Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate WP_085985143.1 MICLODRAFT_RS06940 sugar ABC transporter substrate-binding protein
Query= reanno::Phaeo:GFF3639 (341 letters) >NCBI__GCF_000262405.1:WP_085985143.1 Length = 363 Score = 129 bits (324), Expect = 1e-34 Identities = 94/291 (32%), Positives = 143/291 (49%), Gaps = 31/291 (10%) Query: 56 YVSADAQSSSAKQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIE 115 Y +ADA S +Q S ++QG +++ D+ A V+ A +GI V+AYDR I Sbjct: 77 YQNADANVS--RQQQQFNSAVSQGAKVIVLDPVDSAAAASLVKQAQGQGIKVIAYDRPIP 134 Query: 116 DGRA-FYLTFDNVEVGRMQARAVLEAQPSGNY--------VMIKGSPTDPNADFLRGGQQ 166 D +A FY++FDN +G+ A ++++ N + I GSPTD A ++ G Sbjct: 135 DAKADFYVSFDNQAIGKSIADSLVQHLKKSNVTAGSGMGVLQINGSPTDAAAGLIKKG-- 192 Query: 167 EIIQAAIDSGDIKIVGEAYTDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAA 226 I +D+ I+ E T W P AQ+ +T + + VVA+NDGTAGG +AA Sbjct: 193 --IHEGLDNSGYPILAEFDTPEWAPPKAQQWASGQITRFNKNILGVVAANDGTAGGAIAA 250 Query: 227 LTAQGMEGI-AVSGQDGDHAALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGD 285 A GM + V+G D AAL + G Q ++ K + + AAAN+A+++ G Sbjct: 251 FKAAGMNPVPPVTGNDATIAALQLIIAGDQYNTISKPSEIVAAAAANVAIQLLGGE---- 306 Query: 286 VAGGAAWTSPAGTEL---TARFLEPIPVTADNLSV-VVDAGWITKEALCQG 332 T A T L ++ P +TADNL +++ T E LC G Sbjct: 307 -------TPKADTTLFNTPSKLFVPAVITADNLKAEIINKNINTAEQLCSG 350 Lambda K H 0.313 0.128 0.362 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: 223 Number of extensions: 13 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: 341 Length of database: 363 Length adjustment: 29 Effective length of query: 312 Effective length of database: 334 Effective search space: 104208 Effective search space used: 104208 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 (21.9 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