Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate 5210198 Shew_2641 PTS system, glucose-like IIB subunint (RefSeq)
Query= BRENDA::P69786 (477 letters) >FitnessBrowser__PV4:5210198 Length = 490 Score = 416 bits (1070), Expect = e-121 Identities = 201/472 (42%), Positives = 305/472 (64%), Gaps = 7/472 (1%) Query: 6 FANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPLIFAI 65 F Q++ ++L+LP+++LP AG+++G+ + ++ A ++ +M G VF+ MP++FA+ Sbjct: 24 FKFAQRLSQALLLPIAILPAAGVMIGLATNPIPFISADLATLMWTVGNLVFSMMPMLFAV 83 Query: 66 GVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGGIISG 125 +A+GF + G++A +AV YG+ +++ +A + HLP E I + DTG+ GG++ G Sbjct: 84 TIAIGFCRDQGIAAFSAVFGYGVFFSSLSALAK-IYHLPTEMILGQATIDTGIAGGMMVG 142 Query: 126 AIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQTFSQW 185 A + RI+LP FF G+R P++ AI + +WP + + I+ S W Sbjct: 143 AFTCLVVKHSERIRLPAVFSFFEGRRSAPLLMLPMAILLAYLFLLLWPLLSNWIEQISNW 202 Query: 186 AAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYMAGDP 245 A YQ P AF +YG +ER L+P GLHHIWN PF +++G+Y N V G++ RY+AGDP Sbjct: 203 AVYQEPASAFAVYGMVERLLIPLGLHHIWNAPFYLEMGQYFNGDEWV-RGEVARYLAGDP 261 Query: 246 TAGKLSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSFM 305 AG L+GG+L KM+GLPAAA+AIW A R +V GIM+SAA +LTG+TEPIEF+FM Sbjct: 262 QAGNLAGGYLIKMWGLPAAALAIWRCADKHERNRVAGIMLSAATACWLTGVTEPIEFAFM 321 Query: 306 FVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIVGIGYA 365 FVAP+L+I+HA++ G+A+ + I L + FSHGL+DF +L G S + F I+G A Sbjct: 322 FVAPLLFILHALMTGIAYAVTISLDIHHSVVFSHGLVDFSLLLGQSRNVEWFLILGPLTA 381 Query: 366 IVYYTIFRVLIKALDLKTPGREDATEDAKATGTSEMAPALVAAFGGKENITNLDACITRL 425 ++YY +FR I A +LKTPGR +A +A S ++ A GG++NI L AC+TRL Sbjct: 382 VIYYLVFRGAILAFNLKTPGRMEAGSGQRAGLIS-----MITALGGQDNINELTACLTRL 436 Query: 426 RVSVADVSKVDQAGLKKLGAAGVVVAGSGVQAIFGTKSDNLKTEMDEYIRNH 477 R+SV VD+A L KLGA GVV+ G+GVQ ++GTK+++++ + Y+ H Sbjct: 437 RISVKHAELVDKAQLNKLGAKGVVLVGNGVQLVYGTKAESIRRLLQRYLDRH 488 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: 641 Number of extensions: 29 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: 477 Length of database: 490 Length adjustment: 34 Effective length of query: 443 Effective length of database: 456 Effective search space: 202008 Effective search space used: 202008 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