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 CCNA_00892 CCNA_00892 phosphoenolpyruvate-protein phosphotransferase PtsP
Query= TCDB::Q9HXN5 (842 letters) >FitnessBrowser__Caulo:CCNA_00892 Length = 754 Score = 250 bits (638), Expect = 2e-70 Identities = 201/614 (32%), Positives = 291/614 (47%), Gaps = 30/614 (4%) Query: 231 DEVEVICRGEDSEAALGALLAALASATA--GAPKDAPRAIAPGEPARPAAVAGTLAGVCA 288 DE EV ED + + +LA + S++ GA + +AP +P R L G Sbjct: 145 DEEEV----EDLQI-IAMVLAEMVSSSELLGADELKDVELAPHKPER-------LKGSRF 192 Query: 289 SPGLASGPLAR----LGAISLPADDGRHRPEEQHLALDQALQRVRDDVQGSLQQARLGGD 344 + GLA G + +L +DD A++ ++ ++G Q L G Sbjct: 193 AEGLAYGVAVLHEQPVAPETLLSDDALAEEARLTYAIEALQTQIDQMLEG---QHGLVGA 249 Query: 345 ENEAAIFSAHLALLEDPGLLDAADMLIDQGVGAAHAWHRAIQAQCEILQALGNLLLAERA 404 E + + D G + + G+ A A R L + L ER Sbjct: 250 SYE--VLETYRLFAHDRGWNRSLQEAVRSGLTAEAAVERVRSEHRARLGQARDPYLRERL 307 Query: 405 NDLRDLEKRVLRVLLGDTAPLR-VPAGAIVAAREITPSDLAPLVDAGAAGLCMAEGGATS 463 +DL DL R+LR L GD +R +P AI+ AR + P+DL G+ + EG A S Sbjct: 308 HDLEDLNDRLLRHLSGDVHHVRQLPEDAILIARNLGPADLLEYDRTKLKGILLEEGSAAS 367 Query: 464 HVAILARSKGLPCLVALGAGLLELEEGRQVVLDAGQGRLELSPDARRLEQVALQVAQREE 523 H I+AR+ +PC+ L + EG VV+DA L P ++ + ++ R + Sbjct: 368 HAGIVARALDIPCVGRLVGLRDRVNEGDPVVVDAETQEAWLRPRPDVVKALKARMEVRAQ 427 Query: 524 QRRRQQADAQREALTRDGRRIEIGANVASPREAAEAFANGADGVGLLRTEFLFLERRAAP 583 ++ +T+DG ++ + N + GA+G+GL RTEF F+ P Sbjct: 428 RKAEFARLRDTPPITKDGSKVTLLMNAGLAVDLDILGETGAEGIGLFRTEFQFMVAEELP 487 Query: 584 DEEEQRNAYQEVLDAMGQRKVIIRTIDVGGDKHLDYLPLPVEENPALGLRGIHLGQARPE 643 E Q Y++VLDA V RT+D+GGDK L Y+ L E+NPALG R + +G RP Sbjct: 488 RLEAQTALYEKVLDAANGMPVTFRTLDLGGDKLLPYMELEREDNPALGWRAVRMGLDRPA 547 Query: 644 LLDQQLRALLRVEPLERCRILLPMVSEVDELRAIRRRLG-ELATQLGIERLP----ELGV 698 LL Q+RAL++ RI+ P+V+ VDE RA R + E+A L R ++G Sbjct: 548 LLRMQIRALIKAANGRPLRIMFPLVANVDEFRAARSFVDQEVAWALKRGRPAPARLDVGA 607 Query: 699 MIEVPSAALLADQLAEHADFLSIGTNDLSQYALAMDRCHAGLADRIDALHPALLRLIAQT 758 MIE PS D L DF+S+GTNDL QY A DR + ++DR D L PA LR + Sbjct: 608 MIEAPSLLWHLDALLPMTDFVSVGTNDLMQYMFAADRGNPRVSDRYDPLSPAALRALKTI 667 Query: 759 CAGAARHGRWVGVCGALASDPLATPVLVGLGVEELSVGPNLVGEIKTRVRQLDAAECRRH 818 A G V VCG +A PL LV LG + LS+ P +G +K V LD RR+ Sbjct: 668 QQACADTGTQVSVCGEMAGRPLEAFALVALGFDRLSMPPAGIGPVKQMVLSLDREAARRN 727 Query: 819 AQALLDLGSARAVR 832 +ALL GS ++R Sbjct: 728 VEALLK-GSGGSLR 740 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: 1477 Number of extensions: 74 Number of successful extensions: 3 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: 842 Length of database: 754 Length adjustment: 41 Effective length of query: 801 Effective length of database: 713 Effective search space: 571113 Effective search space used: 571113 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