Align Glucose kinase (characterized, see rationale)
to candidate Pf1N1B4_600 Glucokinase (EC 2.7.1.2)
Query= uniprot:Q8P6M4 (344 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_600 Length = 319 Score = 140 bits (352), Expect = 6e-38 Identities = 101/316 (31%), Positives = 155/316 (49%), Gaps = 17/316 (5%) Query: 23 LAADVGGTHVRVGRVSHGADAPIELSQYRTYRCADHASLDAILADFLRD----SRAVDAV 78 L D+GGT+ R + +L + ADHAS + +A +L ++ +V Sbjct: 5 LVGDIGGTNARFALWKNQ-----QLESVQVLATADHASPEEAIALYLSGLGLAPGSIGSV 59 Query: 79 VIASAG-VALDDGRFISNNLPWTIAPRQLRDTLGVRAVHLVNDFEAVAYAAPQMEQRAVV 137 ++ AG V+ D+ +F +N+ W ++ + TL V + LVNDF A+A +++ Sbjct: 60 CLSVAGPVSGDEFKFTNNH--WRLSRQGFCKTLQVDQLLLVNDFSAMALGMTRLQPGEFR 117 Query: 138 QLSGPTPRHAQPGGPILVVGPGTGLGAAVWIN-GPRQPTVLATEAGQVALASNDPDTAQV 196 + TP +P P +V+GPGTGLG ++ G + L E G V L + P Q+ Sbjct: 118 VVCEGTP---EPLRPAVVIGPGTGLGVGTLLDLGEGRFAPLPGEGGHVDLPLSSPRETQL 174 Query: 197 LRILARDASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALHSDDALARRC 256 + + + ++ E LSG GL +Y A+C + TP+ P IT A L + D +A Sbjct: 175 WQHIFNEIGHVSAETALSGSGLPRVYRAICAVDGHTPVLDTPEAITKAGL-AGDPIALEV 233 Query: 257 LQLFCALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAKGRMRPVLER 316 L+ FC LG G+ L GA GGVY+ GG++P F S F F KG M + Sbjct: 234 LEQFCCWLGRVAGNNVLTTGARGGVYIVGGVIPRFADFFIESGFARCFADKGCMSDYFKG 293 Query: 317 IPVKLVEHGQLGVLGA 332 IPV LV G++GA Sbjct: 294 IPVWLVTAPYSGLVGA 309 Lambda K H 0.321 0.136 0.410 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: 317 Number of extensions: 16 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: 344 Length of database: 319 Length adjustment: 28 Effective length of query: 316 Effective length of database: 291 Effective search space: 91956 Effective search space used: 91956 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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