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 WP_012385783.1 BIND_RS14440 sugar ABC transporter ATP-binding protein
Query= TCDB::G4FGN3 (494 letters) >NCBI__GCF_000019845.1:WP_012385783.1 Length = 518 Score = 426 bits (1094), Expect = e-123 Identities = 233/495 (47%), Positives = 338/495 (68%), Gaps = 10/495 (2%) Query: 4 ILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE-II 62 ILE++++ K F V AL+ VS+E GE+HA++GENGAGKSTLMKI++G Y PD G I+ Sbjct: 11 ILEMRNVSKTFGSVKALRDVSLEIREGEIHALMGENGAGKSTLMKILSGAYIPDPGSTIL 70 Query: 63 YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122 + + V P A GI ++QEL++ NL+VAENI++G E +RG +D M + Sbjct: 71 LDNKPVSITGPLAARELGISIIYQELALAPNLTVAENIYLGREIRRGGLVDRAAMIAGSA 130 Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182 K + + G ++ + SIA +Q+VEIARAV+ +++L++DEPT++LT++ET++LFE Sbjct: 131 KVL-QRLGATFQAKDLVQSLSIAERQLVEIARAVHAHSRILVMDEPTTTLTERETDRLFE 189 Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242 V++L+E G++II+ISHR+ EI+ + D+VS+LRDG YIGT + +T + +V+MMVGR L Sbjct: 190 TVRALREDGLSIIYISHRMNEIYALSDRVSILRDGTYIGTLDHDEITPDAVVKMMVGRDL 249 Query: 243 EKFYIKE--AHEP-GEVVLEVKNLS-GERFENVSFSLRRGEILGFAGLVGAGRTELMETI 298 FY KE AH+ G ++L VKN+ +R + SF L GE+LG AGLVG+GRTEL I Sbjct: 250 TSFYKKEHDAHDGRGNIILSVKNIGDSKRIFDCSFDLHEGEVLGIAGLVGSGRTELARLI 309 Query: 299 FGFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDR 358 +G +R G I + G+ +I +AIE G+ + EDRK+LGL L MS+ N++L R Sbjct: 310 YGVDRRRSGIIMLNGESKKIASVSEAIEAGLLYLTEDRKQLGLFLDMSVGENINLGVASR 369 Query: 359 -IKKGPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILI 417 KG F+ + +E AD AI I+ P V LSGGNQQKV+L++ L LKP++LI Sbjct: 370 DAYKGCFLKLGKARERADAAIGDLSIKVKSPKTPVGALSGGNQQKVLLSRLLELKPRVLI 429 Query: 418 LDEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGII- 476 LDEPTRGID+GAK+EIYR+++ L K G+GVI+ISSELPE++ + DR+ VMS G++AG + Sbjct: 430 LDEPTRGIDIGAKSEIYRLINDLVKSGIGVIVISSELPEIVGVCDRVLVMSEGRIAGTVG 489 Query: 477 --DAKEASQEKVMKL 489 DA +QE ++ L Sbjct: 490 GPDAPPITQENIIAL 504 Score = 87.4 bits (215), Expect = 1e-21 Identities = 65/243 (26%), Positives = 123/243 (50%), Gaps = 14/243 (5%) Query: 257 VLEVKNLSG-----ERFENVSFSLRRGEILGFAGLVGAGRTELMETIFG-FRPKRGGEIY 310 +LE++N+S + +VS +R GEI G GAG++ LM+ + G + P G I Sbjct: 11 ILEMRNVSKTFGSVKALRDVSLEIREGEIHALMGENGAGKSTLMKILSGAYIPDPGSTIL 70 Query: 311 IEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKKGPFISFKRE 370 ++ K V I PL A E GI ++ ++ L L +++ N+ L I++G + R Sbjct: 71 LDNKPVSITGPLAARELGISIIYQE---LALAPNLTVAENIYLGR--EIRRGGLVD--RA 123 Query: 371 KELADWAIKTFDIRPAYPDRKVLY-LSGGNQQKVVLAKWLALKPKILILDEPTRGIDVGA 429 +A A + + + ++ LS +Q V +A+ + +IL++DEPT + Sbjct: 124 AMIAGSAKVLQRLGATFQAKDLVQSLSIAERQLVEIARAVHAHSRILVMDEPTTTLTERE 183 Query: 430 KAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEASQEKVMKL 489 ++ + L ++G+ +I IS + E+ +SDR++++ G G +D E + + V+K+ Sbjct: 184 TDRLFETVRALREDGLSIIYISHRMNEIYALSDRVSILRDGTYIGTLDHDEITPDAVVKM 243 Query: 490 AAG 492 G Sbjct: 244 MVG 246 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: 664 Number of extensions: 28 Number of successful extensions: 9 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: 518 Length adjustment: 34 Effective length of query: 460 Effective length of database: 484 Effective search space: 222640 Effective search space used: 222640 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 24 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