Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate H281DRAFT_01853 H281DRAFT_01853 PTS system D-glucose-specific IIB component, Glc family /PTS system D-glucose-specific IIC component, Glc family
Query= reanno::pseudo3_N2E3:AO353_04465 (571 letters) >FitnessBrowser__Burk376:H281DRAFT_01853 Length = 596 Score = 426 bits (1096), Expect = e-123 Identities = 253/591 (42%), Positives = 347/591 (58%), Gaps = 45/591 (7%) Query: 9 LQRLGRALMLPIAILPIAGLLLRLGDTDL------LNIAIIHDAGQVIFANLALIFAIGI 62 LQ++G++LMLP+A+LP+AGLLL LG TD + +A++ +AG VIFANL LIFAIG+ Sbjct: 9 LQKVGKSLMLPVAVLPVAGLLLGLGATDFHGYVPAIVLALMKNAGDVIFANLPLIFAIGV 68 Query: 63 AVGFARDNNGTAGLAGAIGYLVMVSTLKVLDA-------------SINMGMLAGIISGLM 109 A+GF +N+G +G+A IGYLVM +TL V+ SI G+ GI++G + Sbjct: 69 ALGFT-ENDGVSGIAATIGYLVMTATLGVIAKVEGIEPDMIMGIPSIQTGVFGGILAGGL 127 Query: 110 AGALYNRFKDIKLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLL 169 A ++NR+ I LP YL FF G+RFVPI T ++ LG I ++WPPI I +F Q Sbjct: 128 AAWMFNRYYRIALPAYLGFFAGKRFVPIVTAIGSIVLGAILSVVWPPIGSAIKAFSQWAA 187 Query: 170 ESGS-IGAFVFGVFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPK 228 S A V+G RLLI GLHHI N +F GSF DPTTG +V GD+ R+FAGD Sbjct: 188 VSDPRTAATVYGFVERLLIPFGLHHIWNVPFFFEAGSFLDPTTGKVVHGDITRFFAGDRT 247 Query: 229 GGQFMTGMFPMMIFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFM 288 G + G F +FGLPAA +A++ A PE + +GG+ +S ALTSFLTG+TEPIEFAF+ Sbjct: 248 AG-ILAGAFLFKMFGLPAAAIAIWHCAKPENKVAVGGMMVSAALTSFLTGITEPIEFAFL 306 Query: 289 FLAPLLYLLHVLLTGMAMAITNALNIHLGFTFSGGAIDMA---LGWGKSTNGWLVFPVGL 345 F+AP+LYL+H L A + N L + +GFTFS G ID L KST+ W VF +G Sbjct: 307 FVAPVLYLIHACLAASAQFVANTLGMRMGFTFSQGGIDFLMFNLIGNKSTHAWYVFILGP 366 Query: 346 AYAVIYYVVFDFCIRRFNLKTPGREGVVVGEKVVLSE--NQRAGAYIQALGGAENLITVG 403 YAVIYY VF F I RF+LKTPGRE V V + R+ + A GG N+ ++ Sbjct: 367 IYAVIYYGVFRFVITRFDLKTPGREDDTVETAKVSTAGVGGRSRELVLAFGGRSNIDSLD 426 Query: 404 ACTTRLRLEMVDRNKASDSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTA 463 AC TRLR+ + + ++ +LKALGA VVR G G +Q + GPL++++ ++ + + TA Sbjct: 427 ACITRLRISVKNPALVNEGKLKALGAAGVVRVGNG--VQAIFGPLSENMKTDMHEYLKTA 484 Query: 464 GSALVAAV---VVTEEAPKAAPV-------------ETPEAQKWLNAVGGSDNVLQLDCV 507 GS A V E A A + +K A+GG N+ +LD + Sbjct: 485 GSEADLAADGKAVAEAAASTATAIGSAQASAHSTTQQAERVEKIRAALGGVANIQKLDAL 544 Query: 508 AMTRIRLQLADGKALSECQLKDLGCQGVSALDGGVWHLLIGDKALSLSEAL 558 A TR+R+ L D L LK G L G + L++G A +L+ A+ Sbjct: 545 AATRLRVGLRDASQLDTAALKAAGVPATQTLTNGEFDLIVGLDAPNLAGAM 595 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: 890 Number of extensions: 37 Number of successful extensions: 10 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: 596 Length adjustment: 36 Effective length of query: 535 Effective length of database: 560 Effective search space: 299600 Effective search space used: 299600 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