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 AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__azobra:AZOBR_RS31210 Length = 516 Score = 381 bits (978), Expect = e-110 Identities = 221/504 (43%), Positives = 315/504 (62%), Gaps = 14/504 (2%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 LL + +SK+F GV+ALD VD V GE+HALLGENGAGKSTLIK L+ + DAGTVT Sbjct: 12 LLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTL 71 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 G+ + PR Q+L I T+YQE NL P LSVAEN++LGR+P R GLVD +R A+ Sbjct: 72 EGRAIAPRGVE-EAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRRAR 130 Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 A+L GL L+ AP+ +VA QQ+V IA+A+ ++A+++I+DEPTA+L +EV L + Sbjct: 131 AVLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFKV 190 Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242 + L++R + +++V+H L +V A+CDR TV+R+GR V A++ D+V +M+GR +E Sbjct: 191 MRTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGRELE 250 Query: 243 FERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQV---SFAARGGEIVGLAGLVGAGRT 299 + P E P R G R V R GE+VGLAGL+G+GRT Sbjct: 251 AVAHRIAPPADDA---EEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRT 307 Query: 300 DLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359 + ARL+FG D G VD + +RLR PRDAI+ G PEDRK++G S+R N+ Sbjct: 308 ETARLVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENII 367 Query: 360 LPSLKALSALGQW---VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRA 416 L AL A W + + ++ + + + L I+ AE I LSGGNQQK LL R Sbjct: 368 L----ALQARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARW 423 Query: 417 MALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFR 476 +A P++LI+DEPTRGID+GA AE+ +++ L G+A++V+SSEL E++A S R+VV R Sbjct: 424 LATEPRLLILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLR 483 Query: 477 EGVIVADLDAQTATEEGLMAYMAT 500 + VA+L + ++A +A+ Sbjct: 484 DRRHVAELRGGEVAVDRIVAAIAS 507 Score = 72.8 bits (177), Expect = 3e-17 Identities = 71/251 (28%), Positives = 112/251 (44%), Gaps = 25/251 (9%) Query: 11 KSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVL--- 67 + + R+++ DL + GEV L G G+G++ +++ AD G GQ + Sbjct: 275 RGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETARLVFGMDRADRGEAAVDGQAVRLR 334 Query: 68 DPRDA--------PLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLR- 118 PRDA P R++ GI LSV EN+ L + R+ L R R Sbjct: 335 GPRDAIRLGFGFCPEDRKKEGIVGA---------LSVRENIILALQARQGWLRPIPRCRQ 385 Query: 119 ---ADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGRE 175 AD L D+ P + + P++ L+ QQ +A+ + RL+I+DEPT + Sbjct: 386 EEIADRFIRLLDIRTP-HAEQPIQLLSGGNQQKALLARWLATEPRLLILDEPTRGIDVGA 444 Query: 176 VDRLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRL 235 + +I L A ++++ VS L E+ A R V+RD R VA +V V +V Sbjct: 445 HAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAELRGGEVAVDRIVAA 504 Query: 236 MVGRHVEFERR 246 + V E R Sbjct: 505 IASESVPEEPR 515 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: 714 Number of extensions: 41 Number of successful extensions: 8 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: 515 Length of database: 516 Length adjustment: 35 Effective length of query: 480 Effective length of database: 481 Effective search space: 230880 Effective search space used: 230880 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