Align Sucrose porter, IIBC (SacP) (55% identical to 4.A.1.2.1) (characterized)
to candidate 17782 b3722 fused beta-glucoside-specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)
Query= TCDB::P05306 (461 letters) >FitnessBrowser__Keio:17782 Length = 625 Score = 236 bits (603), Expect = 1e-66 Identities = 132/413 (31%), Positives = 217/413 (52%), Gaps = 4/413 (0%) Query: 5 ETAKRLIELLGGKENIISAAHCATRLRLVMKDESKIDQAQVEELDGVKGAFSSSGQYQII 64 E A++++ +GG +NI+S HCATRLR +KDESK +++ G+ S GQ+Q++ Sbjct: 3 ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62 Query: 65 FGTGLVNKVFDAFSKEADIEREEHVNHQDAAKEKLNPAARFAKTLSNIFVPIIPAIVASG 124 G + + VF A + A ++ E +K N RF +S IF P+I + A+G Sbjct: 63 IGNHVAD-VFLAVNSVAGLD--EKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATG 119 Query: 125 LLMGLLGMINAFHWMSKDSALLQLLDMFSSAAFIFLPILIGVSASKEFGSNPYLGAVIGG 184 +L G+L + F W ++ S +L S A F F PI++G +A K FG NP+ VIGG Sbjct: 120 ILKGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGG 179 Query: 185 IMIHPNLLNPWGLAE-ATPDYMHLFGFDIALLGYQGTVIPVLLAVYVMSKVEKWTRKVVP 243 ++HP +L + + A + G + LL Y +VIP++ + ++ S +E+ +P Sbjct: 180 ALVHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLP 239 Query: 244 HAVDLLVTPFVTVIVTGFVAFIAIGPLGRALGSGITVALTYVYDHAGFVAGLIFGGTYSL 303 A+ TP + ++V V F+ +GPL + I ++Y AG + GG + + Sbjct: 240 SAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQI 299 Query: 304 IVLTGVHHSFHAIEAGLIADIGKNYLLPIWSMANVAQGGAGLAVFFMAKKAKTKEIALPA 363 V+ G+H + +G + ++P+ A +AQ GA L VF + A+ K +A A Sbjct: 300 FVMFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSA 359 Query: 364 AFSAFLGITEPVIFGVNLRYRKPFIAAMIGGALGGAYVVFTHVAANAYGLTGI 416 A ++ GITEP ++GVNL + PF+ A I GALG + + ++GL I Sbjct: 360 ALTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSI 412 Lambda K H 0.325 0.140 0.411 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: 765 Number of extensions: 40 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: 461 Length of database: 625 Length adjustment: 35 Effective length of query: 426 Effective length of database: 590 Effective search space: 251340 Effective search space used: 251340 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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