Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate 6936677 Sama_0864 phosphoenolpyruvate-protein phosphotransferase PtsP (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__SB2B:6936677 Length = 744 Score = 305 bits (780), Expect = 8e-87 Identities = 203/563 (36%), Positives = 301/563 (53%), Gaps = 15/563 (2%) Query: 276 LLRGVCASAGSAFGYVVQVA-ERTLEMPEFAA-DQQLERESLERALMHATQALQRLR--- 330 L G AS G A + + + E +LE PE A D E L A+ + AL L Sbjct: 169 LFTGTSASTGVAIAHALVIGGEISLEQPEACATDVDAEVNRLRLAMGRSRDALTALAQKF 228 Query: 331 DNAAGEAQADIFKAHQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTL 390 +N + + IF + Q LLED SL + Q + G SA A + + F+++ Sbjct: 229 ENDHDDELSSIFTSLQSLLEDASLGGEYQREVLAGWSAETAVSRVSLRYVAQFETMEDAY 288 Query: 391 LAERALDLMDVGQRVLKLILGVPDGVWELPDQ-AILIAEQLTPSQTAALDTGKVLGFATV 449 L ERA D+ D+GQRVL+ ++ P + PD+ IL+ + S A K+ G T Sbjct: 289 LRERASDIRDLGQRVLRQLIE-PGRMMLDPDKPVILVTREADTSMLAEFPRQKLAGIVTE 347 Query: 450 GGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAK 509 GG SH AILARALG+PA+ G+ + + ++L+A +G L + P+ +V+++ Sbjct: 348 AGGVNSHAAILARALGVPAIMGVEQVLQANLDKQLLVLNASRGILMVSPSPTVVDEYRNL 407 Query: 510 RQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQ 569 Q+ + E A+T DGH + N ++ ++ GA+G+GL R+E + Sbjct: 408 ISAQKALDRQYAEELKEPALTLDGHRIHLYLNAGLMSGVSSEIADGADGVGLYRTEIPFM 467 Query: 570 QRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIR 629 + PS EQ Y ++ ++ R +V+RTLDVGGDKPL Y P+ SE NPFLG RGIR Sbjct: 468 LQQRFPSESEQIKVYRSVLQSAAG-RPVVMRTLDVGGDKPLPYFPI-SEENPFLGWRGIR 525 Query: 630 LCLERPQLLREQFRAILSSAG-LARLHIMLPMVSQLSELRLARLMLEEEALALGLRELPK 688 L L+ P+L Q RA+L +AG L I+LPMVS L E+ A L L++ L P Sbjct: 526 LSLDHPELFLVQLRAMLQAAGDTDNLKILLPMVSSLDEIDEALLYLDQAFSELRADVNPS 585 Query: 689 L-----GIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPS 743 L G+M+EVPA A V+F S+G+NDLTQY LA+DR++PR++S DS+HP Sbjct: 586 LARPPVGVMLEVPALLYQLREVAQRVEFVSVGSNDLTQYLLAVDRNNPRVSSLYDSYHPG 645 Query: 744 VLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREV 803 VLR + ++ H V VCG LA E + LL+ +G DELS++ + I +R V Sbjct: 646 VLRALQLALQECRQHKLDVSVCGELAGEPMGALLLVAMGYDELSMNQGSLAKINYLLRRV 705 Query: 804 ELSDCQAIAHQVLGLESAEQVRE 826 E S+ + + V+ + + + VRE Sbjct: 706 ERSELEQLLALVMQMSNGQDVRE 728 Lambda K H 0.318 0.132 0.370 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: 1170 Number of extensions: 51 Number of successful extensions: 6 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: 844 Length of database: 744 Length adjustment: 41 Effective length of query: 803 Effective length of database: 703 Effective search space: 564509 Effective search space used: 564509 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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