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 Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2881 Length = 496 Score = 364 bits (935), Expect = e-105 Identities = 213/501 (42%), Positives = 299/501 (59%), Gaps = 12/501 (2%) Query: 4 LDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFA 63 ++ V+K F VR L V + G V+ LLGENGAGKSTL+KIL+ + G V Sbjct: 5 VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64 Query: 64 GQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQA 123 G V P + GI I+QEFNL +L++A+N++LG E +R +D +R + Sbjct: 65 GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMREKTRE 124 Query: 124 LLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAII 183 L +GLPL+PD VR L VAE+Q+VEIA+A+ NARL+IMDEPTA L+ E +RL A++ Sbjct: 125 ALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFALM 184 Query: 184 AGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE- 242 AGLKA V++IY+SH+L EV+ D VMRDG VA A V M LMVGR + Sbjct: 185 AGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGRELAD 244 Query: 243 -FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301 F + GA + V G+T PG+ V F R GEI+G AGLVGAGRT+L Sbjct: 245 LFPPKLPAPQDGAPAITVRGLT-------VPGWAEGVDFEVRRGEILGFAGLVGAGRTEL 297 Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361 + G P AG V + +P++L+SPRDA + G+ + EDRK +G + +R NL+L Sbjct: 298 FEGLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLM 357 Query: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421 +L+ + W+D AE+ + Q+ I+ E LSGGNQQK+ L + + P Sbjct: 358 ALERYAK--PWLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHPGP 415 Query: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481 V+++DEPTRG+D+GAK E++ ++ LA+ G+AV+VISSEL E++ + R+ V R G + Sbjct: 416 SVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGRLQ 475 Query: 482 ADLDAQTATEEGLMAYMATGT 502 L TEE L+A+ ATGT Sbjct: 476 TTLQEPHLTEEELIAH-ATGT 495 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: 681 Number of extensions: 39 Number of successful extensions: 7 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: 515 Length of database: 496 Length adjustment: 34 Effective length of query: 481 Effective length of database: 462 Effective search space: 222222 Effective search space used: 222222 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