Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_086509385.1 BZY95_RS07825 glucokinase
Query= reanno::WCS417:GFF4431 (318 letters) >NCBI__GCF_002151265.1:WP_086509385.1 Length = 322 Score = 229 bits (583), Expect = 9e-65 Identities = 136/314 (43%), Positives = 174/314 (55%), Gaps = 6/314 (1%) Query: 4 ALVGDIGGTNARFALWRDQELHSIRVHAT---ADHSSPEDAIKVYLKEEGLEIGDIGA-V 59 AL+GDIGGTNARFAL E H+ R AD+ +A++ YL GL D Sbjct: 5 ALIGDIGGTNARFALVTPGE-HAPRESIALPCADYPGVVEAVRDYLARVGLAADDAPRQA 63 Query: 60 CLSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVV 119 CL+ A P+ GD TNNHW S+ L ++ L ++NDF+A ALG+ L P+E V Sbjct: 64 CLAFACPIDGDRVVMTNNHWSFSRREAQTALGLERLKVINDFTAQALGVPHLAPEELVEV 123 Query: 120 CEGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIY 179 G +VIGPGTGLGV + G + LP EGGHV + RE L +H Sbjct: 124 QPGVAREHATCLVIGPGTGLGVAGIFP-GRHAWIPLPTEGGHVTYAPTDEREQNLLRHFR 182 Query: 180 TEIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSI 239 G VS E L G GL LY A C++ G P +TP +TAA GD +A + L +F Sbjct: 183 NRYGRVSVERILCGQGLLDLYLAHCSLKGANPSCQTPPEVTAAAAGGDAIARDTLLRFLK 242 Query: 240 WLGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLV 299 LG V G+ LT G RGGVY+ GG++PR D+ S F ++F KG MSDY + IPV +V Sbjct: 243 ILGDVCGDAALTMGARGGVYLCGGILPRLLDWLPQSRFVEAFTAKGRMSDYNRAIPVRVV 302 Query: 300 TAPYSGLTGAGVAL 313 TAP+ GL GA AL Sbjct: 303 TAPWPGLLGAAEAL 316 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: 290 Number of extensions: 22 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: 318 Length of database: 322 Length adjustment: 28 Effective length of query: 290 Effective length of database: 294 Effective search space: 85260 Effective search space used: 85260 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_086509385.1 BZY95_RS07825 (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.22064.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-88 283.2 0.0 1.6e-88 283.0 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086509385.1 BZY95_RS07825 glucokinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086509385.1 BZY95_RS07825 glucokinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 283.0 0.0 1.6e-88 1.6e-88 1 315 [] 6 313 .. 6 313 .. 0.93 Alignments for each domain: == domain 1 score: 283.0 bits; conditional E-value: 1.6e-88 TIGR00749 1 lvgdiGGtnarlalvevapgeieqv..ktyssedfpsleavvrvyleeakvelkd.pikgcfaiatPii 66 l+gdiGGtnar+alv +pge + ++ + d+p ++++vr yl + d p ++c+a a+Pi lcl|NCBI__GCF_002151265.1:WP_086509385.1 6 LIGDIGGTNARFALV--TPGEHAPResIALPCADYPGVVEAVRDYLARVGLAADDaPRQACLAFACPID 72 79************6..44444443115689**********************99999*********** PP TIGR00749 67 gdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGt 135 gd v +tn++W++s e + l+l++l++indf+a+a++++ l e+l+ ++ + e a+ ++G+Gt lcl|NCBI__GCF_002151265.1:WP_086509385.1 73 GDRVVMTNNHWSFSRREAQTALGLERLKVINDFTAQALGVPHLAPEELVEVQPGVAREHATCLVIGPGT 141 ********************************************************************* PP TIGR00749 136 GlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskr 204 GlGva + + + + l++eGghv +aP++e e ll+ r++ygrvs+er+l G+Gl +y a lcl|NCBI__GCF_002151265.1:WP_086509385.1 142 GLGVAGIFP-GRHAWIPLPTEGGHVTYAPTDEREQNLLRHFRNRYGRVSVERILCGQGLLDLYLAHCSL 209 *********.99***************************************************887666 PP TIGR00749 205 kgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrf 273 kg + + +++ +++ aa +g d++ar +l fl ilG ++g+ al++garGGvy++GGi+Pr+ lcl|NCBI__GCF_002151265.1:WP_086509385.1 210 KGAN------PSCQTPPEVTAAA-AGGDAIARDTLLRFLKILGDVCGDAALTMGARGGVYLCGGILPRL 271 6433......2456788998766.677899*************************************** PP TIGR00749 274 iellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315 +++l +s f +af kGr+ ++ iPv+vv +GllGa+ lcl|NCBI__GCF_002151265.1:WP_086509385.1 272 LDWLPQSRFVEAFTAKGRMSDYNRAIPVRVVTAPWPGLLGAA 313 ****************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (315 nodes) Target sequences: 1 (322 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 11.24 // [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