Align Maltodextrin-binding protein (characterized, see rationale)
to candidate WP_061059304.1 M988_RS19105 maltose/maltodextrin ABC transporter substrate-binding protein MalE
Query= uniprot:Q9RHZ6 (427 letters) >NCBI__GCF_001655005.1:WP_061059304.1 Length = 396 Score = 175 bits (443), Expect = 3e-48 Identities = 127/404 (31%), Positives = 206/404 (50%), Gaps = 20/404 (4%) Query: 28 TSNGGQNTSPSTSSSSAKGEASALPKGQTITVWSWQTGPE-LQDVKQIAAQWAKAHGDKV 86 T G T ++ ++ +SA K + + W G + + +I ++ K G KV Sbjct: 2 TKKSGIRTLALSALATLVLSSSAFAKIEEGKLVIWINGDKGYNGLAEIGKKFEKETGIKV 61 Query: 87 IVVDQSSNPKGFQFYATAARTGKGPDVVFGMPHDNNGVFAEEGLMAPV-PSGVLNTGLYA 145 +V K + Y A TG GPD++F HD G +A+ GL+A + PS LY Sbjct: 62 LVEHPD---KLEEKYPQVAATGDGPDIIF-WAHDRFGGYAQSGLLAEIHPSKAFQDKLY- 116 Query: 146 PNTIDAIKVNGTMYSVPVSVQVAAIYYNKKLVPQPPQTWAEFV---KDANAHG---FMYD 199 P T DA++ NG + + PV+V+ ++ YNK ++P+PP+TW E K+ A G M++ Sbjct: 117 PFTWDAVRYNGKLIAYPVAVEALSLIYNKDILPEPPKTWEEIPALDKELRAKGKSAIMWN 176 Query: 200 QANLYFDYAIIGGYGGYVFKDNNGTLDPNNIGLDTPGAVQAYTLMRDMVSKYHWMTPSTN 259 YF + II GGY FK +NGT + ++G++ G+ + D+V H + T+ Sbjct: 177 LQEPYFTWPIIAADGGYAFKYDNGTYNIKDVGVNNAGSQAGLQFIVDLVKNKH-INADTD 235 Query: 260 GSIAKAEFLAGKIGMYVSGPWDTADIEKAKIDFGVTPWPTLPNGKHATPFLGVITAFVNK 319 SIA+A F G+ M ++GPW ++I+K+ I++GV PT G + PF+GV++A +N Sbjct: 236 YSIAEAAFNKGQTAMTINGPWAWSNIDKSNINYGVALLPTF-KGHPSKPFVGVLSAGINA 294 Query: 320 ES--KTQAADWSLVQALTSAQAQQMYFRDSQQIPALLSVQRSSAVQSSPTFKAFVEQLRY 377 S K A ++ +T+A +Q+ AL S Q + ++ P A ++ + Sbjct: 295 ASPNKELATEFLENYLMTNAGLEQINKDKPLGAVALKSYQET--LEKDPKIAATMQNAQK 352 Query: 378 AVPMPNIPQMQAVWQA-MSILQNIIAGKVSPEQGAKDFVQNIQK 420 MPNIPQM A W A S + N + G+ S ++ Q I K Sbjct: 353 GEIMPNIPQMSAFWYAERSAIINAVNGRQSVKEALTGAEQRITK 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: 440 Number of extensions: 32 Number of successful extensions: 6 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 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