGADAFLSVTGLSWHNPDPFGCS-LKNIDFDVRSGEIVGVAGVAGNGQDEL 306 Query: 302 ARLIFGADPIA---AGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNL 358 L+ G + + + + +P+ P + G+ VP +R G + S+ N Sbjct: 307 LALLSGEERLPRDDSATISFGGQPVAHLRPDARRKLGLAFVPAERLGHGAVPELSLADNA 366 Query: 359 SLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMA 418 L + + V + L E ++ +K D+ LSGGN QK +LGR + Sbjct: 367 LLTAFQQGLVSHGLVQRGKVQALAEDIIRRFGVKTPDSLAPARSLSGGNLQKFILGREIL 426 Query: 419 LTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRI 472 PK+L+ PT G+D+GA A +H+ L L D G A++VIS +L E+ + DR+ Sbjct: 427 QQPKLLVAAHPTWGVDVGAAATIHRALIALRDAGAAILVISEDLDELFQICDRL 480 Score = 71.2 bits (173), Expect = 8e-17 Identities = 59/233 (25%), Positives = 107/233 (45%), Gaps = 13/233 (5%) Query: 18 ALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAA---DAGTVTFAGQVLDPRDAPL 74 +L +D V GE+ + G G G+ L+ +LS D+ T++F GQ + P Sbjct: 279 SLKNIDFDVRSGEIVGVAGVAGNGQDELLALLSGEERLPRDDSATISFGGQPV-AHLRPD 337 Query: 75 RRQQLGIATIYQE---FNLFPELSVAENMYLGREPRRL---GLVDWSRLRADAQALLNDL 128 R++LG+A + E PELS+A+N L + L GLV +++A A+ ++ Sbjct: 338 ARRKLGLAFVPAERLGHGAVPELSLADNALLTAFQQGLVSHGLVQRGKVQALAEDIIRRF 397 Query: 129 GLPLNPD--APVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGL 186 G+ PD AP R L+ Q + + + +L++ PT + +H + L Sbjct: 398 GVK-TPDSLAPARSLSGGNLQKFILGREILQQPKLLVAAHPTWGVDVGAAATIHRALIAL 456 Query: 187 KARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGR 239 + +++ +S L E+ +CDR + G+ D ++D+ M G+ Sbjct: 457 RDAGAAILVISEDLDELFQICDRLGALCGGQLSPLQATVDTHLSDVGGWMAGQ 509 Score = 62.8 bits (151), Expect = 3e-14 Identities = 58/209 (27%), Positives = 97/209 (46%), Gaps = 12/209 (5%) Query: 272 PGYLRQ--VSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPR 329 PG L + + GEI L G GAG++ L ++I+G +G ++ + + +R+P Sbjct: 24 PGCLANDAIDLSIAPGEIHALLGENGAGKSTLMKIIYGVTHADSGEMIWQGQRVTMRNPA 83 Query: 330 DAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWVDERAERDLVETYRQKL 389 A GI +V + F S+ +N++L A Q E R++ + Y L Sbjct: 84 QARGLGIGMVFQ---HFSLFETLSVAQNIALAMGAAAGTPKQL--EPKIREVSQRYGMAL 138 Query: 390 RIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLA 449 + E + LS G +Q+V + R + ++LI+DEPT + E+ L LA Sbjct: 139 -----EPERLVHSLSIGERQRVEIIRCLMQDIRLLILDEPTSVLTPQEADELFVTLRRLA 193 Query: 450 DLGVAVVVISSELAEVMAVSDRIVVFREG 478 G +++ IS +L EV A+ V R G Sbjct: 194 AEGCSILFISHKLGEVRALCHSATVLRGG 222 Lambda K H 0.320 0.136 0.380 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: 602 Number of extensions: 29 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 515 Length of database: 521 Length adjustment: 35 Effective length of query: 480 Effective length of database: 486 Effective search space: 233280 Effective search space used: 233280 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