Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate 7025094 Shewana3_2257 phosphoenolpyruvate--protein phosphotransferase (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__ANA3:7025094 Length = 567 Score = 296 bits (759), Expect = 2e-84 Identities = 201/570 (35%), Positives = 301/570 (52%), Gaps = 25/570 (4%) Query: 277 LRGVCASAGSAFGYVVQV--AERTLE---MPEFAADQQLER-----ESLERALMHATQAL 326 + G+ S+G AFG + + AE L+ +P QQ + ++L++ L H+ L Sbjct: 3 ITGIIVSSGIAFGQALHLTQAEHHLDYRPIPLSRIPQQQSKFVKALQALQQQLSHSQTKL 62 Query: 327 QRLRDNAAGEAQADIFKAHQELLEDPSLLEQAQALIAEGK-SAAFAWNSATEATATLFKS 385 +N + +A LLED L++Q + I + SA+ A A +S Sbjct: 63 DPQSENY------QLIEADLLLLEDEELIDQVKEAIRTLQLSASVAVERIFAHQANELES 116 Query: 386 LGSTLLAERALDLMDVGQRVLKLILGVPD-GVWELPDQAILIAEQLTPSQTAALDTGKVL 444 L LA RA D+ +GQR++ I G D G+ +L + IL+A+ LTP++ A L ++ Sbjct: 117 LDDPYLANRAQDVRCLGQRLVTAINGRLDQGLAQLTEPTILLAQDLTPAEFALLPKEQLS 176 Query: 445 GFATVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIE 504 G GG TSH AILARA G+PA+ + +GT ++LDA GEL ++PA + Sbjct: 177 GIVLKTGGLTSHTAILARAAGIPAILSCQFDAEFIPNGTPLVLDALSGELFVNPAPELQA 236 Query: 505 QLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRS 564 +L ++ R A T+DGH + ANV +L + +GA+GIGL R+ Sbjct: 237 RLTVTLHHEQARRAALQAYRDVPAKTQDGHLVGLMANVGNLNDITHVGDVGADGIGLFRT 296 Query: 565 EFLYQQRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLG 624 EF+ S P Q Y ALG + +RTLD+G DK L + + E NP LG Sbjct: 297 EFMLMHTSTLPDEKAQYNLYCEALHALGG-KTFTIRTLDIGADKELPCLCQEVEDNPALG 355 Query: 625 MRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLSELRLARLMLEEEALAL--- 681 +RG+R L P+L + Q RAIL +A + +M PMV+Q+ EL ++ E AL Sbjct: 356 LRGVRYTLAHPELFKTQLRAILRAANHGPIRLMFPMVNQVEELDQIFALIAECQDALEEE 415 Query: 682 --GLRELPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADS 739 G EL GI++E PAA + P +DF SIGTNDLTQY +A DR +P+L S Sbjct: 416 EKGFGEL-SYGIVVETPAAVMNLASMLPRLDFVSIGTNDLTQYAMAADRTNPQLTRDYPS 474 Query: 740 FHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAA 799 P++L LI TV A A G V +CG LAS L VPLL+G+G+DELSV++ + +KAA Sbjct: 475 LSPAILGLIKMTVDQAKAAGVKVSLCGELASSPLMVPLLIGMGLDELSVNLSALLEVKAA 534 Query: 800 IREVELSDCQAIAHQVLGLESAEQVREALS 829 + + +L+ A+AH + ++++ ++ Sbjct: 535 VCQGQLTKFSALAHTAMQQNRISELQQCIT 564 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: 1003 Number of extensions: 48 Number of successful extensions: 5 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: 567 Length adjustment: 39 Effective length of query: 805 Effective length of database: 528 Effective search space: 425040 Effective search space used: 425040 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: 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