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 N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 354 bits (909), Expect = e-102 Identities = 218/506 (43%), Positives = 303/506 (59%), Gaps = 23/506 (4%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 +L + K F ALD VDL + GEVHAL+G+NGAGKSTLIK+L+ D G+V Sbjct: 12 VLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVEL 71 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRR--LGLVDWSRLRAD 120 G+V+ P P+ Q+ GI T+YQE NL P LSVAEN+Y GR PRR L ++DW ++R Sbjct: 72 DGRVIAP-STPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMIDWRQVRDG 130 Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180 A++LL L L L+ DAP+ VA +QMV IA+A+ ++AR++I+DEPT++L EV L Sbjct: 131 ARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELF 190 Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRH 240 +IA L+ R +++++V+H L +V A+ DR TV+RDG V VAD+ A +V MVGR Sbjct: 191 RVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVNAMVGRD 250 Query: 241 ---VEFERRKRRRPPGAVVLKVEGVTPA--APRLSAPGYLRQVSFAARGGEIVGLAGLVG 295 V +R PP A PA A L G L V R GE++GL GL+G Sbjct: 251 LPTVAGADAERAPPPDA--------PPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLG 302 Query: 296 AGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIR 355 +GRT+LARL+FG D G + + + + L+ P DA+ G+ L PE+RK G + S+R Sbjct: 303 SGRTELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVR 362 Query: 356 RNLSLPSLKALSALGQW--VDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLL 413 N+ L AL A W + + +L Q L IK AD ET +G LSGGNQQKV+L Sbjct: 363 ENIVL----ALQARQGWRGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVML 418 Query: 414 GRAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIV 473 R + P++LI+DEPTRGID+ AK E+ ++ A G+AV+ IS+E E+ DRI Sbjct: 419 ARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIA 478 Query: 474 VFREGVIVADLDAQTATEEGLMAYMA 499 V RE +L +TE ++A +A Sbjct: 479 VMRERRKAGELPG-GSTEARVLAMIA 503 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: 691 Number of extensions: 44 Number of successful extensions: 9 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: 505 Length adjustment: 34 Effective length of query: 481 Effective length of database: 471 Effective search space: 226551 Effective search space used: 226551 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 Apr 09 2024. 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