Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_017222136.1 A923_RS0113155 glucokinase
Query= ecocyc::GLUCOKIN-MONOMER (321 letters) >NCBI__GCF_000276805.1:WP_017222136.1 Length = 319 Score = 325 bits (832), Expect = 1e-93 Identities = 158/316 (50%), Positives = 215/316 (68%) Query: 5 ALVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAIA 64 ++V DVGGTN RLA+CD+ +G +S+ K ++ ++ +LEA + Y E+ C+ IA Sbjct: 3 SVVADVGGTNIRLAVCDLETGALSELKEFACAEFVTLEAALAQYFAALSGEITHLCVGIA 62 Query: 65 CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124 CP+ D V MTN W FS ++ L + L IIND+TA+S+A+P L E IQ G E Sbjct: 63 CPVENDHVVMTNLNWEFSKQALQDKLKLASLHIINDYTAISLAVPFLSAEEKIQIGAGEC 122 Query: 125 VEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHV 184 AV+G GTGLGV+H+V +W+SL GEGGHV F PN+ E+A IL +L+ + GHV Sbjct: 123 QTDGVTAVFGPGTGLGVSHIVKAAGKWISLDGEGGHVSFTPNTPEQADILCLLQTQFGHV 182 Query: 185 SAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRF 244 SAER+LSG GLVNLY+ + + + +PKD+T+ AL SC R++L++FC +MG F Sbjct: 183 SAERILSGQGLVNLYKCLCTLSEQEAKFDQPKDVTKAALDGSCDIARKSLAVFCQVMGGF 242 Query: 245 GGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNP 304 GNLALNL GG++IAGGIVPRF++FF+AS FR FE+KGRFK+Y+ IP +LI HDNP Sbjct: 243 AGNLALNLACTGGIYIAGGIVPRFVDFFQASEFRRCFEEKGRFKDYLTAIPTFLITHDNP 302 Query: 305 GLLGSGAHLRQTLGHI 320 GLLG+ +LRQ L I Sbjct: 303 GLLGASVYLRQELTSI 318 Lambda K H 0.322 0.141 0.426 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: 337 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: 321 Length of database: 319 Length adjustment: 28 Effective length of query: 293 Effective length of database: 291 Effective search space: 85263 Effective search space used: 85263 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: 48 (23.1 bits)
Align candidate WP_017222136.1 A923_RS0113155 (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.3342883.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-106 339.6 0.2 1.1e-105 339.4 0.2 1.0 1 NCBI__GCF_000276805.1:WP_017222136.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000276805.1:WP_017222136.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 339.4 0.2 1.1e-105 1.1e-105 2 314 .. 5 307 .. 4 308 .. 0.98 Alignments for each domain: == domain 1 score: 339.4 bits; conditional E-value: 1.1e-105 TIGR00749 2 vgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrltn 74 v+d+GGtn rla+++ +g ++ +k + + +f lea++ +y e+ + c+ ia+P+ +d v +tn NCBI__GCF_000276805.1:WP_017222136.1 5 VADVGGTNIRLAVCDLETGALSELKEFACAEFVTLEAALAQYFAALSGEITH---LCVGIACPVENDHVVMTN 74 89*****************************************999999988...9***************** PP TIGR00749 75 ldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqsd 147 l+W++s + l+ +l la l++ind++a+++a++ l e+ iq+g+ ++++++ a++G+GtGlGv+++++ + NCBI__GCF_000276805.1:WP_017222136.1 75 LNWEFSKQALQDKLKLASLHIINDYTAISLAVPFLSAEEKIQIGAGECQTDGVTAVFGPGTGLGVSHIVK-AA 146 *********************************************************************9.99 PP TIGR00749 148 grykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelke 220 g++ +l geGghv+f+P+ ++++ +l +l++++g+vsaer+lsG+Glv++y+ l ++ +k+ ++ NCBI__GCF_000276805.1:WP_017222136.1 147 GKWISLDGEGGHVSFTPNTPEQADILCLLQTQFGHVSAERILSGQGLVNLYKCLCTLS--EQEAKFD----QP 213 ******************************************************9887..4456766....8* PP TIGR00749 221 kdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlk 293 kd+++aal+gs+ +ar++l +f+ ++G +agnlal+l GG+y+aGGivPrf++++++s fr fe+kGr+k NCBI__GCF_000276805.1:WP_017222136.1 214 KDVTKAALDGSCDIARKSLAVFCQVMGGFAGNLALNLACTGGIYIAGGIVPRFVDFFQASEFRRCFEEKGRFK 286 ************************************************************************* PP TIGR00749 294 ellasiPvqvvlkkkvGllGa 314 ++l+ iP ++ ++++GllGa NCBI__GCF_000276805.1:WP_017222136.1 287 DYLTAIPTFLITHDNPGLLGA 307 ********************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (319 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 19.33 // [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