Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate 7025672 Shewana3_2822 PTS system, glucose-like IIB subunint (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_04465 (571 letters) >FitnessBrowser__ANA3:7025672 Length = 452 Score = 258 bits (659), Expect = 4e-73 Identities = 177/463 (38%), Positives = 257/463 (55%), Gaps = 36/463 (7%) Query: 23 LPIAGLLLRLGDT------DLLNIAIIHDAGQVIFANLALIFAIGIAVGFARDNNGTAGL 76 +P AG++L L + ++L + ++ G++IFA + ++FA+ +A+GF RD G A Sbjct: 1 MPAAGVMLGLTVSPIPFMPEVLTVLMLA-VGKLIFAIMPILFAVAVAIGFCRDQ-GIAAF 58 Query: 77 AGAIGYLVMVSTLKVL------DASINMGMLA---GIISGLMAGAL------YNRFKDIK 121 GY VM +TL L + +GM GI G++ G + ++++ I+ Sbjct: 59 TAVFGYGVMTATLAALADLYQLPTQLLLGMETLDTGIAGGMLIGGVTCFAVRWSQY--IR 116 Query: 122 LPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQ-LLLESGSIGAFVFG 180 LP +FF GRR + A+GLG I +WPP+ I + + +I V+G Sbjct: 117 LPAIFSFFEGRRSASLLIIPLAMGLGYILAHVWPPLSLLIERVSDWAVYQKPAIAFGVYG 176 Query: 181 VFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMM 240 RLLI GLHHI N + G + +V G++ARY AGDP+ G + G + + Sbjct: 177 ALERLLIPLGLHHIWNAPFYLEVGQY-QLQNSEVVRGEVARYLAGDPQAGN-LAGGYLIK 234 Query: 241 IFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVL 300 ++GLPAA LA++R A P R + GI LS A S+LTGVTEPIEFAFMF+AP L+L+HVL Sbjct: 235 MWGLPAAALAIWRCAEPSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPFLFLIHVL 294 Query: 301 LTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTN-GWLVFPVGLAYAVIYYVVFDFCI 359 L+G+A + L+IH FS G +D L + S N GW VF +G AVIYY++F I Sbjct: 295 LSGLAYFVCIMLDIHHSIVFSHGLVDFTLLFSLSRNTGWFVF-LGPLTAVIYYLLFRGSI 353 Query: 360 RRFNLKTPGREGVVVGEKVVLSENQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKA 419 FNLKTPGR + E E+ R A I ALGG EN++ + AC TRLRL + Sbjct: 354 LAFNLKTPGR--LEPDEPHGAKESLR--AIIAALGGRENIVELNACLTRLRLSVHSPELV 409 Query: 420 SDSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPT 462 + L LGA V+ GKG +QVV G A+++ +++ + T Sbjct: 410 NKVRLSQLGAKGVIVMGKG--VQVVYGTKAETLRKVLQRYLDT 450 Score = 38.9 bits (89), Expect = 4e-07 Identities = 21/66 (31%), Positives = 42/66 (63%), Gaps = 2/66 (3%) Query: 494 AVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDGGVWHLLIGDKALS 553 A+GG +N+++L+ +TR+RL + + +++ +L LG +GV + GV ++ G KA + Sbjct: 382 ALGGRENIVELNA-CLTRLRLSVHSPELVNKVRLSQLGAKGVIVMGKGV-QVVYGTKAET 439 Query: 554 LSEALE 559 L + L+ Sbjct: 440 LRKVLQ 445 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: 618 Number of extensions: 36 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 571 Length of database: 452 Length adjustment: 34 Effective length of query: 537 Effective length of database: 418 Effective search space: 224466 Effective search space used: 224466 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