Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate WP_038210079.1 Q392_RS16455 glycerol kinase GlpK
Query= SwissProt::O66131 (496 letters) >NCBI__GCF_000745855.1:WP_038210079.1 Length = 497 Score = 558 bits (1437), Expect = e-163 Identities = 278/495 (56%), Positives = 353/495 (71%), Gaps = 5/495 (1%) Query: 4 YMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASVL 63 Y+LA+DQGT+SSR+I+F+ G IV MAQ+E Q +PQPGWVEH+ EIW LA VL Sbjct: 3 YLLALDQGTSSSRSIVFDAAGRIVAMAQRELPQIYPQPGWVEHDPMEIWQGQLATAREVL 62 Query: 64 SEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYDPLF 123 ++A++KP + IGITNQRETT+VWE+ TG P+++AIVWQ R+ +C +L+A G + Sbjct: 63 AKAKLKPTDIRAIGITNQRETTLVWERATGRPVHHAIVWQDRRAEPLCAKLRADGMEDTI 122 Query: 124 RKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVTDYS 183 R+KTGL+IDAYFS TK+ W+LD+V G R RAERGEL FGT+D+WLIW+L+GG+VHVTD S Sbjct: 123 REKTGLVIDAYFSATKLVWLLDNVPGLRARAERGELAFGTVDSWLIWQLTGGKVHVTDVS 182 Query: 184 NASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAGAAG 243 NASRT++FN+H WD +LL L VP A++PEVRPSS +A A G +PI G AG Sbjct: 183 NASRTMLFNVHRNAWDADLLAALKVPAALMPEVRPSSCHFA-DADAALLGAPLPIGGVAG 241 Query: 244 DQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVEYALEG 303 DQQAALFGQACF GMAKNTYGTGCF+LM+TGEK S++GLL T A + +YA+EG Sbjct: 242 DQQAALFGQACFGPGMAKNTYGTGCFLLMHTGEKFQPSRNGLLVTSAAQTSAQPQYAMEG 301 Query: 304 SIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSEVRGAV 363 S+FV G+ +QWLRDGL+ I+ + + AE V GV VVPAF GLG PYW ++ RG + Sbjct: 302 SVFVGGAVVQWLRDGLQAIQGSGQVQALAESVPDAGGVMVVPAFTGLGAPYWKADARGTI 361 Query: 364 FGLTRGTTKEHFIRATLESLAYQTKDVLAVM----EADSGISLTTLRVDGGAVKNNFLMQ 419 GLTRGTT H RA LES+AYQ+ +L M EA G + LRVDGGA N+ LMQ Sbjct: 362 TGLTRGTTVAHIARAALESIAYQSAALLFAMSRDAEAAGGAPVAELRVDGGASVNDLLMQ 421 Query: 420 FQSDLLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKRT 479 FQ+DLL +PV RP V ETTALGAAYLAGLA G + ++++ QW+ +RRF P M + Sbjct: 422 FQADLLGIPVVRPEVVETTALGAAYLAGLACGVYAGTEELSRQWRAQRRFMPTMSRAQAD 481 Query: 480 MLYDGWKKAVRAAMA 494 W+ AVR A A Sbjct: 482 EAMARWEHAVRQATA 496 Lambda K H 0.319 0.134 0.406 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: 735 Number of extensions: 27 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: 496 Length of database: 497 Length adjustment: 34 Effective length of query: 462 Effective length of database: 463 Effective search space: 213906 Effective search space used: 213906 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 (21.7 bits) S2: 52 (24.6 bits)
Align candidate WP_038210079.1 Q392_RS16455 (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.170098.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-215 700.1 0.1 6.7e-215 700.0 0.1 1.0 1 NCBI__GCF_000745855.1:WP_038210079.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000745855.1:WP_038210079.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 700.0 0.1 6.7e-215 6.7e-215 2 493 .. 3 494 .. 2 497 .] 0.99 Alignments for each domain: == domain 1 score: 700.0 bits; conditional E-value: 6.7e-215 TIGR01311 2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaai 74 +++a+DqGt+ssr ivfd+ g++va aq+el qi+p++gwvEhdp+ei++ ++++++e+l+k++ k+++i ai NCBI__GCF_000745855.1:WP_038210079.1 3 YLLALDQGTSSSRSIVFDAAGRIVAMAQRELPQIYPQPGWVEHDPMEIWQGQLATAREVLAKAKLKPTDIRAI 75 89*********************************************************************** PP TIGR01311 75 GitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnvee 147 GitnqREtt+vW+++tg+p+++aivWqd+r + ++++l++++ e+++rektGL++++YfsatKl Wlldnv++ NCBI__GCF_000745855.1:WP_038210079.1 76 GITNQRETTLVWERATGRPVHHAIVWQDRRAEPLCAKLRADGMEDTIREKTGLVIDAYFSATKLVWLLDNVPG 148 ************************************************************************* PP TIGR01311 148 vrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssev 220 +r++ae+gel fGtvd+wli++Ltggkvhvtdv+NASRt+l+n+++++wd +ll+++k+p++l+Pe+r+ss + NCBI__GCF_000745855.1:WP_038210079.1 149 LRARAERGELAFGTVDSWLIWQLTGGKVHVTDVSNASRTMLFNVHRNAWDADLLAALKVPAALMPEVRPSSCH 221 ************************************************************************* PP TIGR01311 221 ygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklgg 293 +++ +++ ll++ +pi gv+Gdqqaal+gq+c+ +g+aKntYgtGcFll++tGek + s++glL t a +++ NCBI__GCF_000745855.1:WP_038210079.1 222 FADADAA-LLGAPLPIGGVAGDQQAALFGQACFGPGMAKNTYGTGCFLLMHTGEKFQPSRNGLLVTSAAQTSA 293 *****99.*************************************************************9998 PP TIGR01311 294 kkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGl 366 + +ya+EGsv+v+Ga+vqwlrd l+ i+ + +v++la+sv+d +gv++VPaf+GL+aPyW++dArgti+Gl NCBI__GCF_000745855.1:WP_038210079.1 294 QP--QYAMEGSVFVGGAVVQWLRDGLQAIQGSGQVQALAESVPDAGGVMVVPAFTGLGAPYWKADARGTITGL 364 76..6******************************************************************** PP TIGR01311 367 trkttkehiaraaleavafqardileamekdag....vevkvLkvDGglsknnllmqiqadilgvkverpkva 435 tr+tt +hiaraale++a+q+ ++l am++da+ + v++L+vDGg+s n+llmq+qad+lg++v+rp+v+ NCBI__GCF_000745855.1:WP_038210079.1 365 TRGTTVAHIARAALESIAYQSAALLFAMSRDAEaaggAPVAELRVDGGASVNDLLMQFQADLLGIPVVRPEVV 437 ********************************988888999******************************** PP TIGR01311 436 ettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeavers 493 ettalGaA++agla gv+ +eel+++++a+ ++f p+m++++ ++ +++w++av+++ NCBI__GCF_000745855.1:WP_038210079.1 438 ETTALGAAYLAGLACGVYAGTEELSRQWRAQ-RRFMPTMSRAQADEAMARWEHAVRQA 494 *****************************97.***********************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (496 nodes) Target sequences: 1 (497 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 32.09 // [ok]
This GapMind analysis is from Apr 09 2024. 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