Alignments for a candidate for glpK in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Pseudomonas putida KT2440

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate PP_1075 PP_1075 glycerol kinase

Query= reanno::WCS417:GFF1099
         (501 letters)



>FitnessBrowser__Putida:PP_1075
          Length = 499

 Score =  906 bits (2341), Expect = 0.0
 Identities = 437/498 (87%), Positives = 464/498 (93%)

Query: 1   MTDIQNKNYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQ 60
           MTD Q+KNYIIALDQGTTSSRAIIFDRDANVV T+QREFAQHYPQAGWVEHDPMEIFATQ
Sbjct: 1   MTDTQDKNYIIALDQGTTSSRAIIFDRDANVVGTSQREFAQHYPQAGWVEHDPMEIFATQ 60

Query: 61  SAVMVEALAQAGLHHDQVAAIGITNQRETTVVWDKVTGRPIYNAIVWQCRRSTEICQQLK 120
           SA MVEALAQAG+ H QVAA+GITNQRETTVVWDK TGRP+YNAIVWQCRRSTEIC QLK
Sbjct: 61  SATMVEALAQAGISHAQVAALGITNQRETTVVWDKETGRPVYNAIVWQCRRSTEICAQLK 120

Query: 121 RDGHEQYISDTTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGG 180
           RDGHE YI +TTGLVTDPYFSGTKLKWILDNV+G+RERA  GELLFGT+D+WLIWK TGG
Sbjct: 121 RDGHEDYIRETTGLVTDPYFSGTKLKWILDNVDGARERAERGELLFGTIDTWLIWKLTGG 180

Query: 181 KTHVTDYTNASRTMLFNIHTLEWDAKMLEILDIPREMLPEVKSSSEIYGRTKSGIAIGGI 240
           K HVTDYTNASRT++FNIH+L+WD K+LEIL IPR+MLPEV+ SSE+YG TKSGIAI GI
Sbjct: 181 KVHVTDYTNASRTLMFNIHSLQWDDKLLEILGIPRQMLPEVRPSSEVYGHTKSGIAIAGI 240

Query: 241 AGDQQAALFGQMCVEAGQAKNTYGTGCFLLMNTGDKAVKSKHGMLTTIACGPRGEVAYAL 300
           AGDQQ+ALFGQMCVE GQAKNTYGTGCFLLMNTGD+AVKS HG+LTTIACGPRGEVAYAL
Sbjct: 241 AGDQQSALFGQMCVEPGQAKNTYGTGCFLLMNTGDQAVKSSHGLLTTIACGPRGEVAYAL 300

Query: 301 EGAVFNGGSTVQWLRDELKIINDAHDTEYFAGKVKDSNGVYLVPAFTGLGAPYWDPYARG 360
           EGAVFNGGSTVQWLRDELKI+NDA DTEYFA KVKDSNGVYLVPAFTGLGAPYWDPYARG
Sbjct: 301 EGAVFNGGSTVQWLRDELKIVNDALDTEYFASKVKDSNGVYLVPAFTGLGAPYWDPYARG 360

Query: 361 ALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQ 420
           ALFGLTRGV+VDHIIRAALESIAYQTRDVLDAMQQD G+RL  LRVDGGAVANNFLMQFQ
Sbjct: 361 ALFGLTRGVKVDHIIRAALESIAYQTRDVLDAMQQDCGQRLSELRVDGGAVANNFLMQFQ 420

Query: 421 ADILGTQVERPQMRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDEAAKEKL 480
           ADILGT VERPQMRETTALGAAYLAGLACGFW  L+ELR KA+IEREF PQLDE  KEKL
Sbjct: 421 ADILGTCVERPQMRETTALGAAYLAGLACGFWSGLDELRDKAIIEREFSPQLDETQKEKL 480

Query: 481 YAGWQKAVSRTRDWEPHE 498
           YAGW+KAV RTRDWE HE
Sbjct: 481 YAGWKKAVERTRDWEDHE 498


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: 875
Number of extensions: 21
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: 499
Length adjustment: 34
Effective length of query: 467
Effective length of database: 465
Effective search space:   217155
Effective search space used:   217155
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 PP_1075 PP_1075 (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.7162.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-230  748.9   0.2   1.1e-229  748.8   0.2    1.0  1  lcl|FitnessBrowser__Putida:PP_1075  PP_1075 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1075  PP_1075 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  748.8   0.2  1.1e-229  1.1e-229       1     496 []       8     494 ..       8     494 .. 0.99

  Alignments for each domain:
  == domain 1  score: 748.8 bits;  conditional E-value: 1.1e-229
                           TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiG 75 
                                         ++i+a+DqGttssrai+fd+++++v+++q+e+ q++p++gwvEhdp+ei++++ +++ eal++++i+ +++aa+G
  lcl|FitnessBrowser__Putida:PP_1075   8 NYIIALDQGTTSSRAIIFDRDANVVGTSQREFAQHYPQAGWVEHDPMEIFATQSATMVEALAQAGISHAQVAALG 82 
                                         59************************************************************************* PP

                           TIGR01311  76 itnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevrk 150
                                         itnqREttvvWdketg+p++naivWq++r ++i+++lk++++e+++re+tGL+ ++Yfs+tKl+W+ldnv+++r+
  lcl|FitnessBrowser__Putida:PP_1075  83 ITNQRETTVVWDKETGRPVYNAIVWQCRRSTEICAQLKRDGHEDYIRETTGLVTDPYFSGTKLKWILDNVDGARE 157
                                         *************************************************************************** PP

                           TIGR01311 151 aaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevygeie 225
                                         +ae+gellfGt+dtwli+kLtggkvhvtd+tNASRtl++n+++l+wd++lle+++ip+++lPe+r+ssevyg+++
  lcl|FitnessBrowser__Putida:PP_1075 158 RAERGELLFGTIDTWLIWKLTGGKVHVTDYTNASRTLMFNIHSLQWDDKLLEILGIPRQMLPEVRPSSEVYGHTK 232
                                         *************************************************************************99 PP

                           TIGR01311 226 ekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkya 300
                                         +       + i+g++Gdqq+al+gq+c+++g+aKntYgtGcFll+ntG+++v s+hglLtt+a+   g+ +  ya
  lcl|FitnessBrowser__Putida:PP_1075 233 SG------IAIAGIAGDQQSALFGQMCVEPGQAKNTYGTGCFLLMNTGDQAVKSSHGLLTTIACGPRGEVA--YA 299
                                         87......********************************************************9999886..** PP

                           TIGR01311 301 lEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehi 375
                                         lEG+v+ +G++vqwlrd+lk++++a ++e +a++v+ds+gvy+VPaf+GL+aPyWd+ Arg+++Gltr+++  hi
  lcl|FitnessBrowser__Putida:PP_1075 300 LEGAVFNGGSTVQWLRDELKIVNDALDTEYFASKVKDSNGVYLVPAFTGLGAPYWDPYARGALFGLTRGVKVDHI 374
                                         *************************************************************************** PP

                           TIGR01311 376 araaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglav 450
                                         +raale++a+q+rd+l+am++d+g+++++L+vDGg+++nn+lmq+qadilg+ verp++ ettalGaA++agla 
  lcl|FitnessBrowser__Putida:PP_1075 375 IRAALESIAYQTRDVLDAMQQDCGQRLSELRVDGGAVANNFLMQFQADILGTCVERPQMRETTALGAAYLAGLAC 449
                                         *************************************************************************** PP

                           TIGR01311 451 gvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                         g+w+ ++el+++a  e ++f+p+ de+++ek y+ wk+aver+++w
  lcl|FitnessBrowser__Putida:PP_1075 450 GFWSGLDELRDKAIIE-REFSPQLDETQKEKLYAGWKKAVERTRDW 494
                                         ***********99997.**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (499 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: 00:00:00.03
# Mc/sec: 7.77
//
[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
the source code
instructions for running GapMind on your computer

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