Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate 14863 b0731 fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)
Query= BRENDA::O31645 (650 letters) >FitnessBrowser__Keio:14863 Length = 658 Score = 278 bits (710), Expect = 7e-79 Identities = 176/463 (38%), Positives = 258/463 (55%), Gaps = 29/463 (6%) Query: 3 LLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIIIA 62 ++ +T+CP GIAHTYMAAE L+KA +LGV++ VE QG G+E +LT +++ A A I A Sbjct: 186 IVCVTACPAGIAHTYMAAEYLEKAGRKLGVNVYVEKQGANGIEGRLTADQLNSATACIFA 245 Query: 63 ADRSVNK-DRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRS-ATKSESGNHQEKK- 119 A+ ++ + +RF G LSV V + IR E LIQ+AL + RS T++ + Q K Sbjct: 246 AEVAIKESERFNGIPALSVPVAEPIRHAEALIQQALT----LKRSDETRTVQQDTQPVKS 301 Query: 120 -QNPIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIEQIGSAS 178 + + + L++G+SF VP IV GG ++AVA+ L + L ++S+ ++G Sbjct: 302 VKTELKQALLSGISFAVPLIVAGGTVLAVAVLLSQIFGLQDLFNEENSWLWMYRKLGGGL 361 Query: 179 FSF-MIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYA 237 M+P+LA Y AYS+ADKP L PG G A + G+GFLG ++ G +AGY Sbjct: 362 LGILMVPVLAAYTAYSLADKPALAPGFAAGLAA-------NMIGSGFLGAVVGGLIAGYL 414 Query: 238 ALWIKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGS 296 W+K L++ + + PV +L G +F++G PVA I SLT WL G+ GS Sbjct: 415 MRWVKNHLRLSSKFNGFLTFYLYPVLGTLGAGSLMLFVVGEPVAWINNSLTAWLNGLSGS 474 Query: 297 SSILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIG---LGI 353 +++LL ILG M SFD+GGPVNK A+ F + G Y GP A+ + + + Sbjct: 475 NALLLGAILGFMCSFDLGGPVNKAAYAFCLGAMANGVY---GPYAIFASVKMVSAFTVTA 531 Query: 354 ATFLGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMI 413 +T L R F+ + E GK+ + +GL GITEGAIP A +DPLRVI S + GSM I Sbjct: 532 STMLAPRLFKEFEIETGKSTWLLGLAGITEGAIPMAIEDPLRVIGSFVLGSMVTGAIVGA 591 Query: 414 GNVGDRVAHGGPIVAVL------GAVDHVLMFFIAVIAGSLVT 450 N+G G L G V + +F A + G+ ++ Sbjct: 592 MNIGLSTPGAGIFSLFLLHDNGAGGVMAAIGWFGAALVGAAIS 634 Score = 88.2 bits (217), Expect = 1e-21 Identities = 46/148 (31%), Positives = 78/148 (52%), Gaps = 1/148 (0%) Query: 502 LTDIISPELIEPNLSGETSDDIIDELIQKLSRRGALLSESGFKQAILNREQQGTTAIGMN 561 LT + + + N + ++ I L Q+L+ G + S F + + RE G TA+G Sbjct: 23 LTTLTHRDALCLNARFTSREEAIHALTQRLAALGKISSTEQFLEEVYRRESLGPTALGEG 82 Query: 562 IAIPHGKSEAVREPSVAFGIKRSGVDWNSLDGSEA-KLIFMIAVPKESGGNQHLKILQML 620 +A+PHGK+ AV+E + A + W +DG EA L+ ++A+P G H+++L L Sbjct: 83 LAVPHGKTAAVKEAAFAVATLSEPLQWEGVDGPEAVDLVVLLAIPPNEAGTTHMQLLTAL 142 Query: 621 SRKLMDDNYRERLLSVQTTEEAYKLLEE 648 + +L DD R R+ S T +E L++ Sbjct: 143 TTRLADDEIRARIQSATTPDELLSALDD 170 Lambda K H 0.319 0.137 0.386 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: 925 Number of extensions: 50 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: 650 Length of database: 658 Length adjustment: 38 Effective length of query: 612 Effective length of database: 620 Effective search space: 379440 Effective search space used: 379440 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: 54 (25.4 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