Align The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)
Query= TCDB::Q8DS05 (729 letters) >FitnessBrowser__SB2B:6936959 Length = 485 Score = 206 bits (524), Expect = 2e-57 Identities = 169/552 (30%), Positives = 265/552 (48%), Gaps = 95/552 (17%) Query: 10 FEFWQKFGKCLMVVIAVMPAAGLMVSIG-NSLALI-DPKSTLLVTVANIIAQIGWGVINN 67 F F Q+ + L++ IA++PAAG+M+ I N L I D + L+++V +I I Sbjct: 20 FRFAQRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANVLMLSVGKLIFDI------- 72 Query: 68 LHILFAVAIGGSWAKERAGGAFAAALAFILINLITGNFYGISLEMIADKTSYVHNIFGGK 127 + +LFA+A+ + +++ AF+AA YG+ L +A H Sbjct: 73 MPMLFAIAVAIGFCRDQGIAAFSAAFG-----------YGVLLSTLAAAAKVYHL----P 117 Query: 128 MHVADYFINVLGQPALNMGVFVGIISGFVGATAYNKYYNFRKLPDVLSFFNGKRFVPFVV 187 H+ V G P ++ G+ G++ G + A R LP V SFF G+R P ++ Sbjct: 118 SHI------VWGTPTIDTGIAGGMLVGGITCVAVRLSEKLR-LPAVFSFFEGRRSAPLIM 170 Query: 188 IVRSTIVALILSVFWPIVQSGINGFGMWIASSQHTAPFLAPFLYGTLERLLLPFGLHHML 247 I ++A++L+ WP + I W + P +A YG +ERLLLP GLHH+ Sbjct: 171 IPLVMLLAVMLAFIWPPLALSIERLSDWAVYQE---PAIAFGFYGMVERLLLPLGLHHIW 227 Query: 248 TIPMNYTQLGGTYVVLTGAQAGKHVLGQDPLWLAWVQDLIHLKGAGHMSQYHHLLTSVTP 307 P Y ++G A G+ V G+ + A +L G Sbjct: 228 NAPF-YLEVGQY------AHDGEIVRGEMARYFAGDPSAGNLAG---------------- 264 Query: 308 ARFKVGQMIGSSGILMGLTLAMYRNVDPDKKEKYKGMFLSAAVAVFLTGVTEPLEYMFMF 367 G +I G L LA++R D +++ + G+ LSAA A +LTGVTEP+E+ F+F Sbjct: 265 -----GYLIKMWG-LPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAFLF 318 Query: 368 AALPLYLVYAVVQGLAFASA---DLIHLRVHSFGNIEFLTRTPMAIKAGLA--MDIVNFI 422 A LYL +A++ GLA++ A D+ H V S G ++F+ P + + + F+ Sbjct: 319 VAPLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTHWIWFLGPLTFV 378 Query: 423 VVSVVFGVAMYFITNFMIKKFNLATSGRNGNYDTGDDASDETASNSNAGTANANSQIVKI 482 + ++F + I FNL T GR DTG ++ I Sbjct: 379 IYYILFRAS--------ILAFNLKTPGR-FEADTGQ-----------------KRNLIAI 412 Query: 483 INLLGGKENISDVDACMTRLRITVTDVAKVGDEAAWKKAGAMGLIVKGNGVQAVYGPKAD 542 ++ LGG NI+D+ AC+TRLRI+V D ++V D GA G+IV G+GVQ V+G KA+ Sbjct: 413 VSALGGGGNIADLSACLTRLRISVADPSQV-DRQRLMSLGAKGVIVVGSGVQLVFGTKAE 471 Query: 543 VLKSDIQDLLDS 554 L+ +Q LD+ Sbjct: 472 TLRKLLQRYLDT 483 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: 733 Number of extensions: 38 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: 729 Length of database: 485 Length adjustment: 37 Effective length of query: 692 Effective length of database: 448 Effective search space: 310016 Effective search space used: 310016 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: 53 (25.0 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