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_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)
Query= TCDB::B8H229 (515 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 Length = 514 Score = 383 bits (984), Expect = e-111 Identities = 224/501 (44%), Positives = 316/501 (63%), Gaps = 14/501 (2%) Query: 9 VSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD 68 + K+FPGV+ALD + V G+VHAL+GENGAGKSTL+KIL A+ +G + Q Sbjct: 21 IGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIGEQ--- 77 Query: 69 PRDAPLRRQQLG--IATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQALLN 126 R +G +A I+QE +L PE++VAEN++LG P GL++ LR A A L Sbjct: 78 KRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRGVLRQQALACLK 137 Query: 127 DLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHAIIAGL 186 L ++P V L++ ++Q+VEIAKA++ A +I DEPT++LS RE+DRL AII L Sbjct: 138 GLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIGRL 197 Query: 187 KARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVAS-GDVADVEVADMVRLMVGRHVEFER 245 + V+YVSHR+ EV +C+ TV +DGRFV + D++ + +V MVGR ++ Sbjct: 198 RDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQDIY 257 Query: 246 RKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLI 305 R RP GAV LKV+G L PG VSF A GEI+GL GLVGAGRT+L R++ Sbjct: 258 DYRSRPRGAVALKVDG-------LLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRML 310 Query: 306 FGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKA 365 G AGR+ + + L+L SPRDAI AGI+L PEDRK++G S+ N+++ + A Sbjct: 311 SGLTRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGA 370 Query: 366 LSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLI 425 S G + E+D + + L++K +A I LSGGNQQK +LGR +++ KVL+ Sbjct: 371 HSTFGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLL 430 Query: 426 VDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLD 485 +DEPTRGIDIGAKAE++Q++ +LA G+AV+V+SS+L EVM +SDRI+V EG + +L Sbjct: 431 LDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELT 490 Query: 486 AQTATEEGLMAYMATGTDRVA 506 + A E L+ +A RVA Sbjct: 491 REQANESNLL-QLALPRQRVA 510 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: 678 Number of extensions: 30 Number of successful extensions: 8 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: 514 Length adjustment: 35 Effective length of query: 480 Effective length of database: 479 Effective search space: 229920 Effective search space used: 229920 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