Align The Maltose group translocator, MalT of 470 aas and 10 TMSs. Takes up extracellular maltose, releasing maltose-phosphate into the cytoplasm (characterized)
to candidate AO353_04465 AO353_04465 PTS N-acetyl-D-glucosamine transporter
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04465 Length = 571 Score = 221 bits (562), Expect = 8e-62 Identities = 166/536 (30%), Positives = 258/536 (48%), Gaps = 87/536 (16%) Query: 10 QKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAIITNLHILFA 69 Q+ G+AL++ +A++P AGL++ +G D + ++ ++ D G I NL ++FA Sbjct: 10 QRLGRALMLPIAILPIAGLLLRLG--------DTDLLNIA--IIHDAGQVIFANLALIFA 59 Query: 70 VAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDLIVKDY 129 + I +A+D G T + G ++ S KV Sbjct: 60 IGIAVGFARDNNG---------------TAGLAGAIGYLVMVSTLKVLDA---------- 94 Query: 130 FTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVIVWSTV 189 ++NMG+ GII+G + LYN++ + KLP+ LAFF G+RFVP + Sbjct: 95 --------SINMGMLAGIISGLMAGALYNRFKDI-KLPEYLAFFGGRRFVPIATGFSAVG 145 Query: 190 TAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLTIPMNY 249 ++ L+WP IQ G+N FG+ + S + FV+G RLL+ GLHH+L + Sbjct: 146 LGVIFGLIWPPIQHGINSFGQLLLESGS----IGAFVFGVFNRLLIVTGLHHILNNMAWF 201 Query: 250 TELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPARFKAG 309 + G++T T G +V G DL A GD K +F G Sbjct: 202 --IFGSFTDPT---TGAIVTG----------DLARYFA-GDPKG----------GQFMTG 235 Query: 310 QVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFIAPVLY 369 L AM+RN E+R +FLS AL FLTGVTEPIEF FMF+AP+LY Sbjct: 236 MFPMMIFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLY 295 Query: 370 VVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVIVSLVFFGLNF 429 +++ + TG+A A+ + +N+ + GF M + G + + V L + + + Sbjct: 296 LLHVLLTGMAMAITNALNIHL---GFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYY 352 Query: 430 TLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKENIADVDAC 489 +F+F I++FNL TPGR G + + SE A I LGG EN+ V AC Sbjct: 353 VVFDFCIRRFNLKTPGREGVVVGEKVVLSE-------NQRAGAYIQALGGAENLITVGAC 405 Query: 490 MTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKG--VQAVYGPKADVLKSDIQDML 543 TRLR+ + D + A +++ K GA+ ++ KG +Q V GP AD + +I+ + Sbjct: 406 TTRLRLEMVDRN-KASDSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAM 460 Lambda K H 0.325 0.140 0.416 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: 747 Number of extensions: 48 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: 545 Length of database: 571 Length adjustment: 36 Effective length of query: 509 Effective length of database: 535 Effective search space: 272315 Effective search space used: 272315 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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