Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate AO356_18250 AO356_18250 glycerol kinase
Query= reanno::WCS417:GFF1099 (501 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_18250 Length = 501 Score = 992 bits (2564), Expect = 0.0 Identities = 488/501 (97%), Positives = 492/501 (98%) Query: 1 MTDIQNKNYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQ 60 MTDIQNKNYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQ Sbjct: 1 MTDIQNKNYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQ 60 Query: 61 SAVMVEALAQAGLHHDQVAAIGITNQRETTVVWDKVTGRPIYNAIVWQCRRSTEICQQLK 120 SAVMVEALAQAGLHHDQVAAIGITNQRETTVVWDK TGRPIYNAIVWQCRRSTEICQQLK Sbjct: 61 SAVMVEALAQAGLHHDQVAAIGITNQRETTVVWDKTTGRPIYNAIVWQCRRSTEICQQLK 120 Query: 121 RDGHEQYISDTTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGG 180 RDGHEQYIS TTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGG Sbjct: 121 RDGHEQYISQTTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGG 180 Query: 181 KTHVTDYTNASRTMLFNIHTLEWDAKMLEILDIPREMLPEVKSSSEIYGRTKSGIAIGGI 240 K HVTDYTNASRT+LFNIH+LEWDAKMLEILDIPREMLPEVKSSSEIYGRTKSGIAIGGI Sbjct: 181 KVHVTDYTNASRTLLFNIHSLEWDAKMLEILDIPREMLPEVKSSSEIYGRTKSGIAIGGI 240 Query: 241 AGDQQAALFGQMCVEAGQAKNTYGTGCFLLMNTGDKAVKSKHGMLTTIACGPRGEVAYAL 300 AGDQQAALFGQMCVE GQAKNTYGTGCFLLMNTG KAVKS HGMLTTIACGPRGEVAYAL Sbjct: 241 AGDQQAALFGQMCVEPGQAKNTYGTGCFLLMNTGKKAVKSNHGMLTTIACGPRGEVAYAL 300 Query: 301 EGAVFNGGSTVQWLRDELKIINDAHDTEYFAGKVKDSNGVYLVPAFTGLGAPYWDPYARG 360 EGAVFNGGSTVQWLRDELKIINDA DTEYFA KVKDSNGVYLVPAFTGLGAPYWDPYARG Sbjct: 301 EGAVFNGGSTVQWLRDELKIINDALDTEYFANKVKDSNGVYLVPAFTGLGAPYWDPYARG 360 Query: 361 ALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQ 420 ALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERL+ALRVDGGAVANNFLMQFQ Sbjct: 361 ALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLRALRVDGGAVANNFLMQFQ 420 Query: 421 ADILGTQVERPQMRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDEAAKEKL 480 ADILGTQVERP+MRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDEAAKEKL Sbjct: 421 ADILGTQVERPKMRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDEAAKEKL 480 Query: 481 YAGWQKAVSRTRDWEPHEGAE 501 YAGWQKAVSRTRDWEPHE AE Sbjct: 481 YAGWQKAVSRTRDWEPHEDAE 501 Lambda K H 0.319 0.134 0.408 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: 910 Number of extensions: 13 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: 501 Length of database: 501 Length adjustment: 34 Effective length of query: 467 Effective length of database: 467 Effective search space: 218089 Effective search space used: 218089 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: 52 (24.6 bits)
Align candidate AO356_18250 AO356_18250 (glycerol kinase)
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.26274.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-229 746.2 0.4 7.2e-229 746.1 0.4 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18250 AO356_18250 glycerol kinase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18250 AO356_18250 glycerol kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 746.1 0.4 7.2e-229 7.2e-229 1 496 [] 8 494 .. 8 494 .. 0.99 Alignments for each domain: == domain 1 score: 746.1 bits; conditional E-value: 7.2e-229 TIGR01311 1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealek 63 ++i+a+DqGttssrai+fd+++++v++aq+e+ q++p++gwvEhdp+ei++++ +v+ eal++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18250 8 NYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQSAVMVEALAQ 70 59************************************************************* PP TIGR01311 64 leikaeeiaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektG 126 ++ + +++aaiGitnqREttvvWdk+tg+p++naivWq++r ++i+++lk++++e++++++tG lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18250 71 AGLHHDQVAAIGITNQRETTVVWDKTTGRPIYNAIVWQCRRSTEICQQLKRDGHEQYISQTTG 133 *************************************************************** PP TIGR01311 127 LplstYfsatKlrWlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlll 189 L+ ++Yfs+tKl+W+ldnve+ r++a++gellfGtvd+wli+k+tggkvhvtd+tNASRtll+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18250 134 LVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGGKVHVTDYTNASRTLLF 196 *************************************************************** PP TIGR01311 190 nletlkwdeellelfkipkellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlc 252 n+++l+wd ++le+++ip+e+lPe++ssse+yg +++ + i g++Gdqqaal+gq+c lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18250 197 NIHSLEWDAKMLEILDIPREMLPEVKSSSEIYGRTKSG------IAIGGIAGDQQAALFGQMC 253 *********************************99987......******************* PP TIGR01311 253 lkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkyalEGsvavaGaavqwl 315 +++g+aKntYgtGcFll+ntG+k+v s+hg+Ltt+a+ g+ + yalEG+v+ +G++vqwl lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18250 254 VEPGQAKNTYGTGCFLLMNTGKKAVKSNHGMLTTIACGPRGEVA--YALEGAVFNGGSTVQWL 314 *************************************9999886..***************** PP TIGR01311 316 rdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiara 378 rd+lk+i++a ++e +a++v+ds+gvy+VPaf+GL+aPyWd+ Arg+++Gltr+++ hi+ra lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18250 315 RDELKIINDALDTEYFANKVKDSNGVYLVPAFTGLGAPYWDPYARGALFGLTRGVRVDHIIRA 377 *************************************************************** PP TIGR01311 379 aleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalG 441 ale++a+q+rd+l+am++d+g ++++L+vDGg+++nn+lmq+qadilg++verpk+ ettalG lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18250 378 ALESIAYQTRDVLDAMQQDSGERLRALRVDGGAVANNFLMQFQADILGTQVERPKMRETTALG 440 *************************************************************** PP TIGR01311 442 aAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496 aA++agla g+w s+eel+ +a e ++fep+ de+ +ek y+ w++av+r+++w lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18250 441 AAYLAGLACGFWGSLEELRGKAVIE-REFEPQLDEAAKEKLYAGWQKAVSRTRDW 494 *******************999997.9*************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (496 nodes) Target sequences: 1 (501 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: 00:00:00.02 # Mc/sec: 11.26 // [ok]
This GapMind analysis is from Sep 17 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