Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate GFF4494 PS417_23000 PTS N-acetyl-D-glucosamine transporter
Query= reanno::pseudo3_N2E3:AO353_04465 (571 letters) >FitnessBrowser__WCS417:GFF4494 Length = 568 Score = 928 bits (2398), Expect = 0.0 Identities = 466/569 (81%), Positives = 502/569 (88%), Gaps = 3/569 (0%) Query: 1 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAI 60 MYQ FIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIA++HDAGQ IFANLALIFAI Sbjct: 1 MYQHFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAVMHDAGQAIFANLALIFAI 60 Query: 61 GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDI 120 GIAVGFARDNNGTAGLAGAIGYLVMVSTLKV+D SINMGMLAGI SGLMAG LYNRFKDI Sbjct: 61 GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVMDTSINMGMLAGIASGLMAGGLYNRFKDI 120 Query: 121 KLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFG 180 KLPEYLAFFGGRRFVPI TGFSAVGLGVIFGLIWPPIQHGINSFG LL+ESGS+GAFVFG Sbjct: 121 KLPEYLAFFGGRRFVPIVTGFSAVGLGVIFGLIWPPIQHGINSFGVLLMESGSLGAFVFG 180 Query: 181 VFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMM 240 VFNRLLIVTGLHHILNNMAWF+FGSFTDP TGA+VTGDL RYFAGDPKGGQFMTGMFP+M Sbjct: 181 VFNRLLIVTGLHHILNNMAWFVFGSFTDPVTGAVVTGDLTRYFAGDPKGGQFMTGMFPVM 240 Query: 241 IFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVL 300 +FGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAP LYL+H + Sbjct: 241 LFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPFLYLIHAV 300 Query: 301 LTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR 360 LTG++MA+TN LNIHLGFTFSGG IDM LGWGKSTNGWLVFPVGLAYA+IYY VF++CIR Sbjct: 301 LTGLSMAVTNMLNIHLGFTFSGGFIDMVLGWGKSTNGWLVFPVGLAYALIYYSVFNYCIR 360 Query: 361 RFNLKTPGREGVVVGEKVVLSENQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKAS 420 FNLKTPGRE V + +S+NQRA AYIQALGGA+NL++VGACTTRLRL+MVDRNKA Sbjct: 361 HFNLKTPGREDTQVVQAEAMSDNQRATAYIQALGGAQNLLSVGACTTRLRLDMVDRNKAV 420 Query: 421 DSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPKA 480 D+ELKALGAMAVVRPG GGSLQVVVGP+ADSIADEIR AMP + AA VV K Sbjct: 421 DAELKALGAMAVVRPGNGGSLQVVVGPMADSIADEIRLAMP---GFVAAAPVVVAPVEKP 477 Query: 481 APVETPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDG 540 V EA+KWLNA+GG NV QL+ VAMTR+R++L D LSE L LGCQGVS L+ Sbjct: 478 VAVNVQEAEKWLNALGGRGNVRQLEAVAMTRLRVELGDDSGLSEADLTALGCQGVSQLES 537 Query: 541 GVWHLLIGDKALSLSEALEGLVNRSEVSA 569 GVWHLLIGDKA L EALE LV ++ A Sbjct: 538 GVWHLLIGDKATGLGEALERLVGAQQIGA 566 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: 1130 Number of extensions: 55 Number of successful extensions: 4 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: 568 Length adjustment: 36 Effective length of query: 535 Effective length of database: 532 Effective search space: 284620 Effective search space used: 284620 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