Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate CCNA_00892 CCNA_00892 phosphoenolpyruvate-protein phosphotransferase PtsP
Query= reanno::pseudo3_N2E3:AO353_05485 (953 letters) >FitnessBrowser__Caulo:CCNA_00892 Length = 754 Score = 301 bits (772), Expect = 8e-86 Identities = 209/606 (34%), Positives = 301/606 (49%), Gaps = 16/606 (2%) Query: 363 RAIEEGLGEDIEPLPTVSAQ----SEVI--DEITDVVVAPASGCVIQAVAAAPGIAIGPA 416 R +E ED++ + V A+ SE++ DE+ DV +AP ++ A G+A G A Sbjct: 142 RNYDEEEVEDLQIIAMVLAEMVSSSELLGADELKDVELAPHKPERLKGSRFAEGLAYGVA 201 Query: 417 HIQVLQAIDYPLRGESTAIERERLKTSLADVRRDIEGLI--QRSKAKAIREIFITHQEML 474 + L + E RL ++ ++ I+ ++ Q A E+ T++ Sbjct: 202 VLHEQPVAPETLLSDDALAEEARLTYAIEALQTQIDQMLEGQHGLVGASYEVLETYRLFA 261 Query: 475 DDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAERAADLRDIGRRVLAQL 534 D + ++ G +AEAA V + +D L ER DL D+ R+L L Sbjct: 262 HDRGWNRSLQEAVRSGLTAEAAVERVRSEHRARLGQARDPYLRERLHDLEDLNDRLLRHL 321 Query: 535 CG-IETPSEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGATAHSAIVARALGIPAL 593 G + + + IL+ +GP+D+ D T++ GIL G A +H+ IVARAL IP + Sbjct: 322 SGDVHHVRQLPEDAILIARNLGPADLLEYDRTKLKGILLEEGSAASHAGIVARALDIPCV 381 Query: 594 VGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDNREQRLQAAAAQRHQPAL 653 R+ G P+++D + + ++ + R QR A R P + Sbjct: 382 GRLVGLRDRVNEGDPVVVDAETQEAWLRPRPDVVKALKARMEVRAQRKAEFARLRDTPPI 441 Query: 654 TTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQQAPDEATQEVEYRRVLD 713 T DG V + N G + + E GAEGIGL RTE FM ++ P Q Y +VLD Sbjct: 442 TKDGSKVTLLMNAGLAVDLDILGETGAEGIGLFRTEFQFMVAEELPRLEAQTALYEKVLD 501 Query: 714 GLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQRPQIMEAQLRALLRAAD 773 G P+ RTLD+GGDK LPY + +E+NP LG R +R+ L RP ++ Q+RAL++AA+ Sbjct: 502 AANGMPVTFRTLDLGGDKLLPYMELEREDNPALGWRAVRMGLDRPALLRMQIRALIKAAN 561 Query: 774 NRPLRIMFPMVGSVDEWRQARDMTER-----LRLEIPV-ADLQLGIMIEVPSAALLAPVL 827 RPLRIMFP+V +VDE+R AR ++ L+ P A L +G MIE PS L Sbjct: 562 GRPLRIMFPLVANVDEFRAARSFVDQEVAWALKRGRPAPARLDVGAMIEAPSLLWHLDAL 621 Query: 828 AKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVC 887 DF SVGTNDL QY A DRG+P +S + D L PA L+ + +A G V VC Sbjct: 622 LPMTDFVSVGTNDLMQYMFAADRGNPRVSDRYDPLSPAALRALKTIQQACADTGTQVSVC 681 Query: 888 GELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVR 947 GE+A PL LV LG D LS+ IG VK V L + + AL GS +R Sbjct: 682 GEMAGRPLEAFALVALGFDRLSMPPAGIGPVKQMVLSLDREAARRNVE-ALLKGSGGSLR 740 Query: 948 ALVEAL 953 +E L Sbjct: 741 GEIETL 746 Lambda K H 0.319 0.135 0.383 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: 1385 Number of extensions: 65 Number of successful extensions: 4 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: 953 Length of database: 754 Length adjustment: 42 Effective length of query: 911 Effective length of database: 712 Effective search space: 648632 Effective search space used: 648632 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: 56 (26.2 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