Align The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) (characterized)
to candidate BWI76_RS19555 BWI76_RS19555 PTS beta-glucoside transporter subunit EIIBCA
Query= TCDB::Q8NMD6 (661 letters) >FitnessBrowser__Koxy:BWI76_RS19555 Length = 619 Score = 326 bits (835), Expect = 2e-93 Identities = 211/660 (31%), Positives = 333/660 (50%), Gaps = 48/660 (7%) Query: 1 MDHKDLAQRILRDIGGEDNIVAAAHCATRLRLVLKDTKDVDRQSLDDDPDLKGTFETGGM 60 M++K LAQ IL +GG +NIV+ HCATRLR LKD+K D + L +P + E+GG Sbjct: 1 MEYKALAQDILTRVGGRENIVSLVHCATRLRFKLKDSKKADAEGLKANPGVIMVVESGGQ 60 Query: 61 FQIIVGPGDVDHVFKELDDATSKDIAVSTEQLKDVVANNANWFSRAVKVLADIFVPLIPI 120 FQ+++G +HV S+ + V + + + +++ IF P I + Sbjct: 61 FQVVIG----NHVHDVWLAVRSEAGLTDDSEPVAVKGEKVSLIGQLIDIVSGIFTPFIGV 116 Query: 121 LVGGGLLMAINNVLVAQDLFGPQSLVEMFPQISGVAEMINLMASAPFAFLPVLVGFTATK 180 L G+L + + V Q ++ + A F F P+ +G+TA K Sbjct: 117 LAASGILKGLLALAVVCGWLTTQQ---------ATYKIWFAASDALFFFFPLFLGYTAGK 167 Query: 181 RFGGNEFLGAGIGMAMVFPSLVNGYDVAATMAAGEMPMWSLFGLDVAQAGYQGTVLPVLV 240 +FGGN F+ IG A+ P ++ +D A+MA G + L G+ V Y +V+P+++ Sbjct: 168 KFGGNPFITMVIGGALTHPLMIQAFD--ASMAPGAATEYFL-GIPVTFINYSSSVIPIIL 224 Query: 241 VSWILATIEKFLHKRLKGTADFLITPVLTLLLTGFLTFIAIGPAMRWVGDVLAHGLQGLY 300 SW+ IEK + L + TP + L + LTF+ IGP W+ +LA+G Q +Y Sbjct: 225 ASWVSCWIEKRSNAILPSSMKNFFTPAICLAVVVPLTFLIIGPVATWLSQLLANGYQLIY 284 Query: 301 DFGGPVGGLLFGLVYSPIVITGLHQSFPPIELE-LFNQGGSFIFATASMANIAQGAACLA 359 + G G ++ VI GLH P+ + L G + A + Q A L Sbjct: 285 QVAPWLAGAAMGALWQVCVIFGLHWGLIPLMINNLAVLGHDSMMPMLLPAVMGQVGAALG 344 Query: 360 VFFLAKSEKLKGLAGASGVSAVLGITEPAIFGVNLRLRWPFFIGIGTAAIGGALIALFNI 419 +F + + K LAG++ + + G+TEPAI+G+NL LR PF G AIGGA++ + Sbjct: 345 IFLRTRDARQKVLAGSAVSAGIFGVTEPAIYGLNLPLRRPFIFGCVAGAIGGAMVGFSDS 404 Query: 420 KAVALGAAGFLGVVSIDAPDMVMFLVCAVVTFFIAFGAAIAYGLYLVRRNGSIDPDATAA 479 + G + + P+ + V GAA + ++ A Sbjct: 405 HVYSFGFGNIFTLAQMIPPEGIDATVWG--------GAAGMFASLII---------ACVL 447 Query: 480 PVPAGTTKAEAE------APAEFSNDSTIIQAPLTGEAIALSSVSDAMFASGKLGSGVAI 533 + AG ++ AE APA ND I AP+TG +AL V D+ FASG LG GVAI Sbjct: 448 TLVAGLPRSSAEQAAVVVAPAS-END---ILAPMTGSVLALDQVPDSTFASGLLGQGVAI 503 Query: 534 VPTKGQLVSPVSGKIVVAFPSGHAFAVRTKAEDGSNVDILMHIGFDTVNLNGTHFNPLKK 593 +P+ G++++P SG++ F + HA + + S +++L+H+G DTV L+G F K Sbjct: 504 IPSVGKVIAPFSGEVASIFQTKHAIGLLSD----SGIELLIHVGIDTVKLDGAPFTAHVK 559 Query: 594 QGDEVKAGELLCEFDIDAIKAAGYEVTTPIVVSNYKKTGPVNTYGLGEIEAGANLLNVAK 653 +GD++KAG+LL EFD AI AGY++ TPI++SN ++ ++AG LL+V++ Sbjct: 560 EGDKIKAGDLLLEFDRQAILDAGYDLATPIIISNSDDFRTLDMVSASAVDAGQPLLSVSR 619 Lambda K H 0.322 0.139 0.408 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: 912 Number of extensions: 48 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: 661 Length of database: 619 Length adjustment: 38 Effective length of query: 623 Effective length of database: 581 Effective search space: 361963 Effective search space used: 361963 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 (21.9 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