Align Fructokinase; EC 2.7.1.4 (characterized)
to candidate PfGW456L13_3908 Ribokinase (EC 2.7.1.15)
Query= SwissProt::P26420 (307 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 Length = 305 Score = 85.5 bits (210), Expect = 1e-21 Identities = 93/323 (28%), Positives = 134/323 (41%), Gaps = 42/323 (13%) Query: 1 MNGKIWVLGDAVVDL------LPDGEGRLL-----QCPGGAPANVAVGVARLGGDSGFIG 49 M+ K+ V+G +DL LP G L+ GG AN AV ARLG IG Sbjct: 1 MSAKVVVIGSLNMDLVTRAPRLPKGGETLIGQSFTTVSGGKGANQAVAAARLGAQVSMIG 60 Query: 50 RVGDDPFGRFMRHTLAQEQVDVNYMR-LDAAQRTSTVVVDLDSHGERTFTFMVRPSADLF 108 VG+D +G +R L EQ+D + +D + + +VVD S + ++ P A+ Sbjct: 61 CVGNDAYGEALRGALLAEQIDCRAVSTVDGSSGVALIVVDDSSQN----SIVIVPGANGA 116 Query: 109 LQPEDLPPFAA---GQWLHVCSIALSAEPSRSTTFAALEAIKRAGGYVSFDPNIRSDLWQ 165 L E + F + + +C + E ++ AL+ + G V +P S Sbjct: 117 LTAETIDRFDSVIRAADVLICQL----EVPDASVGHALKRGRELGKTVILNPAPAS---- 168 Query: 166 DPQDLRDCLDRALALADAIKLSEEELAFISG----SDDIVSGIARLNARFQPTLLLVTQG 221 R A D + +E E + +SG S D A +++T G Sbjct: 169 -----RPLPSDWYASIDYLIPNESEASALSGLSVDSLDTAQAAATRLIALGAGKVIITLG 223 Query: 222 KAGVQAALRGQVSHFPARPVVAVDTTGAGDAFVAGLLAGLAAHGIPDNLAALAPDLALAQ 281 G A + HFPA V AVDTT AGD FV G A LAA A + Q Sbjct: 224 AQGSLFADGQRFEHFPAPVVKAVDTTAAGDTFVGGFAAALAAGNDE------AQAIRFGQ 277 Query: 282 TCGALATTAKGAMTALPYKDDLQ 304 AL+ T GA ++P D+Q Sbjct: 278 VAAALSVTRAGAQPSIPALSDVQ 300 Lambda K H 0.321 0.137 0.406 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: 190 Number of extensions: 8 Number of successful extensions: 2 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: 307 Length of database: 305 Length adjustment: 27 Effective length of query: 280 Effective length of database: 278 Effective search space: 77840 Effective search space used: 77840 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 (21.8 bits) S2: 48 (23.1 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