Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate AZOBR_RS30470 AZOBR_RS30470 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::pseudo3_N2E3:AO353_05485 (953 letters) >FitnessBrowser__azobra:AZOBR_RS30470 Length = 590 Score = 367 bits (943), Expect = e-106 Identities = 230/581 (39%), Positives = 336/581 (57%), Gaps = 23/581 (3%) Query: 393 VVAPASGCVIQAVAAAPGIAIGPAHIQVLQAI---DYPLRGESTAIERERLKTSLADVRR 449 V A G ++ + +PGIAIGPAH+ AI +Y L + E R + RR Sbjct: 5 VPAAGQGRSLRGLGVSPGIAIGPAHVVESGAIRVPEYTLTADQVEAEAARFADACGKARR 64 Query: 450 DIEGL------IQRSKAKAIREIFITHQEMLDDPELTDEVDTRLKQG-ESAEAAWMAVID 502 I L + S ++ I + H M+ + LT V+ R++Q +AEAA A I Sbjct: 65 QIRKLKAKALVLPGSASEEIGFLLDAHLAMVTNSRLTRGVERRIQQELVNAEAAVQAEIA 124 Query: 503 AAARQQESLQDALLAERAADLRDIGRRVLAQLCGIETP--SEPDQPYILVMDEVGPSDVA 560 A+ S++D+ LA R AD+R++GRR++ L E S + +++ +E+ P+D A Sbjct: 125 TIAQTFASMEDSYLAGRIADVREVGRRLIRNLMRHEYQAFSMLNPGAVILAEELTPADTA 184 Query: 561 RLDPTRVAGILTARGGATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHV 620 LDP RVAG T GGA H+AI+AR+LGIPA++G G + L +G +++DG +GR+ + Sbjct: 185 LLDPRRVAGFATVLGGAEGHTAIMARSLGIPAVLGVGGLLAGLKNGITVIVDGVQGRVII 244 Query: 621 DADAATLQRAAEERDNREQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGA 680 D L+ + R RE+ + R PA+T D AV + AN+ + A+E GA Sbjct: 245 DPTPEVLEDYRQRRAEREREREQLKGLRKLPAVTRDNTAVTLQANLELPRDLDHALENGA 304 Query: 681 EGIGLLRTELIFMAHQQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAK 740 +GIGLLRTE +FM Q PDE Q R +++G+ GR + RT+DVGG+K L W + Sbjct: 305 QGIGLLRTEFLFMNRDQLPDEDEQYTVLRSIVEGMGGRTVTARTMDVGGEK-LAGWMAGR 363 Query: 741 ---EENPFLGVRGIRLTLQRPQIMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDM- 796 NP LG+R +RL L+ P+++E QL A+LRA + PLRI+ PM+ SV E ++ R+M Sbjct: 364 YGEPANPALGLRAVRLGLREPKLLETQLAAMLRAGVHGPLRILLPMICSVAEVQRVREMM 423 Query: 797 ---TERLRLE-IPVAD--LQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDR 850 RLR +P+AD +G+M+EVP AAL A LA DFFS+GTNDLTQYTLAIDR Sbjct: 424 GQVARRLRRRGVPIADPLPPVGVMVEVPGAALSADALAYAADFFSIGTNDLTQYTLAIDR 483 Query: 851 GHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSV 910 G +++ D LHPAVL+LI T+ AA V VCGE+A D +L+GLGV +LS+ Sbjct: 484 GDEQVASLYDPLHPAVLRLIQFTIEAALRARIPVSVCGEIAGDSRYTALLLGLGVRDLSM 543 Query: 911 SARSIGEVKARVRELSLAQVKHLAQLALAVGSANEVRALVE 951 +I VK R+R+L L + A++ + + + AL++ Sbjct: 544 VPPAIPLVKRRIRKLDLQEATRRARVIMDQSDSGRIAALLD 584 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: 1067 Number of extensions: 46 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: 590 Length adjustment: 40 Effective length of query: 913 Effective length of database: 550 Effective search space: 502150 Effective search space used: 502150 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