Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate HSERO_RS22730 HSERO_RS22730 sugar ABC transporter substrate-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__HerbieS:HSERO_RS22730 Length = 446 Score = 207 bits (528), Expect = 4e-58 Identities = 130/404 (32%), Positives = 195/404 (48%), Gaps = 13/404 (3%) Query: 26 AESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGGGSTAMTVLKSRAVAG 85 A + GS++V+HWWTS E+ A++V+ Q+ K W+D A+ GG G A VLKS +A Sbjct: 48 ATATGSLQVLHWWTSASERQAINVVVNQLAKQDIQWRDVAIPGGAGMGAAKVLKSMVLAN 107 Query: 86 NPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAENWDGLLSKKVSDTVKYEGDYVAVPVN 145 P V Q+ G EW GLL L +V+ NW+ + V + G VA P+ Sbjct: 108 RAPEVTQLNGVVFGEWADLGLLLE--LDNVAVQGNWEKQMFPTVWSLLNNHGHVVAAPLG 165 Query: 146 IHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIALAHGGQPWQDSTVFEDV 205 IHR+N L+ N VFK+ + P T +EF KL+ +G + LA + WQ +T+FE++ Sbjct: 166 IHRINSLYYNVAVFKRYNLSP-PKTWDEFDQIVKKLQGSGVVPLAQSAEAWQLATLFENL 224 Query: 206 VLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYMDPNRAGRDWNIAAADVISG 265 L+ G Y+K V++ M L+ + G M R W A ++SG Sbjct: 225 ALAESGPAYYRKLFVEMSPAAYLDARMLHILKRLRALAGAMAQPVRERPWTEVARSMVSG 284 Query: 266 KAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNIDSMAVFKLKADRKGDIAA 325 +A M +MGDWAK E A + + C PGT + Y+ D++A+F A Sbjct: 285 EAAMLIMGDWAKGELNAWGMEVDQQFGCAPAPGTGEYHLYSTDTLAMF---AGNYAHQPM 341 Query: 326 QQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECAQKSAKDFIADDKTGGLQ 385 Q+ LA++ + Q ++ KGSIPV MD+ CA+ S + F Sbjct: 342 QETLARLTMSPAVQSEYNRIKGSIPVLRAADPHMDR-----CARDSWRTFSKGPMWQA-- 394 Query: 386 PSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASAVK 429 PS+ H MAT + AI V F D+ +A +LA+ + Sbjct: 395 PSLVHRMATDDTTKDAIVAEVQRFFMDRSISEEQAQKRLATIAR 438 Lambda K H 0.314 0.129 0.377 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: 416 Number of extensions: 18 Number of successful extensions: 5 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: 432 Length of database: 446 Length adjustment: 32 Effective length of query: 400 Effective length of database: 414 Effective search space: 165600 Effective search space used: 165600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 51 (24.3 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