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 WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= TCDB::B8H229 (515 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 284 bits (726), Expect = 6e-81 Identities = 176/507 (34%), Positives = 278/507 (54%), Gaps = 16/507 (3%) Query: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 ++++ + K FPG+ A D V L V GE+HALLGENGAGKSTL+ +L + + G + Sbjct: 4 VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63 Query: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 G+ + D P +LGI ++Q F L + +V EN+ LG+EP G ++ + + Sbjct: 64 KGKPVKITD-PNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVE 122 Query: 123 ALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAI 182 + GL ++P A ++ ++V QQ VEI K + A ++I DEPTAAL+ +E+ L I Sbjct: 123 TISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182 Query: 183 IAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHVE 242 + L + S+I ++H+L E+ +CDR TV+R GR + + D+++ + +MVGR V Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242 Query: 243 FERRKRRRPPGAVVLKVEGVTPAAPR-LSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301 F K P VL+++ + R ++A + + GEI+G+AG+ G G+T+L Sbjct: 243 FSVEKDPAQPKDAVLQIKDLVVKDSRDITA---VNDLHLEVHAGEILGVAGVDGNGQTEL 299 Query: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361 I G G + ++ + + +PR AG+ +P+DR + G LD ++ N+ L Sbjct: 300 IEAITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQ 359 Query: 362 SL--KALSALG----QWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGR 415 + K S G + ++A +L+E Y ++ T LSGGNQQK ++ R Sbjct: 360 TYYQKPYSTSGVLNFNEIYKKA-NELIEDY----DVRTPSEHTLARALSGGNQQKAIIAR 414 Query: 416 AMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF 475 + +P +LI +PTRG+D+GA +H L D G AV++IS EL EV+ VSDRI V Sbjct: 415 EVDRSPDLLIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVI 474 Query: 476 REGVIVADLDAQTATEEGLMAYMATGT 502 EG IVA +DA E L MA G+ Sbjct: 475 YEGKIVAIVDADKTNENELGLLMAGGS 501 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: 557 Number of extensions: 21 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: 509 Length adjustment: 35 Effective length of query: 480 Effective length of database: 474 Effective search space: 227520 Effective search space used: 227520 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