Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_043744689.1 AMB_RS14985 transcriptional regulator
Query= reanno::SB2B:6938110 (299 letters) >NCBI__GCF_000009985.1:WP_043744689.1 Length = 297 Score = 291 bits (746), Expect = 9e-84 Identities = 155/296 (52%), Positives = 186/296 (62%), Gaps = 8/296 (2%) Query: 2 MRMGVDLGGTKIELVALGEDGSELFRKRIATPR-EYQGTLNAVVTLVNEAEATLGTQGSL 60 +R+G+DLGGTK E +AL G EL R+R+AT R Y GT+ + LV E+ LG S+ Sbjct: 3 LRIGIDLGGTKTEAIALDLSGRELARQRVATARGSYDGTIATIKGLVEGLESRLGAAASV 62 Query: 61 GIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAA 120 GIGIPG ISP TGL+KNANSTW+ G PLDRDL L R VR+ANDA+CFA+SEA DGA A Sbjct: 63 GIGIPGTISPRTGLIKNANSTWLIGKPLDRDLETALGRPVRLANDADCFALSEATDGAGA 122 Query: 121 GKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLPWMRPDEFNTTECFCGNKDC 180 G VFG ILGTG G G+ GR+ G N I GEWGHNPLPW E C+CG C Sbjct: 123 GFDTVFGVILGTGVGGGIVAHGRLLSGPNAIAGEWGHNPLPWPEDAERPGPACYCGRSGC 182 Query: 181 IETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHVINML 240 IETF+SG G RD GG G L + D A RY RLAR+LA VIN++ Sbjct: 183 IETFLSGPGLARD---HGG----GLSAEQLATSDDAAAGAALARYERRLARALAAVINVI 235 Query: 241 DPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNLYGCSSGVRGAAWLW 296 DP IVLGGG+S + +Y +PA+ +V T + +G SSGVRGAAWLW Sbjct: 236 DPHVIVLGGGLSKLDRLYRNVPALWEGFVFSDHVDTLLRPPRHGDSSGVRGAAWLW 291 Lambda K H 0.320 0.139 0.429 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: 306 Number of extensions: 16 Number of successful extensions: 3 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: 299 Length of database: 297 Length adjustment: 27 Effective length of query: 272 Effective length of database: 270 Effective search space: 73440 Effective search space used: 73440 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