Align PTS system glucose-specific EIICBA component; EIICBA-Glc; EII-Glc; EIICBA-Glc 1; EC 2.7.1.199 (characterized)
to candidate WP_009141894.1 HMPREF9452_RS09360 PTS transporter subunit EIIC
Query= SwissProt::Q57071 (675 letters) >NCBI__GCF_000225705.1:WP_009141894.1 Length = 530 Score = 266 bits (679), Expect = 2e-75 Identities = 172/541 (31%), Positives = 279/541 (51%), Gaps = 62/541 (11%) Query: 8 QLQRIGKALMLPVAILPAAGLLLALGNAFQGDALQSLM--PFIKAEGFQNVAKMMEGAGG 65 ++Q+ G A+ PV + AG+++ G F + + + P G NV +++G G Sbjct: 4 KIQKFGGAMFTPVMLFAFAGVVIGFGTLFTTEVIFGPLAAPGTMWYGVWNV--ILQG-GW 60 Query: 66 IIFDNLAIIFALGVAIGLASGDGV-AAIAAFVGFIVLN---KTM----GMFLGVTPEKAA 117 +F+ L ++FA+ + IGLA+ + A VG++ TM G F GV Sbjct: 61 TVFNQLPLLFAVSLPIGLANKQNARCCMEALVGYLTFQYFVSTMLSQWGGFFGVDFAAEV 120 Query: 118 DAATGFANVLGIPTLQTGVFGGIIIGALAAWCYNKFYNISLPSYLGFFAGKRFVPIMMAT 177 +G A + I TL G+ G + + + +NKFY + LP +LG FAG FV I+ Sbjct: 121 GGTSGLAMIASIKTLDMGMIGALAVSGIIIAIHNKFYEVELPEWLGVFAGSTFVYIITFF 180 Query: 178 CSFILAFPMAIIWPSIQGGLNAFSEGLLASNTGLAVFLFGFIKRLLIPFGLHHIFHAPFW 237 +AF + WP +Q G+ AF +G +A+ L V +F F++R LIPFGLHH+ ++PF+ Sbjct: 181 VMLPVAFVACLGWPHVQDGIRAF-QGFVATTGTLGVGVFAFLERALIPFGLHHLMYSPFY 239 Query: 238 FE--------FGSYKNAAGQIIHGDQRIFIEQIRDNVPLTAGKFMQGEFPVMMFGLPAAA 289 ++ + ++ A QI + +++ T + + +FG P A Sbjct: 240 YDNAVVDGGIYTAFATALPQIAASTDSL--KELAPYAAFTCSTWSK------IFGCPGIA 291 Query: 290 LAIYQTAKKENKKVVAGLMLSGALTSFLTGITEPLEFSFLFVAPLLFFIHAVLDGLSFLI 349 LA + TAK E KK + L++ LT+ G+TEP+EF+FLF+AP LF +H VL L + Sbjct: 292 LAFFVTAKPEKKKELLSLLIPITLTAVFCGVTEPIEFTFLFIAPPLFIVHCVLAALLAMA 351 Query: 350 LYLLDLHLGYTFSGGFIDFFLLGILPNKTQWW----LVIPVGLVYAAIYYIIFRFLIVKF 405 + ++ +G F+GG I+ L +P W + + VGLV+ I++++FRFLIVKF Sbjct: 352 INMVGC-VG-VFAGGIIEISSLNFIPLMANHWQQYAMALVVGLVFTVIWFVVFRFLIVKF 409 Query: 406 NFKTPGRED-------------KEVKSSNVAASE------------LPFKVLDAMGGKAN 440 +FKTPGRED + K+ +A+ E + +VL+ +GG N Sbjct: 410 DFKTPGREDDDEQVKFRSKAEYRAAKNGELASGEGAKVDESDPYAVMAAEVLELLGGADN 469 Query: 441 IKHLDACITRLRVEVNDKAKV-DVQELKDLGASGVLEVGNNMQAIFGPKSDQIKHDMQQI 499 I + C+TRLRV V D+ V D + K +G SG+ + G MQ I G K +++ + + Sbjct: 470 IVDVTNCVTRLRVNVKDETLVADDPDFKSIGTSGIAKNGKGMQVIIGLKVPKVRDRFEAL 529 Query: 500 M 500 + Sbjct: 530 L 530 Lambda K H 0.324 0.143 0.421 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: 850 Number of extensions: 47 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: 675 Length of database: 530 Length adjustment: 37 Effective length of query: 638 Effective length of database: 493 Effective search space: 314534 Effective search space used: 314534 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: 41 (22.0 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 24 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