Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate WP_007798050.1 AFK65_RS00625 glycerol kinase GlpK
Query= CharProtDB::CH_121461 (502 letters) >NCBI__GCF_001277175.1:WP_007798050.1 Length = 505 Score = 957 bits (2473), Expect = 0.0 Identities = 463/501 (92%), Positives = 489/501 (97%) Query: 2 TEKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTL 61 TEKKYIVALDQGTTSSRAVV+DHDANI+SVSQREFEQIYP+PGWVEHDPMEIWA+QSSTL Sbjct: 4 TEKKYIVALDQGTTSSRAVVLDHDANIVSVSQREFEQIYPRPGWVEHDPMEIWASQSSTL 63 Query: 62 VEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGL 121 VE LAKADISSDQIAAIGITNQRET +VWE+ETGKPI+NAIVWQCRRT+EICE LKRDG+ Sbjct: 64 VEALAKADISSDQIAAIGITNQRETAVVWERETGKPIHNAIVWQCRRTSEICEKLKRDGM 123 Query: 122 EDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHV 181 EDY+R TGLVIDPYFSGTKVKWILDHV+G+RERA+RGELLFGTVDTWLIWKMTQGRVHV Sbjct: 124 EDYVRQATGLVIDPYFSGTKVKWILDHVDGARERAKRGELLFGTVDTWLIWKMTQGRVHV 183 Query: 182 TDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPIS 241 TDYTNASRTMLFNIH LDWDD+MLE LDIPR MLP+VR+SSEVYGQTNIGGKGGTRIPI+ Sbjct: 184 TDYTNASRTMLFNIHELDWDDRMLEALDIPRAMLPQVRKSSEVYGQTNIGGKGGTRIPIA 243 Query: 242 GIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNY 301 GIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAV S +GLLTTIACGP GEVNY Sbjct: 244 GIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVASTHGLLTTIACGPRGEVNY 303 Query: 302 ALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYA 361 ALEGAVFMAGASIQWLRDEMKLI+DA+DSEYFATKV++TNGVYVVPAFTGLGAPYWDPYA Sbjct: 304 ALEGAVFMAGASIQWLRDEMKLISDAFDSEYFATKVKDTNGVYVVPAFTGLGAPYWDPYA 363 Query: 362 RGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQ 421 RGAIFGLTRGVN+NHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQ Sbjct: 364 RGAIFGLTRGVNSNHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQ 423 Query: 422 FQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERN 481 FQSDILGTRVERPEVREVTALGAAYLAGLAVG+WQNLDELQEKAVIEREFRPGIETTERN Sbjct: 424 FQSDILGTRVERPEVREVTALGAAYLAGLAVGYWQNLDELQEKAVIEREFRPGIETTERN 483 Query: 482 YRYAGWKKAVKRAMAWEEHDE 502 YRY GW+KAVKRAMAWEEHD+ Sbjct: 484 YRYEGWRKAVKRAMAWEEHDK 504 Lambda K H 0.318 0.134 0.404 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: 977 Number of extensions: 22 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: 502 Length of database: 505 Length adjustment: 34 Effective length of query: 468 Effective length of database: 471 Effective search space: 220428 Effective search space used: 220428 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
Align candidate WP_007798050.1 AFK65_RS00625 (glycerol kinase GlpK)
to HMM TIGR01311 (glpK: glycerol kinase (EC 2.7.1.30))
# 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/TIGR01311.hmm # target sequence database: /tmp/gapView.3433710.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01311 [M=496] Accession: TIGR01311 Description: glycerol_kin: glycerol kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-234 764.6 0.8 1.9e-234 764.4 0.8 1.0 1 NCBI__GCF_001277175.1:WP_007798050.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001277175.1:WP_007798050.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 764.4 0.8 1.9e-234 1.9e-234 1 496 [] 7 499 .. 7 499 .. 0.99 Alignments for each domain: == domain 1 score: 764.4 bits; conditional E-value: 1.9e-234 TIGR01311 1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaa 73 k+i+a+DqGttssra+v+d+++++v+ +q+e++qi+p++gwvEhdp+ei++s+ ++l eal+k++i++++iaa NCBI__GCF_001277175.1:WP_007798050.1 7 KYIVALDQGTTSSRAVVLDHDANIVSVSQREFEQIYPRPGWVEHDPMEIWASQSSTLVEALAKADISSDQIAA 79 69*********************************************************************** PP TIGR01311 74 iGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnve 146 iGitnqREt+vvW++etgkp++naivWq++rt++i+e+lk+++ e+++r+ tGL++++Yfs+tK++W+ld+v+ NCBI__GCF_001277175.1:WP_007798050.1 80 IGITNQRETAVVWERETGKPIHNAIVWQCRRTSEICEKLKRDGMEDYVRQATGLVIDPYFSGTKVKWILDHVD 152 ************************************************************************* PP TIGR01311 147 evrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirssse 219 ++r++a++gellfGtvdtwli+k+t+g+vhvtd+tNASRt+l+n+++l+wd+++le+++ip+++lP++r+sse NCBI__GCF_001277175.1:WP_007798050.1 153 GARERAKRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHELDWDDRMLEALDIPRAMLPQVRKSSE 225 ************************************************************************* PP TIGR01311 220 vygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklg 292 vyg+++ ++++pi+g++Gdqqaal+gqlc+k+g+aKntYgtGcF+l+ntGek+v s+hglLtt+a+ NCBI__GCF_001277175.1:WP_007798050.1 226 VYGQTNIGGKGGTRIPIAGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVASTHGLLTTIACGPR 298 ********9*************************************************************999 PP TIGR01311 293 gkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivG 365 g+ +yalEG+v++aGa +qwlrd++kli++a ++e +a++v+d++gvy+VPaf+GL+aPyWd+ Arg+i+G NCBI__GCF_001277175.1:WP_007798050.1 299 GEV--NYALEGAVFMAGASIQWLRDEMKLISDAFDSEYFATKVKDTNGVYVVPAFTGLGAPYWDPYARGAIFG 369 877..6******************************************************************* PP TIGR01311 366 ltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaett 438 ltr+++++hi+ra+le++a+q+rd+leam++d+g+++++L+vDGg+++nn+lmq+q+dilg++verp+v e+t NCBI__GCF_001277175.1:WP_007798050.1 370 LTRGVNSNHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVT 442 ************************************************************************* PP TIGR01311 439 alGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496 alGaA++aglavg+w++++el+++a e ++f+p ++++er+ +y+ w++av+r++ w NCBI__GCF_001277175.1:WP_007798050.1 443 ALGAAYLAGLAVGYWQNLDELQEKAVIE-REFRPGIETTERNYRYEGWRKAVKRAMAW 499 ************************9997.**************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (496 nodes) Target sequences: 1 (505 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: 30.56 // [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