Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate Ac3H11_2062 ABC-type sugar transport system, periplasmic component
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2062 Length = 416 Score = 426 bits (1096), Expect = e-124 Identities = 223/414 (53%), Positives = 279/414 (67%), Gaps = 12/414 (2%) Query: 18 ALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGGGSTAMTV 77 A+ L+ + S G VEV+H+WTSGGE +V LK ++ G TW+D AVAGGGG +AMTV Sbjct: 11 AVGLAAAMSASAGEVEVLHYWTSGGEAKSVAELKKIMQGKGHTWRDFAVAGGGGDSAMTV 70 Query: 78 LKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAENWDGLLSKKVSDTVKYEG 137 LKSR ++GNPP AQ KGP IQEW S G+L+ + ++KAE WD LL K V+D +KY+G Sbjct: 71 LKSRVISGNPPSAAQTKGPAIQEWASEGVLAN--MDTLAKAEKWDELLPKVVADVMKYKG 128 Query: 138 DYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIALAHGGQPWQ 197 YVA PVN+HRVNW+W + E KKAG+ P T +EF+AA DKLKAAG + +AHGGQ WQ Sbjct: 129 AYVAAPVNVHRVNWMWGSSEALKKAGVAAMPKTWDEFFAAADKLKAAGLVPVAHGGQNWQ 188 Query: 198 DSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYMDPNRAGRDWNI 257 D T FE VVL V GA Y+ ALV LD L+ M KS ++I GY DP GRDWN+ Sbjct: 189 DFTTFESVVLGVGGAKFYQDALVKLDNTALTSDTMKKSLETFRRIKGYTDPGAPGRDWNL 248 Query: 258 AAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNIDSMAVFKLK- 316 A A +I GKAG Q+MGDWAK E+ AA K GKD+ C A PG+ AFT+N+DS +FKLK Sbjct: 249 ATAMLIQGKAGFQLMGDWAKGEFLAAGKAPGKDFLCAAAPGSANAFTFNVDSFILFKLKD 308 Query: 317 -ADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECAQKSAKDF 375 A +K AQ DLA + FQ+VF++NKGSIPVR MDK FD+CA+ SAKDF Sbjct: 309 AAAQK----AQSDLASSIMSPAFQEVFNLNKGSIPVRAG--QPMDK--FDDCAKASAKDF 360 Query: 376 IADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASAVK 429 + K+GGL PS AH MA + A +GAI DVV+ F ND A A ++A+A K Sbjct: 361 VDTAKSGGLVPSAAHGMAIAPATEGAIKDVVSQFWNDDKVSVADAMKKIAAAAK 414 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: 611 Number of extensions: 25 Number of successful extensions: 4 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: 416 Length adjustment: 32 Effective length of query: 400 Effective length of database: 384 Effective search space: 153600 Effective search space used: 153600 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