Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate GFF1918 PGA1_c19500 putative sugar-binding periplasmic protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__Phaeo:GFF1918 Length = 414 Score = 220 bits (560), Expect = 7e-62 Identities = 148/424 (34%), Positives = 205/424 (48%), Gaps = 23/424 (5%) Query: 13 LASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGAVAGGGGS 72 LA ++ L ++ A EV+HWW S GE AA+ V +G W D + GGG Sbjct: 8 LAGVATLAMTSAATADGIRAEVIHWWVSAGEAAAIKVFADAYTANGGEWIDNGIGGGG-- 65 Query: 73 TAMTVLKSRAVAGNPPGVAQIK-GPDIQEWGSTGLLSTDALKDVSKAENWDGLLSKKVSD 131 A T +R + G+ P V Q + +E GLL + L ++A NW L + + Sbjct: 66 -AKTTFVNRLMGGDAPQVGQFNTSREFEEIVDAGLLHS--LDAEAEAGNWSALFPGIIDN 122 Query: 132 TVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAGFIALAH 191 VK +G Y AVPVNIH NWLW N +V AG++ PT + F+ A + LK AG I LA Sbjct: 123 VVKRDGSYYAVPVNIHGSNWLWHNNQVMADAGLD-VPTDWDSFFEAAETLKEAGIIPLAV 181 Query: 192 GGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSF---AELKKITGYMDP 248 GG+ WQ+ F V+LSV G D Y + + D L+ EM + F + L+ + DP Sbjct: 182 GGEAWQERLTFNSVLLSVGGQDLYLRLFEEKDTTALTSDEMKEVFDVYSRLRTLVRETDP 241 Query: 249 NRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTYNID 308 GR WN A VI+G+A MQ+MGDWAK E+ +A G +Y C P Y I Sbjct: 242 GSPGRSWNDATNMVITGQAAMQIMGDWAKGEFLSAGMTPGVEYGCT--PAVIAGSPYMIS 299 Query: 309 SMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFDECA 368 K + D AQ +A L + Q F+ KGSIPVR D +D D C Sbjct: 300 GDVFVFPKTGNEEDREAQSLMATTMLDAEVQVAFNNIKGSIPVRPD----VDTSQLDVCG 355 Query: 369 QKS-AKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLASA 427 Q++ A D G Q ++ ++A GA+ DV T F N + +A L+ A Sbjct: 356 QQAIALTSNPDTHVGVTQMYISSDLA------GALQDVYTQFWNSETMTTEEAITLLSQA 409 Query: 428 VKAA 431 + A Sbjct: 410 YEIA 413 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: 467 Number of extensions: 20 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