Align D-gluconate TRAP transporter, periplasmic component (characterized)
to candidate WP_090448376.1 BLS63_RS24280 TRAP transporter substrate-binding protein
Query= reanno::psRCH2:GFF2082 (338 letters) >NCBI__GCF_900100495.1:WP_090448376.1 Length = 337 Score = 544 bits (1401), Expect = e-159 Identities = 274/337 (81%), Positives = 306/337 (90%), Gaps = 1/337 (0%) Query: 1 MKRLLISTLAAALLGSTLSLGYAQAADDIRPRMIRFGYGLNEDSNQGRAAKLLAEEVAKA 60 M+R LI+ LAAA+L S L+ AQA D+IRPRMIRFGYGLNEDSNQGRAAKLLAEEVA+A Sbjct: 1 MRRFLIAGLAAAILSSPLAALAAQA-DEIRPRMIRFGYGLNEDSNQGRAAKLLAEEVARA 59 Query: 61 SGGKLKVRTFASASLGSDDQMQNALIGGAQEMMVGSTATLVGISKEMAVWDTPFLFTDPR 120 S GKLK+RTF +ASLG+D+QMQNALIGGAQEMMVGSTATLVGISKEMAVWDTPFLF+ + Sbjct: 60 SDGKLKLRTFGAASLGADNQMQNALIGGAQEMMVGSTATLVGISKEMAVWDTPFLFSSEQ 119 Query: 121 QADQVLDGPVGRQVMDKLEEKGLVGLVYWENGFRNVTNSARPIEKLEDFNGVKLRVMPNP 180 QAD VLDGPVGRQVMDKLEEKGLVGLVYWENGFRN+TN+ RPI KLE+F+G+KLRVMPNP Sbjct: 120 QADAVLDGPVGRQVMDKLEEKGLVGLVYWENGFRNMTNNVRPITKLEEFSGIKLRVMPNP 179 Query: 181 VFIDTFKRMGANAVPLPFSELFTALETKAVDGQENPFNTILSSKFYEVQKYLSVTNHVYS 240 VF++TFK MGANAVPLPFSELFTALETKAVDGQENP+NTILSSKFYEVQKYL+VTNHVYS Sbjct: 180 VFLETFKLMGANAVPLPFSELFTALETKAVDGQENPYNTILSSKFYEVQKYLTVTNHVYS 239 Query: 241 PWIVTVSKRWWDGLSATEQGILMEAAEKARDAEREDTRREASQALAALKERGMQINEVSP 300 PWIVT SKRWWDGLS TEQGI+M AA KARD ER+DTR EA++AL L+ GMQ+N++S Sbjct: 240 PWIVTASKRWWDGLSQTEQGIIMAAAIKARDFERQDTRAEAAKALEQLQANGMQVNQISA 299 Query: 301 DEIQRMREKAQPAIQTVIDAVGQELFDQVQAEVEKAA 337 +E QRMR+KAQPAIQ VID+VGQELFDQVQAE KAA Sbjct: 300 EETQRMRDKAQPAIQQVIDSVGQELFDQVQAEAAKAA 336 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: 397 Number of extensions: 9 Number of successful extensions: 2 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: 337 Length adjustment: 28 Effective length of query: 310 Effective length of database: 309 Effective search space: 95790 Effective search space used: 95790 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 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