Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)
Query= TCDB::Q9HXN4 (570 letters) >FitnessBrowser__SB2B:6936959 Length = 485 Score = 291 bits (745), Expect = 4e-83 Identities = 178/470 (37%), Positives = 262/470 (55%), Gaps = 31/470 (6%) Query: 10 QRLGRALMLPIAILPIAGLLLRLGDVDLLDIP-----LVHDAGKAIFANLALIFAIGIAV 64 QRL + L++PIAILP AG+++ + L IP L+ GK IF + ++FAI +A+ Sbjct: 24 QRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANVLMLSVGKLIFDIMPMLFAIAVAI 83 Query: 65 GFARDNNGTAGLAGAIGYLVMISVLKVI-------------DPGIDMGVLSGIISGLVAG 111 GF RD G A + A GY V++S L P ID G+ G++ G + Sbjct: 84 GFCRDQ-GIAAFSAAFGYGVLLSTLAAAAKVYHLPSHIVWGTPTIDTGIAGGMLVGGITC 142 Query: 112 ALYNRFKDVKLPEYLAFFGGRRFVPIATGISAVCLGLLFGVIWPPLQQGINGLGQLMLES 171 + ++LP +FF GRR P+ + L ++ IWPPL I L + Sbjct: 143 VAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPLALSIERLSDWAVYQ 202 Query: 172 GSFGAFAF-GVLNRLLIVTGLHHILNNLVWFVFGSFTDPETGRVVTGDLARYFAGDPKGG 230 AF F G++ RLL+ GLHHI N + G + G +V G++ARYFAGDP G Sbjct: 203 EPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYA--HDGEIVRGEMARYFAGDPSAG 260 Query: 231 QFMAGMFPVMMFGLPAACLAMYRNARPERRKLIGGLLLSMALTAFLTGVTEPVEFAFMFL 290 +AG + + M+GLPAA LA++R A +R + G++LS A ++LTGVTEP+EFAF+F+ Sbjct: 261 N-LAGGYLIKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAFLFV 319 Query: 291 APLLYLLHALLTGLSMALTDLLDIRLGFTFSGGAIDLALGWGRSTHGWMLWPLGLLYAGI 350 APLLYL HALLTGL+ ++ LLD+ FS G +D L + +S++ +W LG L I Sbjct: 320 APLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLFPQSSNTHWIWFLGPLTFVI 379 Query: 351 YYLVFDFCIRRFNLKTPGREDDASSESGDNAEAERAPAFIRALGGAANLEVVDACTTRLR 410 YY++F I FNLKTPGR + D + A + ALGG N+ + AC TRLR Sbjct: 380 YYILFRASILAFNLKTPGRFE------ADTGQKRNLIAIVSALGGGGNIADLSACLTRLR 433 Query: 411 LRLVDRNKASDAQLKALGAMAVVRPGKAGSLQVVVGPQADSIADEIRRAL 460 + + D ++ +L +LGA V+ G +Q+V G +A+++ ++R L Sbjct: 434 ISVADPSQVDRQRLMSLGAKGVIVVG--SGVQLVFGTKAETLRKLLQRYL 481 Score = 47.8 bits (112), Expect = 1e-09 Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 2/73 (2%) Query: 496 AWLGALGGAGNLREVRDVALTRLRVSVADERKLATEQLRRLGGQGVSSLAGGICHILVGP 555 A + ALGG GN+ ++ LTRLR+SVAD ++ ++L LG +GV + G+ ++ G Sbjct: 411 AIVSALGGGGNIADL-SACLTRLRISVADPSQVDRQRLMSLGAKGVIVVGSGV-QLVFGT 468 Query: 556 RAAALSQALQPLL 568 +A L + LQ L Sbjct: 469 KAETLRKLLQRYL 481 Lambda K H 0.326 0.143 0.428 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: 633 Number of extensions: 30 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: 570 Length of database: 485 Length adjustment: 35 Effective length of query: 535 Effective length of database: 450 Effective search space: 240750 Effective search space used: 240750 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