Align Putative PTS system glucosamine-specific EIICBA component; EC 2.7.1.193 (characterized)
to candidate WP_009141894.1 HMPREF9452_RS09360 PTS transporter subunit EIIC
Query= SwissProt::P39816 (631 letters) >NCBI__GCF_000225705.1:WP_009141894.1 Length = 530 Score = 229 bits (584), Expect = 2e-64 Identities = 166/533 (31%), Positives = 261/533 (48%), Gaps = 72/533 (13%) Query: 7 QILQQLGRALMTPVAVLPAAGLLLRFGDKDLLNI----------------PIIKDAGGVV 50 Q +Q+ G A+ TPV + AG+++ FG + +I G V Sbjct: 3 QKIQKFGGAMFTPVMLFAFAGVVIGFGTLFTTEVIFGPLAAPGTMWYGVWNVILQGGWTV 62 Query: 51 FDNLPLIFAVGVAIGLAGGEGV-AGLAAVIGYL----ILTVTLDNMGKLLGLQPPYE--G 103 F+ LPL+FAV + IGLA + + A++GYL ++ L G G+ E G Sbjct: 63 FNQLPLLFAVSLPIGLANKQNARCCMEALVGYLTFQYFVSTMLSQWGGFFGVDFAAEVGG 122 Query: 104 AEHL--------IDMGVFGGIIIGLLAAYLYKRFSSIELHPVLGFFSGKRFVPIITSVSS 155 L +DMG+ G + + + ++ +F +EL LG F+G FV IIT Sbjct: 123 TSGLAMIASIKTLDMGMIGALAVSGIIIAIHNKFYEVELPEWLGVFAGSTFVYIITFFVM 182 Query: 156 LVIGVIFSFVWPLIQNGINAASSLIADS-TVGLFFYATIYRLLIPFGLHHIFYTPFYFMM 214 L + + WP +Q+GI A +A + T+G+ +A + R LIPFGLHH+ Y+PFY+ Sbjct: 183 LPVAFVACLGWPHVQDGIRAFQGFVATTGTLGVGVFAFLERALIPFGLHHLMYSPFYYDN 242 Query: 215 -----GEYTDPSTGNTVTGDLTRFFAGDPTAGRFMMGDFPYMIFCLPAVALAIIHTARPE 269 G YT +T T F + + C P +ALA TA+PE Sbjct: 243 AVVDGGIYTAFATALPQIAASTDSLKELAPYAAFTCSTWSKIFGC-PGIALAFFVTAKPE 301 Query: 270 KKKMISGVMISAALTSMLTGITEPVEFSFLFVAPVLYLINSILAGVIFVVCDLFHVRHGY 329 KKK + ++I LT++ G+TEP+EF+FLF+AP L++++ +LA ++ + ++ V Sbjct: 302 KKKELLSLLIPITLTAVFCGVTEPIEFTFLFIAPPLFIVHCVLAALLAMAINM--VGCVG 359 Query: 330 TFSGGGIDY-VLNY-GLSTNGW----VVIPVGIVFAFIYYYLFRFAILKWNLKTPGRETD 383 F+GG I+ LN+ L N W + + VG+VF I++ +FRF I+K++ KTPGRE D Sbjct: 360 VFAGGIIEISSLNFIPLMANHWQQYAMALVVGLVFTVIWFVVFRFLIVKFDFKTPGREDD 419 Query: 384 -----------------------EDGQNEEKAPVAKDQLAFHVLQALGGQQNIANLDACI 420 E + +E P A +A VL+ LGG NI ++ C+ Sbjct: 420 DEQVKFRSKAEYRAAKNGELASGEGAKVDESDPYA--VMAAEVLELLGGADNIVDVTNCV 477 Query: 421 TRLRVTVHQPSQVCKD-ELKRLGAVGVLEVNNNFQAIFGTKSDALKDDIKTIM 472 TRLRV V + V D + K +G G+ + Q I G K ++D + ++ Sbjct: 478 TRLRVNVKDETLVADDPDFKSIGTSGIAKNGKGMQVIIGLKVPKVRDRFEALL 530 Lambda K H 0.324 0.142 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: 823 Number of extensions: 45 Number of successful extensions: 7 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: 631 Length of database: 530 Length adjustment: 36 Effective length of query: 595 Effective length of database: 494 Effective search space: 293930 Effective search space used: 293930 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