Alignments for a candidate for glpK in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Pseudomonas fluorescens GW456-L13

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate PfGW456L13_1734 Glycerol kinase (EC 2.7.1.30)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734
          Length = 501

 Score =  982 bits (2538), Expect = 0.0
 Identities = 482/501 (96%), Positives = 488/501 (97%)

Query: 1   MTDIQNKNYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQ 60
           MTD QNKNYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQ
Sbjct: 1   MTDTQNKNYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQ 60

Query: 61  SAVMVEALAQAGLHHDQVAAIGITNQRETTVVWDKVTGRPIYNAIVWQCRRSTEICQQLK 120
           SAVMVEALAQAGLHHDQVAAIGITNQRETTVVWDK TGRPIYNAIVWQCRRSTEICQQLK
Sbjct: 61  SAVMVEALAQAGLHHDQVAAIGITNQRETTVVWDKNTGRPIYNAIVWQCRRSTEICQQLK 120

Query: 121 RDGHEQYISDTTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGG 180
           RDGHEQYISDTTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGG
Sbjct: 121 RDGHEQYISDTTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGG 180

Query: 181 KTHVTDYTNASRTMLFNIHTLEWDAKMLEILDIPREMLPEVKSSSEIYGRTKSGIAIGGI 240
           K HVTDYTNASRTMLFNIHTLEWDAKMLE+LDIPREMLP+VKSSSEIYG TKSGIAIGGI
Sbjct: 181 KVHVTDYTNASRTMLFNIHTLEWDAKMLEVLDIPREMLPQVKSSSEIYGHTKSGIAIGGI 240

Query: 241 AGDQQAALFGQMCVEAGQAKNTYGTGCFLLMNTGDKAVKSKHGMLTTIACGPRGEVAYAL 300
           AGDQQAALFGQMCVE GQAKNTYGTGCFLLMNTGDKAVKS+HGMLTTIACGPRGEVAYAL
Sbjct: 241 AGDQQAALFGQMCVEPGQAKNTYGTGCFLLMNTGDKAVKSQHGMLTTIACGPRGEVAYAL 300

Query: 301 EGAVFNGGSTVQWLRDELKIINDAHDTEYFAGKVKDSNGVYLVPAFTGLGAPYWDPYARG 360
           EGAVFNGGSTVQWLRDELKIINDAHDTEYFA KVKDSNGVYLVPAFTGLGAPYWDPYARG
Sbjct: 301 EGAVFNGGSTVQWLRDELKIINDAHDTEYFANKVKDSNGVYLVPAFTGLGAPYWDPYARG 360

Query: 361 ALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQ 420
           ALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQ
Sbjct: 361 ALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQ 420

Query: 421 ADILGTQVERPQMRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDEAAKEKL 480
           ADILGTQVERPQMRETTALGAAYLAGLACGFWGSLEELRGKAVIER+FEP LDE AKEKL
Sbjct: 421 ADILGTQVERPQMRETTALGAAYLAGLACGFWGSLEELRGKAVIERKFEPTLDETAKEKL 480

Query: 481 YAGWQKAVSRTRDWEPHEGAE 501
           YAGW+KAVSRTRDW   +  E
Sbjct: 481 YAGWKKAVSRTRDWAAEDETE 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: 905
Number of extensions: 11
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 PfGW456L13_1734 (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.26230.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   4.5e-230  750.0   0.8   5.1e-230  749.8   0.8    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734  Glycerol kinase (EC 2.7.1.30)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734  Glycerol kinase (EC 2.7.1.30)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  749.8   0.8  5.1e-230  5.1e-230       1     496 []       8     494 ..       8     494 .. 0.99

  Alignments for each domain:
  == domain 1  score: 749.8 bits;  conditional E-value: 5.1e-230
                                               TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvk 55 
                                                             ++i+a+DqGttssrai+fd+++++v++aq+e+ q++p++gwvEhdp+ei++++ +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734   8 NYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQSA 62 
                                                             59***************************************************** PP

                                               TIGR01311  56 vlaealekleikaeeiaaiGitnqREttvvWdketgkplvnaivWqdtrtakive 110
                                                             v+ eal++++ + +++aaiGitnqREttvvWdk+tg+p++naivWq++r ++i++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734  63 VMVEALAQAGLHHDQVAAIGITNQRETTVVWDKNTGRPIYNAIVWQCRRSTEICQ 117
                                                             ******************************************************* PP

                                               TIGR01311 111 elkeetkeeelrektGLplstYfsatKlrWlldnveevrkaaeegellfGtvdtw 165
                                                             +lk++++e++++++tGL+ ++Yfs+tKl+W+ldnve+ r++a++gellfGtvd+w
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734 118 QLKRDGHEQYISDTTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSW 172
                                                             ******************************************************* PP

                                               TIGR01311 166 liykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssev 220
                                                             li+k+tggkvhvtd+tNASRt+l+n++tl+wd ++le+++ip+e+lP+++ssse+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734 173 LIWKFTGGKVHVTDYTNASRTMLFNIHTLEWDAKMLEVLDIPREMLPQVKSSSEI 227
                                                             ******************************************************* PP

                                               TIGR01311 221 ygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGek 275
                                                             yg++++       + i g++Gdqqaal+gq+c+++g+aKntYgtGcFll+ntG+k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734 228 YGHTKSG------IAIGGIAGDQQAALFGQMCVEPGQAKNTYGTGCFLLMNTGDK 276
                                                             ***9987......****************************************** PP

                                               TIGR01311 276 kviskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeevek 330
                                                             +v s+hg+Ltt+a+   g+ +  yalEG+v+ +G++vqwlrd+lk+i++a+++e 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734 277 AVKSQHGMLTTIACGPRGEVA--YALEGAVFNGGSTVQWLRDELKIINDAHDTEY 329
                                                             **************9999886..******************************** PP

                                               TIGR01311 331 laksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavaf 385
                                                             +a++v+ds+gvy+VPaf+GL+aPyWd+ Arg+++Gltr+++  hi+raale++a+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734 330 FANKVKDSNGVYLVPAFTGLGAPYWDPYARGALFGLTRGVRVDHIIRAALESIAY 384
                                                             ******************************************************* PP

                                               TIGR01311 386 qardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettal 440
                                                             q+rd+l+am++d+g ++k+L+vDGg+++nn+lmq+qadilg++verp++ ettal
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734 385 QTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQADILGTQVERPQMRETTAL 439
                                                             ******************************************************* PP

                                               TIGR01311 441 GaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslk 495
                                                             GaA++agla g+w s+eel+ +a  e ++fep+ de+ +ek y+ wk+av+r+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734 440 GAAYLAGLACGFWGSLEELRGKAVIE-RKFEPTLDETAKEKLYAGWKKAVSRTRD 493
                                                             ********************999997.9*************************99 PP

                                               TIGR01311 496 w 496
                                                             w
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1734 494 W 494
                                                             8 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: 11.52
//
[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