Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate WP_009141894.1 HMPREF9452_RS09360 PTS transporter subunit EIIC
Query= BRENDA::P69786 (477 letters) >NCBI__GCF_000225705.1:WP_009141894.1 Length = 530 Score = 226 bits (577), Expect = 1e-63 Identities = 153/524 (29%), Positives = 247/524 (47%), Gaps = 62/524 (11%) Query: 9 LQKVGKSLMLPVSVLPIAGILLGVGS-----ANFSWLPAV------VSHVMAEAGGSVFA 57 +QK G ++ PV + AG+++G G+ F L A V +V+ + G +VF Sbjct: 5 IQKFGGAMFTPVMLFAFAGVVIGFGTLFTTEVIFGPLAAPGTMWYGVWNVILQGGWTVFN 64 Query: 58 NMPLIFAIGVALGFTNNDG----VSALAAVVAYGIMVKTMA----------VVAPLVLHL 103 +PL+FA+ + +G N + AL + + V TM A + Sbjct: 65 QLPLLFAVSLPIGLANKQNARCCMEALVGYLTFQYFVSTMLSQWGGFFGVDFAAEVGGTS 124 Query: 104 PAEEIASKHLADTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIF 163 IAS D G++G + I + N+FY ++LPE+LG FAG FV II+ + Sbjct: 125 GLAMIASIKTLDMGMIGALAVSGIIIAIHNKFYEVELPEWLGVFAGSTFVYIITFFVMLP 184 Query: 164 TGVVLSFIWPPIGSAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIG 223 V WP + I+ F + A + G++ F+ER L+PFGLHH+ PF Sbjct: 185 VAFVACLGWPHVQDGIRAFQGFVATTG-TLGVGVFAFLERALIPFGLHHLMYSPFYYDNA 243 Query: 224 EYTNAAGQVFHGDIPRYMAGDPTAGKLSGGFLF------KMYGLPAAAIAIWHSAKPENR 277 F +P+ A + +L+ F K++G P A+A + +AKPE + Sbjct: 244 VVDGGIYTAFATALPQIAASTDSLKELAPYAAFTCSTWSKIFGCPGIALAFFVTAKPEKK 303 Query: 278 AKVGGIMISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGL---AFPICILLGMRDG 334 ++ ++I LT+ G+TEPIEF+F+F+AP L+I+H +LA L A + +G+ G Sbjct: 304 KELLSLLIPITLTAVFCGVTEPIEFTFLFIAPPLFIVHCVLAALLAMAINMVGCVGVFAG 363 Query: 335 TSFSHGLIDFIVLSGNSSKLWLFP-IVGIGYAIVYYTIFRVLIKALDLKTPGREDATEDA 393 ++FI L N + + +VG+ + ++++ +FR LI D KTPGRED E Sbjct: 364 GIIEISSLNFIPLMANHWQQYAMALVVGLVFTVIWFVVFRFLIVKFDFKTPGREDDDEQV 423 Query: 394 KATGTSE-------------------------MAPALVAAFGGKENITNLDACITRLRVS 428 K +E MA ++ GG +NI ++ C+TRLRV+ Sbjct: 424 KFRSKAEYRAAKNGELASGEGAKVDESDPYAVMAAEVLELLGGADNIVDVTNCVTRLRVN 483 Query: 429 VADVSKV-DQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMD 471 V D + V D K +G +G+ G G+Q I G K ++ + Sbjct: 484 VKDETLVADDPDFKSIGTSGIAKNGKGMQVIIGLKVPKVRDRFE 527 Lambda K H 0.325 0.140 0.422 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: 648 Number of extensions: 36 Number of successful extensions: 8 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: 477 Length of database: 530 Length adjustment: 34 Effective length of query: 443 Effective length of database: 496 Effective search space: 219728 Effective search space used: 219728 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 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