Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate WP_068006982.1 PsAD2_RS14045 carbohydrate ABC transporter substrate-binding protein
Query= reanno::WCS417:GFF4324 (428 letters) >NCBI__GCF_001623255.1:WP_068006982.1 Length = 413 Score = 206 bits (525), Expect = 8e-58 Identities = 140/416 (33%), Positives = 207/416 (49%), Gaps = 27/416 (6%) Query: 1 MNAINRLAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWK 60 M +N L V ++ L++ +EV HWWTSGGE AAV V V G W Sbjct: 1 MKGLNALLVTAAL-----LASTTFTQAADLEVTHWWTSGGEAAAVRVFADAVNNSGHTWV 55 Query: 61 DGAVAGGGGATAMTVLKSRAVAGNPPGVAQIK-GPDIQEWASTGLLDTDVLKDVAKEEKW 119 D A+AGG A + + SR G+P Q+ G D ++ GL+ TD L +VA++E W Sbjct: 56 DSAIAGGDNARPVII--SRISGGDPMQATQLNTGRDAEDLIRAGLM-TD-LTEVAEKEGW 111 Query: 120 -DSLLDKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDK 178 D + K+ D+ +YEG VPVNIH W+W+N +V+++ G+ PT EF + Sbjct: 112 ADIIRPAKLLDSCRYEGRIYCVPVNIHSFQWMWLNRKVYEQNGLAV-PTNWSEFVQSAPT 170 Query: 179 LKAAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELK 238 L+ G PLA GG+PWQ S + ++V G D Y+K A +GPEM K Sbjct: 171 LRDKGITPLAVGGEPWQLSGMSGVFQVAVGGVDLYRKIKAQKSVEAASGPEMRKVFQAFA 230 Query: 239 KVATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTD 298 D G+ WN VI GKA QIMGDWA+ E++ A++VAGKDY+C+ G + Sbjct: 231 DARDLGDNGHVGRAWNNATSMVITGKAAAQIMGDWAQGEFSMAEQVAGKDYDCLPGLGMN 290 Query: 299 KAFTYNIDSLAVFKQKDKG----TAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNK 354 DS F K G Q ++A +++ + Q F++ KGS+PVR D Sbjct: 291 PVLDTGGDSF--FFPKPVGDQPDVVKAQLEMASLLVSKAVQVDFNLKKGSLPVRGD---- 344 Query: 355 MDSYGFDSCAQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPK 410 +D +SC + L+D + + P+ + ++ QG D+ + N P+ Sbjct: 345 VDLNAANSCMKKGIA-ILSDPE--NILPATEQSFSSD--TQGQLEDLWVEFFNAPE 395 Lambda K H 0.314 0.131 0.388 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: 487 Number of extensions: 21 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: 428 Length of database: 413 Length adjustment: 32 Effective length of query: 396 Effective length of database: 381 Effective search space: 150876 Effective search space used: 150876 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: 42 (22.0 bits) S2: 50 (23.9 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