Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate SMc04396 SMc04396 periplasmic binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__Smeli:SMc04396 Length = 414 Score = 362 bits (930), Expect = e-105 Identities = 189/422 (44%), Positives = 260/422 (61%), Gaps = 12/422 (2%) Query: 11 ISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGG 70 ++ +++AL L+ AA + +VEV+HWWTSGGE AA+DVLK +E G +W D VAGGG Sbjct: 5 MTTTAVAALMLAATAARAAENVEVLHWWTSGGEAAALDVLKKDLESKGISWTDMPVAGGG 64 Query: 71 GSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAENWDGLLSKKVS 130 G+ AMTVL++R AGN P Q+ G DI +W G L L +V+ E WD ++ + Sbjct: 65 GTEAMTVLRARVTAGNAPTAVQMLGFDILDWAKEGALGN--LDEVAAKEGWDKVVPAALQ 122 Query: 131 DTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIALA 190 KY+G ++A PVN+H NW+WIN KAG K PTT EE A DK K G +A Sbjct: 123 QFSKYDGHWIAAPVNVHSTNWVWINKAALDKAGA-KEPTTWEELIALLDKFKEQGITPIA 181 Query: 191 HGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGYMDPNR 250 HGGQPWQD+T+F+ VVLS +G D YK+A +DLD L G +M ++F + K+ Y+D N Sbjct: 182 HGGQPWQDATIFDAVVLS-LGNDFYKQAFIDLDPAALGGDKMKEAFDRMTKLRSYVDDNF 240 Query: 251 AGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNIDSM 310 +GRDWN+A+A VI KAG+Q MGDWAK E+ AKK+ G D+ C+ FPGT+ + T+N D Sbjct: 241 SGRDWNLASAMVIENKAGLQFMGDWAKGEFLKAKKVPGTDFVCMRFPGTQGSVTFNSDQF 300 Query: 311 AVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECAQK 370 A+FK+ D+ + AQ +A FQ F++ KGS+P R D + FD C +K Sbjct: 301 AMFKVSEDK---VPAQLQMASAIESPAFQSAFNVVKGSVPARTD----VPDTDFDACGKK 353 Query: 371 SAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASAVKA 430 KD + G L SMAH A AV+ AI+DVVT N + + +A +L +AV+A Sbjct: 354 GIKDLAEANTNGTLFGSMAHGHANPAAVKNAIYDVVTRQFNG-ELNSEEAVTELVAAVEA 412 Query: 431 AQ 432 A+ Sbjct: 413 AK 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: 521 Number of extensions: 24 Number of successful extensions: 6 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: 414 Length adjustment: 32 Effective length of query: 400 Effective length of database: 382 Effective search space: 152800 Effective search space used: 152800 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: 50 (23.9 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