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 H281DRAFT_01976 H281DRAFT_01976 PTS system N-acetylglucosamine-specific IIB component, Glc family /PTS system N-acetylglucosamine-specific IIC component, Glc family
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__Burk376:H281DRAFT_01976 Length = 599 Score = 229 bits (585), Expect = 2e-64 Identities = 180/538 (33%), Positives = 260/538 (48%), Gaps = 87/538 (16%) Query: 10 QKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARVMEDIGWAIITNLHILFA 69 Q+ G+AL++ +AV+P AGL++ +G+ D+ + IA D G AI NL +LFA Sbjct: 10 QRLGRALMLPIAVLPVAGLLLRLGQ------PDVFNIKMIA----DAGGAIFDNLPLLFA 59 Query: 70 VAIGGSWAKDRAGGAFAALLAFVLTNRITGAI-FGVNAEMLADSKAKVSSVLAGDLIVKD 128 + + +AKD G A + GAI + + ++ D K Sbjct: 60 IGVAVGFAKDNNGVA-----------GLAGAIGYLIEVAVMKDINDK------------- 95 Query: 129 YFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVIVWST 188 LNMGV GI+ G + LYN+Y + KLP LAFF GKRFVP V V Sbjct: 96 ----------LNMGVLSGIVAGIVAGLLYNRYKDI-KLPDYLAFFGGKRFVPIVTGVVCL 144 Query: 189 VTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLTIPMN 248 I+ +W +QS ++ G W+ +A + FV+G L RLLL GLHH+L Sbjct: 145 ALGILFGYVWQPVQSVIDTAGHWLT----TAGALGAFVFGVLNRLLLVTGLHHILNSLTW 200 Query: 249 YTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPARFKA 308 + + GT+T G+ V DL+ A GD A F Sbjct: 201 F--VFGTFTPPGGAAV--------------TGDLHRFFA-GDPTA----------GTFMT 233 Query: 309 GQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFIAPVL 368 G L AMF KE+RA + S AL FLTGVTEPIEF FMF+APVL Sbjct: 234 GFFPVMMFGLPAACLAMFHEAPKERRAIVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVL 293 Query: 369 YVVYAITTGLAFALADLINLRVHAFGFIELITRTPMMVNAGLTRDLINFVIVSLVFFGLN 428 YV++A+ TGLA A+ + + + GF ++N GL+ + V +V+ + Sbjct: 294 YVIHALLTGLALAICSALGIHL---GFTFSAGAIDYVLNYGLSTKGWLAIPVGIVYAVVY 350 Query: 429 FTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGS-----LATKVIDLLGGKENI 483 + LF F I+KFN+ TPGR D + ++ G V + A + I LGG N+ Sbjct: 351 YGLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGAAVPRAQRYIAALGGAANL 410 Query: 484 ADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKD-KGVQAVYGPKADVLKSDIQ 540 + VDAC TRLR++V D V+ E + K GA G++ + VQ + GP+AD++ +I+ Sbjct: 411 SVVDACTTRLRLSVVDSGKVS-ENELKTIGARGVLKRGATNVQVIIGPEADIIADEIR 467 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: 860 Number of extensions: 49 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 545 Length of database: 599 Length adjustment: 36 Effective length of query: 509 Effective length of database: 563 Effective search space: 286567 Effective search space used: 286567 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