Align D-gluconate TRAP transporter, periplasmic component (characterized)
to candidate WP_086509696.1 BZY95_RS09480 TRAP transporter substrate-binding protein
Query= reanno::psRCH2:GFF2082 (338 letters) >NCBI__GCF_002151265.1:WP_086509696.1 Length = 331 Score = 214 bits (544), Expect = 3e-60 Identities = 123/328 (37%), Positives = 190/328 (57%), Gaps = 8/328 (2%) Query: 1 MKRLLISTLAAALLGSTLSL-GYAQAAD--DIRPRMIRFGYGLNEDSNQGRAAKLLAEEV 57 MK STLA LG +L+L AQA+D D+ P +R + +NE AA E V Sbjct: 1 MKIFARSTLA---LGISLALVSTAQASDFADMDPVTLRLAHVVNEQDGFHIAAVKFQELV 57 Query: 58 AKASGGKLKVRTFASASLGSDDQMQNALIGGAQEMMVGSTATLVGISKEMAVWDTPFLFT 117 A+ + G + V + +ASLG + + + G +M V + + +EMAV++ PFLF Sbjct: 58 AERTEGAVSVDIYPNASLGDERTLLEGMQIGTVDMGVITNGPVANFVEEMAVFELPFLFP 117 Query: 118 DPRQADQVLDGPVGRQVMDKLEEKGLVGLVYWENGFRNVTNSARPIEKLEDFNGVKLRVM 177 P+ A +VLDGP+G++++DKL E L GL Y E GFRN+TNS RP+ ED NG+++RVM Sbjct: 118 SPQAAYEVLDGPIGQELLDKLAEVNLKGLAYAERGFRNLTNSERPVRSPEDLNGLRIRVM 177 Query: 178 PNPVFIDTFKRMGANAVPLPFSELFTALETKAVDGQENPFNTILSSKFYEVQKYLSVTNH 237 NPV+ DTF+ +GANA+P+ ++E TA++ +DGQENP N I S K +E Q +++++ H Sbjct: 178 ENPVYTDTFRELGANAIPMAWTEALTAMQQGTIDGQENPVNVIHSFKLHETQDHMTLSRH 237 Query: 238 VYSPWIVTVSKRWWDGLSATEQGILMEAAEKARDAEREDTRREASQALAALKERGMQINE 297 Y+P + + W+ L Q +L++AA++A + ER + L L+ GMQI Sbjct: 238 TYAPALFVMGMPAWNQLPEAAQEVLVQAAQEAAEHERRVNAEMEAGQLEELRAAGMQI-- 295 Query: 298 VSPDEIQRMREKAQPAIQTVIDAVGQEL 325 V +++ + +P + D G L Sbjct: 296 VDDADLEAFQAAVRPVYEKYGDQFGDYL 323 Lambda K H 0.315 0.131 0.368 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: 208 Number of extensions: 14 Number of successful extensions: 1 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: 338 Length of database: 331 Length adjustment: 28 Effective length of query: 310 Effective length of database: 303 Effective search space: 93930 Effective search space used: 93930 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: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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