Align protein-Npi-phosphohistidine-trehalose phosphotransferase (EC 2.7.1.201); protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate BWI76_RS02965 BWI76_RS02965 PTS trehalose transporter subunit IIBC
Query= BRENDA::A0A0H3F7X9 (473 letters) >FitnessBrowser__Koxy:BWI76_RS02965 Length = 472 Score = 860 bits (2221), Expect = 0.0 Identities = 425/472 (90%), Positives = 454/472 (96%) Query: 2 MSKINQTDIDRLIELVGGRGNIATVSHCITRLRFVLNQPANARPKEIEQLPMVKGCFTNA 61 MSK+NQ DID+LIELVGGR NIATVSHCITRLRFVLN PA A+PK+IEQL MVKGCFTNA Sbjct: 1 MSKVNQQDIDKLIELVGGRDNIATVSHCITRLRFVLNNPAIAKPKDIEQLRMVKGCFTNA 60 Query: 62 GQFQVVIGTNVGDYYQALIASTGQAQVDKEQVKKAARQNMKWHEQLISHFAEIFFPLLPA 121 GQFQVVIGT VGDYY+AL+A+TGQA DKEQ KKAARQNMKWHEQLISHFAEIFFPLLPA Sbjct: 61 GQFQVVIGTEVGDYYKALLATTGQASADKEQAKKAARQNMKWHEQLISHFAEIFFPLLPA 120 Query: 122 LISGGLILGFRNVIGDLPMSNGQTLAQMYPSLQTIYDFLWLIGEAIFFYLPVGICWSAVK 181 LISGGLILGFRNVIGDLPMSNGQTLAQM+PSL+TIYDFLWLIGEAIFFYLPVGICWSAVK Sbjct: 121 LISGGLILGFRNVIGDLPMSNGQTLAQMHPSLKTIYDFLWLIGEAIFFYLPVGICWSAVK 180 Query: 182 KMGGTPILGIVLGVTLVSPQLMNAYLLGQQLPEVWDFGMFSIAKVGYQAQVIPALLAGLA 241 KMGGTPILGIVLGVTLVSPQLMNAYLLGQQ+PEVW+FG+F+I KVGYQAQVIPALLAGLA Sbjct: 181 KMGGTPILGIVLGVTLVSPQLMNAYLLGQQVPEVWNFGLFTIEKVGYQAQVIPALLAGLA 240 Query: 242 LGVIETRLKRIVPDYLYLVVVPVCSLILAVFLAHALIGPFGRMIGDGVAFAVRHLMTGSF 301 LG IETRLKRIVPDYLYLV+VPVCSLILAVFLAHA IGPFGRMIGDGVA+AVRHL+TGSF Sbjct: 241 LGFIETRLKRIVPDYLYLVIVPVCSLILAVFLAHAFIGPFGRMIGDGVAWAVRHLLTGSF 300 Query: 302 APIGAALFGFLYAPLVITGVHQTTLAIDLQMIQSMGGTPVWPLIALSNIAQGSAVIGIII 361 APIGAALFGFLYAPLVITGVHQTTLAID+QMIQSMGGTPVWPLIALSNIAQ SAV+GIII Sbjct: 301 APIGAALFGFLYAPLVITGVHQTTLAIDMQMIQSMGGTPVWPLIALSNIAQASAVVGIII 360 Query: 362 SSRKHNEREISVPAAISAWLGVTEPAMYGINLKYRFPMLCAMIGSGLAGLLCGLNGVMAN 421 +SRK NEREISVPAAISA+LGVTEPAMYGINLKYRFPMLCAM+GSGLAGLLCGLNGVMAN Sbjct: 361 ASRKQNEREISVPAAISAYLGVTEPAMYGINLKYRFPMLCAMVGSGLAGLLCGLNGVMAN 420 Query: 422 GIGVGGLPGILSIQPSYWQVFALAMVIAIIIPIVLTSFIYQRKYRLGTLDIV 473 GIGVGGLPGILSIQP+YWQV+ALAM IA+++PIVLT+ +YQRK+R GTL IV Sbjct: 421 GIGVGGLPGILSIQPTYWQVYALAMAIAVVVPIVLTTVVYQRKFRQGTLQIV 472 Lambda K H 0.326 0.143 0.433 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: 923 Number of extensions: 28 Number of successful extensions: 1 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: 473 Length of database: 472 Length adjustment: 33 Effective length of query: 440 Effective length of database: 439 Effective search space: 193160 Effective search space used: 193160 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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