Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA
Query= TCDB::G4FGN3 (494 letters) >FitnessBrowser__Caulo:CCNA_00903 Length = 515 Score = 374 bits (961), Expect = e-108 Identities = 201/498 (40%), Positives = 319/498 (64%), Gaps = 11/498 (2%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIY 63 +L+V + K FPGV AL V + GEVHA++GENGAGKSTL+KI++ + D G + + Sbjct: 3 LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62 Query: 64 EGRGVR-WNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122 G+ + + P GI T++QE ++ LSVAEN+++G E +R +D+ ++ +A+ Sbjct: 63 AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRADAQ 122 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 + + G+ ++P+ + ++A QQMVEIA+A+ A+++I+DEPT++L+ +E ++L Sbjct: 123 ALLND-LGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLHA 181 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 ++ LK + V++I++SHRL E+ +CD+ +V+RDG ++ + + ++ +V +MVGR + Sbjct: 182 IIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRHV 241 Query: 243 EKFYIKEAHEPGEVVLEVKNLSGER--------FENVSFSLRRGEILGFAGLVGAGRTEL 294 E K PG VVL+V+ ++ VSF+ R GEI+G AGLVGAGRT+L Sbjct: 242 EFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDL 301 Query: 295 METIFGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLP 354 IFG P G + ++ K + + P DAI+ GI LVPEDRK+ G L SI N+SLP Sbjct: 302 ARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLP 361 Query: 355 SLDRIKK-GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKP 413 SL + G ++ + E++L + + I+ A + + LSGGNQQKV+L + +AL P Sbjct: 362 SLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTP 421 Query: 414 KILILDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLA 473 K+LI+DEPTRGID+GAKAE+++++S LA GV V++ISSEL EV+ +SDRI V G + Sbjct: 422 KVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIV 481 Query: 474 GIIDAKEASQEKVMKLAA 491 +DA+ A++E +M A Sbjct: 482 ADLDAQTATEEGLMAYMA 499 Score = 66.2 bits (160), Expect = 3e-15 Identities = 62/241 (25%), Positives = 100/241 (41%), Gaps = 22/241 (9%) Query: 261 KNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGFRPKRGGEIYIEGKRVEIN 319 K+ G R + V + GE+ G GAG++ L++ + G + G+ ++ Sbjct: 11 KSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTFAGQVLD-- 68 Query: 320 HPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKREKELADWAIK 379 P DA P R++LG+ I + P L + R L DW+ Sbjct: 69 -PRDA--------PLRRQQLGIATIYQEFN--LFPELSVAENMYLGREPRRLGLVDWSRL 117 Query: 380 TFDIR--------PAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGAKA 431 D + P PD V L+ QQ V +AK + L +++I+DEPT + Sbjct: 118 RADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVD 177 Query: 432 EIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKLAA 491 ++ I++ L V VI +S L EV M DR VM G+ D + +++L Sbjct: 178 RLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237 Query: 492 G 492 G Sbjct: 238 G 238 Lambda K H 0.318 0.138 0.385 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: 640 Number of extensions: 28 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: 494 Length of database: 515 Length adjustment: 34 Effective length of query: 460 Effective length of database: 481 Effective search space: 221260 Effective search space used: 221260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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