Align Maltodextrin-binding protein (characterized, see rationale)
to candidate BWI76_RS01830 BWI76_RS01830 maltose ABC transporter substrate-binding protein MalE
Query= uniprot:Q9RHZ6 (427 letters) >FitnessBrowser__Koxy:BWI76_RS01830 Length = 396 Score = 180 bits (457), Expect = 6e-50 Identities = 126/383 (32%), Positives = 194/383 (50%), Gaps = 18/383 (4%) Query: 48 ASALPKGQTITVWSWQTGPE-LQDVKQIAAQWAKAHGDKVIVVDQSSNPKGFQFYATAAR 106 ASAL K + + W G + + ++ ++ K G KV V + F A Sbjct: 22 ASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVSVEHPDKLEEKFP---QVAA 78 Query: 107 TGKGPDVVFGMPHDNNGVFAEEGLMAPV-PSGVLNTGLYAPNTIDAIKVNGTMYSVPVSV 165 TG GPD++F HD G +A+ GL+A + P LY P T DA++ NG + + PV+V Sbjct: 79 TGDGPDIIF-WAHDRFGGYAQSGLLAEISPDKAFQDKLY-PFTWDAVRYNGKLIAYPVAV 136 Query: 166 QVAAIYYNKKLVPQPPQTWAEFV---KDANAHG---FMYDQANLYFDYAIIGGYGGYVFK 219 + ++ YNK LVP PP+TW E K+ A G M++ YF + +I GGY FK Sbjct: 137 EALSLIYNKDLVPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFK 196 Query: 220 DNNGTLDPNNIGLDTPGAVQAYTLMRDMVSKYHWMTPSTNGSIAKAEFLAGKIGMYVSGP 279 NG D N+G+D+ GA T + D++ H M T+ SIA+A F G+ M ++GP Sbjct: 197 FENGKYDVKNVGVDSAGAKAGLTFLVDLIKNKH-MNADTDYSIAEAAFNKGETAMTINGP 255 Query: 280 WDTADIEKAKIDFGVTPWPTLPNGKHATPFLGVITAFVNKES-KTQAADWSLVQALTSAQ 338 W ++I+K+K+++GVT PT G + PF+GV++A +N S + A L L + Q Sbjct: 256 WAWSNIDKSKVNYGVTLLPTF-KGNASKPFVGVLSAGINAASPNKELAKEFLENYLMTDQ 314 Query: 339 AQQMYFRDSQQIPALLSVQRSSAVQSSPTFKAFVEQLRYAVPMPNIPQMQAVWQAM-SIL 397 +D + + A+ ++ P A + + MPNIPQM A W A+ + + Sbjct: 315 GLDEVNKD-KPLGAVALKSFQEKLEKDPRIAATMANAQKGEIMPNIPQMSAFWYAVRTAV 373 Query: 398 QNIIAGKVSPEQGAKDFVQNIQK 420 N +G+ + E KD I K Sbjct: 374 INAASGRQTVEAALKDAQSRITK 396 Lambda K H 0.315 0.130 0.392 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: 441 Number of extensions: 35 Number of successful extensions: 7 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: 427 Length of database: 396 Length adjustment: 31 Effective length of query: 396 Effective length of database: 365 Effective search space: 144540 Effective search space used: 144540 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: 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