Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_011913558.1 PST_RS12280 glucokinase
Query= reanno::WCS417:GFF4431 (318 letters) >NCBI__GCF_000013785.1:WP_011913558.1 Length = 320 Score = 398 bits (1022), Expect = e-115 Identities = 196/314 (62%), Positives = 235/314 (74%) Query: 1 MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60 MK ALVGDIGGTNARFALWRDQ + IRV TADH+ PE AI+ YL E G + + AVC Sbjct: 1 MKTALVGDIGGTNARFALWRDQRIEQIRVLPTADHARPELAIRAYLDEVGQPLDALEAVC 60 Query: 61 LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120 L+ AGPVSGD F+FTNNHW+LS+ AFC+ L + +LLL+NDF+AMALGMTRL+ DE V Sbjct: 61 LACAGPVSGDHFRFTNNHWQLSRQAFCRELGLKDLLLINDFTAMALGMTRLRDDERVTVR 120 Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180 EG PEP RP +VIGPGTGLGV LL L G + ALPGEGGH+ LP+ S RE +W ++ Sbjct: 121 EGEPEPGRPRLVIGPGTGLGVAGLLPLVGGGWRALPGEGGHICLPIGSEREAAIWTQLHR 180 Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240 GHV+AE LSG GL LYRA CA+DG ++P IT A LAG+P A+ VL+QF W Sbjct: 181 AQGHVNAEAVLSGPGLLTLYRACCALDGRAAEHDSPAGITKAALAGEPYAVAVLEQFCRW 240 Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300 LGR+ G+NVLT G RGGVYIVGGV+PRFA+FF++SGF + +KG MS YF +PVWLVT Sbjct: 241 LGRIVGDNVLTLGARGGVYIVGGVVPRFAEFFMHSGFCDALCEKGQMSGYFDRLPVWLVT 300 Query: 301 APYSGLTGAGVALE 314 APY GL GAGVAL+ Sbjct: 301 APYPGLEGAGVALQ 314 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: 386 Number of extensions: 14 Number of successful extensions: 1 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: 318 Length of database: 320 Length adjustment: 28 Effective length of query: 290 Effective length of database: 292 Effective search space: 84680 Effective search space used: 84680 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)
Align candidate WP_011913558.1 PST_RS12280 (glucokinase)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR00749.hmm # target sequence database: /tmp/gapView.697217.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00749 [M=315] Accession: TIGR00749 Description: glk: glucokinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-80 254.6 0.0 8.2e-80 254.4 0.0 1.0 1 NCBI__GCF_000013785.1:WP_011913558.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000013785.1:WP_011913558.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 254.4 0.0 8.2e-80 8.2e-80 1 315 [] 5 310 .. 5 310 .. 0.97 Alignments for each domain: == domain 1 score: 254.4 bits; conditional E-value: 8.2e-80 TIGR00749 1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrlt 73 lvgdiGGtnar+al ++ieq++++ + d+ e ++r yl+e l c+a a+P+ gd r+t NCBI__GCF_000013785.1:WP_011913558.1 5 LVGDIGGTNARFAL--WRDQRIEQIRVLPTADHARPELAIRAYLDEVGQPLDALEAVCLACAGPVSGDHFRFT 75 89************..8899******************************9997799**************** PP TIGR00749 74 nldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqs 146 n++W+ls + +el+l+ l lindf+a+a++++ l++++ + + ++e++ + ++G+GtGlGva l++ + NCBI__GCF_000013785.1:WP_011913558.1 76 NNHWQLSRQAFCRELGLKDLLLINDFTAMALGMTRLRDDERVTVREGEPEPGRPRLVIGPGTGLGVAGLLPLV 148 ************************************************************************* PP TIGR00749 147 dgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelk 219 g +++l+geGgh+ + se e+ ++ l++ g+v ae vlsG+Gl ++y+a + + e+ NCBI__GCF_000013785.1:WP_011913558.1 149 GGGWRALPGEGGHICLPIGSEREAAIWTQLHRAQGHVNAEAVLSGPGLLTLYRACCALD-----GRAA-EHDS 215 ********************************************************999.....4444.7889 PP TIGR00749 220 ekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrl 292 + i++aal+g+ + a le f+ lG++ g+ l+lgarGGvy++GG+vPrf e++ +s+f a+ +kG++ NCBI__GCF_000013785.1:WP_011913558.1 216 PAGITKAALAGE-PYAVAVLEQFCRWLGRIVGDNVLTLGARGGVYIVGGVVPRFAEFFMHSGFCDALCEKGQM 287 **********97.678899****************************************************** PP TIGR00749 293 kellasiPvqvvlkkkvGllGag 315 ++ +Pv +v +Gl Gag NCBI__GCF_000013785.1:WP_011913558.1 288 SGYFDRLPVWLVTAPYPGLEGAG 310 *********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (320 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 13.69 // [ok]
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