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 3608669 Dshi_2062 PTSINtr with GAF domain, PtsP (RefSeq)
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__Dino:3608669 Length = 747 Score = 233 bits (594), Expect = 3e-65 Identities = 174/547 (31%), Positives = 263/547 (48%), Gaps = 21/547 (3%) Query: 283 LAGVCASPGLASGPL----ARLGAISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQ 338 + G A G+A G + R+ L +DD PE + + L A+ ++R V L Sbjct: 183 IRGGVAQEGIAKGHVYLHEPRVVVTKLVSDD----PEAELVRLRGAVDQLRVSVDEMLDI 238 Query: 339 ARLGGDENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNL 398 A G D + I A+ G + + ID G+ A A + A ++ + + Sbjct: 239 APKG-DAEQLQILEAYRMFANSRGWMRRMEESIDSGLSAEAAVEKEQSAARSRMERVPDA 297 Query: 399 LLAERANDLRDLEKRVLRVLLGDTAPL--RVPAGAIVAAREITPSDLAPLVDAGAA--GL 454 L ER +DL DL R+LR+L G +PA I+ AR I P +L +D G A G+ Sbjct: 298 YLRERLHDLDDLSNRLLRLLTGQGGETGAEIPADPILVARNIGPGEL---LDYGRALKGI 354 Query: 455 CMAEGGATSHVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQV 514 + EG SH AI+AR+ +P +V E G V++D QG + L PD R L Sbjct: 355 ILEEGSVGSHAAIVARALAIPLIVHAKRITTEALNGDLVLVDGEQGIVHLRPDDRVLAHF 414 Query: 515 ALQVAQREEQRRRQQADAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEF 574 ++A + + + R + + A T G I + N + ++GA+GVGL RTE Sbjct: 415 TDKIAMQAKAQERYASIRDKPAETLCGSVISLTMNAGLMADLPSLPSSGAEGVGLFRTEL 474 Query: 575 LFLERRAAPDEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRG 634 FL R P E Y VLDA ++V+ RT+D+G DK L Y+ E NPALG R Sbjct: 475 QFLTRSKVPRRSELAEIYARVLDAADGKRVVFRTLDIGSDKVLPYMKPQDEPNPALGWRA 534 Query: 635 IHLGQARPELLDQQLRALLRVEPLERCRILLPMVSEVDEL-RAIRRRLGELATQLGIER- 692 I +G +P ++ QL+AL+R ++ P +++++E RA L E+ + + R Sbjct: 535 IRVGLDKPGVMRMQLQALIRGANGRPLTVMFPFIAQLEEFTRARDALLREIDREAALGRT 594 Query: 693 LP---ELGVMIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHP 749 LP E+G M+E PS A + E ADF+SIG NDL Q+ A DR + + R D L+ Sbjct: 595 LPESVEIGAMLETPSLAFAPNSFFEMADFVSIGGNDLKQFFFAADRENERVRRRYDTLNV 654 Query: 750 ALLRLIAQTCAGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQ 809 + L LI + G + CG A P+ +G+ LS+ P +G +K +R+ Sbjct: 655 SFLSLIELIVSRCRDVGTPLSFCGEDAGRPIEALCFAAMGLRSLSMRPASIGPVKHLLRR 714 Query: 810 LDAAECR 816 D E R Sbjct: 715 SDLREAR 721 Lambda K H 0.319 0.136 0.390 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: 1410 Number of extensions: 70 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 842 Length of database: 747 Length adjustment: 41 Effective length of query: 801 Effective length of database: 706 Effective search space: 565506 Effective search space used: 565506 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 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