Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate Pf6N2E2_5574 Glycerol kinase (EC 2.7.1.30)
Query= reanno::WCS417:GFF1099 (501 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 Length = 501 Score = 991 bits (2563), Expect = 0.0 Identities = 488/501 (97%), Positives = 491/501 (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 HVTDYTNASRTMLFNIH+LEWDAKML+ILDIPREMLPEVKSSSEIYGRTKSGIAIGGI Sbjct: 181 KVHVTDYTNASRTMLFNIHSLEWDAKMLDILDIPREMLPEVKSSSEIYGRTKSGIAIGGI 240 Query: 241 AGDQQAALFGQMCVEAGQAKNTYGTGCFLLMNTGDKAVKSKHGMLTTIACGPRGEVAYAL 300 AGDQQAALFGQMCVE GQAKNTYGTGCFLLMNTG KAVKS HGMLTTIACGPRGEVAYAL Sbjct: 241 AGDQQAALFGQMCVEPGQAKNTYGTGCFLLMNTGSKAVKSNHGMLTTIACGPRGEVAYAL 300 Query: 301 EGAVFNGGSTVQWLRDELKIINDAHDTEYFAGKVKDSNGVYLVPAFTGLGAPYWDPYARG 360 EGAVFNGGSTVQWLRDELKIINDA DTEYFA KVKDSNGVYLVPAFTGLGAPYWDPYARG Sbjct: 301 EGAVFNGGSTVQWLRDELKIINDALDTEYFANKVKDSNGVYLVPAFTGLGAPYWDPYARG 360 Query: 361 ALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQ 420 ALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQ Sbjct: 361 ALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQ 420 Query: 421 ADILGTQVERPQMRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDEAAKEKL 480 ADILGTQVERP+MRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDE AKEKL Sbjct: 421 ADILGTQVERPKMRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDEPAKEKL 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: 913 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: 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 Pf6N2E2_5574 (Glycerol kinase (EC 2.7.1.30))
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.10241.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.5e-229 745.7 0.3 1.1e-228 745.5 0.3 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 Glycerol kinase (EC 2.7.1.30) Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 Glycerol kinase (EC 2.7.1.30) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 745.5 0.3 1.1e-228 1.1e-228 1 496 [] 8 494 .. 8 494 .. 0.99 Alignments for each domain: == domain 1 score: 745.5 bits; conditional E-value: 1.1e-228 TIGR01311 1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekl 64 ++i+a+DqGttssrai+fd+++++v++aq+e+ q++p++gwvEhdp+ei++++ +v+ eal+++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 8 NYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQSAVMVEALAQA 71 59************************************************************** PP TIGR01311 65 eikaeeiaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLp 128 + + +++aaiGitnqREttvvWdk+tg+p++naivWq++r ++i+++lk++++e++++++tGL+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 72 GLHHDQVAAIGITNQRETTVVWDKTTGRPIYNAIVWQCRRSTEICQQLKRDGHEQYISQTTGLV 135 **************************************************************** PP TIGR01311 129 lstYfsatKlrWlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnle 192 ++Yfs+tKl+W+ldnve+ r++a++gellfGtvd+wli+k+tggkvhvtd+tNASRt+l+n++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 136 TDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGGKVHVTDYTNASRTMLFNIH 199 **************************************************************** PP TIGR01311 193 tlkwdeellelfkipkellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkg 256 +l+wd ++l++++ip+e+lPe++ssse+yg +++ + i g++Gdqqaal+gq+c+++g lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 200 SLEWDAKMLDILDIPREMLPEVKSSSEIYGRTKSG------IAIGGIAGDQQAALFGQMCVEPG 257 ******************************99987......*********************** PP TIGR01311 257 eaKntYgtGcFlllntGekkviskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlk 320 +aKntYgtGcFll+ntG+k+v s+hg+Ltt+a+ g+ + yalEG+v+ +G++vqwlrd+lk lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 258 QAKNTYGTGCFLLMNTGSKAVKSNHGMLTTIACGPRGEVA--YALEGAVFNGGSTVQWLRDELK 319 *********************************9999886..********************** PP TIGR01311 321 likkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleava 384 +i++a ++e +a++v+ds+gvy+VPaf+GL+aPyWd+ Arg+++Gltr+++ hi+raale++a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 320 IINDALDTEYFANKVKDSNGVYLVPAFTGLGAPYWDPYARGALFGLTRGVRVDHIIRAALESIA 383 **************************************************************** PP TIGR01311 385 fqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaagl 448 +q+rd+l+am++d+g ++k+L+vDGg+++nn+lmq+qadilg++verpk+ ettalGaA++agl lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 384 YQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQADILGTQVERPKMRETTALGAAYLAGL 447 **************************************************************** PP TIGR01311 449 avgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496 a g+w s+eel+ +a e ++fep+ de +ek y+ w++av+r+++w lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5574 448 ACGFWGSLEELRGKAVIE-REFEPQLDEPAKEKLYAGWQKAVSRTRDW 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: 11.50 // [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