Align The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)
Query= TCDB::Q8DS05 (729 letters) >FitnessBrowser__Keio:15742 Length = 530 Score = 229 bits (584), Expect = 3e-64 Identities = 175/555 (31%), Positives = 282/555 (50%), Gaps = 53/555 (9%) Query: 10 FEFWQKFGKCLMVVIAVMPAAGLMVSIGNSLALIDPKSTLLVTVANIIAQ--------IG 61 +EF+Q+ GK M+ +A++ G+M+ IG+SL+ D TL+ + N + Q IG Sbjct: 12 WEFFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDV-ITLIPVLGNPVLQAIFTWMSKIG 70 Query: 62 WGVINNLHILFAVAIGGSWAKERAG-GAFAAALAFILINLITGNFYGISLEMIADKTSYV 120 + L ++F +AI A+E G AFA + + ++NL NF+ + ++ + V Sbjct: 71 SFAFSFLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAV-NFWLTNKGILPTTDAAV 129 Query: 121 HNIFGGKMHVADYFINVLGQPALNMGVFVGIISGFVGATAYNKYYNFRKLPDVLSFFNGK 180 A+ ++LG +++ G+ +I+G + + +++N R LPD L+FF G Sbjct: 130 LK--------ANNIQSILGIQSIDTGILGAVIAGIIVWMLHERFHNIR-LPDALAFFGGT 180 Query: 181 RFVPFVVIVRSTIVALILSVFWPIVQSGINGFGMWIASSQHTAPFLAPFLYGTLERLLLP 240 RFVP + + +V L++ + WPI GI+G G I S A P L+GT ERLLLP Sbjct: 181 RFVPIISSLVMGLVGLVIPLVWPIFAMGISGLGHMINS----AGDFGPMLFGTGERLLLP 236 Query: 241 FGLHHMLTIPMNYTQLGGTYVVLTGAQAGKHVLGQDPLWLAWVQDLIHLKGAGHMSQYHH 300 FGLHH+L + +T GGT V +G + Q L H Sbjct: 237 FGLHHILVALIRFTDAGGTQEVCGQTVSGALTIFQAQL---------------SCPTTHG 281 Query: 301 LLTSVTPARF-KVGQMIGSSGILMGLTLAMYRNVDPDKKEKYKGMFLSAAVAVFLTGVTE 359 S T RF G+M G L G LAMY P+ + K KG+ +S +A + G TE Sbjct: 282 FSESAT--RFLSQGKMPAFLGGLPGAALAMYHCARPENRHKIKGLLISGLIACVVGGTTE 339 Query: 360 PLEYMFMFAALPLYLVYAVVQGLAFASADLIHLRV-HSFGNIEFLTRTPMAIKAGLAMDI 418 PLE++F+F A LY+++A++ GL F ++ + + ++ GNI + I GL+ Sbjct: 340 PLEFLFLFVAPVLYVIHALLTGLGFTVMSVLGVTIGNTDGNI--IDFVVFGILHGLSTKW 397 Query: 419 VNFIVVSVVFGVAMYFITNFMIKKFNLATSGRNGNYDTGDDASDETASNSNAGTANANSQ 478 VV+ ++ V Y I F I +FNL T GR D+ +S E A G + N Sbjct: 398 YMVPVVAAIWFVVYYVIFRFAITRFNLKTPGR----DSEVASSIEKAVAGAPGKSGYN-- 451 Query: 479 IVKIINLLGGKENISDVDACMTRLRITVTDVAKVGDEAAWKKAGAMGLI-VKGNGVQAVY 537 + I+ LGG +NI +D C+TRLR++V D++ V +A K A+G++ + + +Q V Sbjct: 452 VPAILEALGGADNIVSLDNCITRLRLSVKDMSLVNVQAL-KDNRAIGVVQLNQHNLQVVI 510 Query: 538 GPKADVLKSDIQDLL 552 GP+ +K ++ L+ Sbjct: 511 GPQVQSVKDEMAGLM 525 Lambda K H 0.322 0.138 0.402 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: 855 Number of extensions: 52 Number of successful extensions: 9 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: 729 Length of database: 530 Length adjustment: 37 Effective length of query: 692 Effective length of database: 493 Effective search space: 341156 Effective search space used: 341156 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 54 (25.4 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