Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate AO353_04465 AO353_04465 PTS N-acetyl-D-glucosamine transporter
Query= reanno::pseudo3_N2E3:AO353_04465 (571 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04465 Length = 571 Score = 1117 bits (2888), Expect = 0.0 Identities = 571/571 (100%), Positives = 571/571 (100%) Query: 1 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAI 60 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAI Sbjct: 1 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAI 60 Query: 61 GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDI 120 GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDI Sbjct: 61 GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDI 120 Query: 121 KLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFG 180 KLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFG Sbjct: 121 KLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFG 180 Query: 181 VFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMM 240 VFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMM Sbjct: 181 VFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMM 240 Query: 241 IFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVL 300 IFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVL Sbjct: 241 IFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVL 300 Query: 301 LTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR 360 LTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR Sbjct: 301 LTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR 360 Query: 361 RFNLKTPGREGVVVGEKVVLSENQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKAS 420 RFNLKTPGREGVVVGEKVVLSENQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKAS Sbjct: 361 RFNLKTPGREGVVVGEKVVLSENQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKAS 420 Query: 421 DSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPKA 480 DSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPKA Sbjct: 421 DSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPKA 480 Query: 481 APVETPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDG 540 APVETPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDG Sbjct: 481 APVETPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDG 540 Query: 541 GVWHLLIGDKALSLSEALEGLVNRSEVSAKV 571 GVWHLLIGDKALSLSEALEGLVNRSEVSAKV Sbjct: 541 GVWHLLIGDKALSLSEALEGLVNRSEVSAKV 571 Lambda K H 0.325 0.142 0.421 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: 1255 Number of extensions: 49 Number of successful extensions: 3 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: 571 Length of database: 571 Length adjustment: 36 Effective length of query: 535 Effective length of database: 535 Effective search space: 286225 Effective search space used: 286225 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