Aligments for a candidate for glpK in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for glpK in Pseudomonas fluorescens FW300-N2C3

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.8686.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.88
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources