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 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)
Query= TCDB::Q63GK8 (545 letters) >FitnessBrowser__SB2B:6936959 Length = 485 Score = 202 bits (513), Expect = 3e-56 Identities = 165/542 (30%), Positives = 260/542 (47%), Gaps = 84/542 (15%) Query: 6 FDFWQKFGKALLVVVAVMPAAGLMISIGKLIGMSAGDINAVHTIARV-MEDIGWAIITNL 64 F F Q+ + LL+ +A++PAAG+MI G++ + + +A V M +G I + Sbjct: 20 FRFAQRLSQTLLIPIAILPAAGVMI------GIATNPLPFIPDVANVLMLSVGKLIFDIM 73 Query: 65 HILFAVAIGGSWAKDRAGGAFAALLAFVLTNRITGAIFGVNAEMLADSKAKVSSVLAGDL 124 +LFA+A+ + +D+ AF+A + GV LA + AKV + + Sbjct: 74 PMLFAIAVAIGFCRDQGIAAFSAAFGY-----------GVLLSTLA-AAAKVYHLPSH-- 119 Query: 125 IVKDYFTSVLGAPALNMGVFVGIITGFLGATLYNKYYNYNKLPQALAFFNGKRFVPFVVI 184 V G P ++ G+ G++ G + + +LP +FF G+R P ++I Sbjct: 120 -------IVWGTPTIDTGIAGGMLVGGITCVAV-RLSEKLRLPAVFSFFEGRRSAPLIMI 171 Query: 185 VWSTVTAIVLSLLWPFIQSGLNEFGRWIAASKDSAPIVAPFVYGTLERLLLPFGLHHMLT 244 + A++L+ +WP + + W + P +A YG +ERLLLP GLHH+ Sbjct: 172 PLVMLLAVMLAFIWPPLALSIERLSDWAVYQE---PAIAFGFYGMVERLLLPLGLHHIWN 228 Query: 245 IPMNYTELGGTYTMLTGSKVGQVVAGQDPLWLAWITDLNNLLANGDTKAYNDLLNNVVPA 304 P Y E+G + G++V G+ + A GD A N Sbjct: 229 APF-YLEVGQY------AHDGEIVRGEMARYFA-----------GDPSAGN--------- 261 Query: 305 RFKAGQVIGSTAALMGIAFAMFRNVDKEKRAKYKPMFLSAALAVFLTGVTEPIEFMFMFI 364 AG + L A A++R D+ +R + + LSAA A +LTGVTEPIEF F+F+ Sbjct: 262 --LAGGYLIKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAFLFV 319 Query: 365 APVLYVVYAITTGLAFALADLINLR---VHAFGFIELITRTPMMVNAGLTRDLINFVIVS 421 AP+LY+ +A+ TGLA+++A L+++ V + G ++ + P N + Sbjct: 320 APLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTHW------IWFLG 373 Query: 422 LVFFGLNFTLFNFLIKKFNLPTPGRAGNYIDNEDEASEGTGNVQDGSLATKVIDLLGGKE 481 + F + + LF I FNL TPGR EA G Q +L ++ LGG Sbjct: 374 PLTFVIYYILFRASILAFNLKTPGRF--------EADTG----QKRNLIA-IVSALGGGG 420 Query: 482 NIADVDACMTRLRVTVKDLDVVAPEAQWKQNGALGLIVKDKGVQAVYGPKADVLKSDIQD 541 NIAD+ AC+TRLR++V D V + GA G+IV GVQ V+G KA+ L+ +Q Sbjct: 421 NIADLSACLTRLRISVADPSQV-DRQRLMSLGAKGVIVVGSGVQLVFGTKAETLRKLLQR 479 Query: 542 ML 543 L Sbjct: 480 YL 481 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: 592 Number of extensions: 31 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: 485 Length adjustment: 35 Effective length of query: 510 Effective length of database: 450 Effective search space: 229500 Effective search space used: 229500 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: 52 (24.6 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