Alignments for a candidate for glpK in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Pseudomonas stutzeri RCH2

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate GFF2719 Psest_2773 glycerol kinase

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



>FitnessBrowser__psRCH2:GFF2719
          Length = 502

 Score =  810 bits (2092), Expect = 0.0
 Identities = 396/496 (79%), Positives = 436/496 (87%), Gaps = 6/496 (1%)

Query: 5   QNKNYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQSAVM 64
           QNK +I+ALDQGTTSSRAI+ DR+ANVV  AQREFAQ YPQ  WVEHDPMEI+ATQS V 
Sbjct: 4   QNKQFIVALDQGTTSSRAIVLDRNANVVTIAQREFAQIYPQPSWVEHDPMEIWATQSGVF 63

Query: 65  VEALAQAGLHHDQVAAIGITNQRETTVVWDKVTGRPIYNAIVWQCRRSTEICQQLKRDGH 124
           VEALAQAG+ ++QVAAIGITNQRET +VWDK+TGRPIYNAIVWQ R+ST IC QLKRDG 
Sbjct: 64  VEALAQAGITNEQVAAIGITNQRETAIVWDKITGRPIYNAIVWQSRQSTPICDQLKRDGM 123

Query: 125 EQYISDTTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGGKTHV 184
           E++I  TTGLV DPYFSGTK+KWILD+VEGSRERAR GELLFGTVD WLIWK T GK HV
Sbjct: 124 EEHIRKTTGLVIDPYFSGTKIKWILDHVEGSRERARRGELLFGTVDCWLIWKMTQGKAHV 183

Query: 185 TDYTNASRTMLFNIHTLEWDAKMLEILDIPREMLPEVKSSSEIYGRT------KSGIAIG 238
           TDYTNASRT+LF+IH L+WD  MLE LDIPREMLPEV+SSSEIYG         +GI I 
Sbjct: 184 TDYTNASRTLLFDIHKLDWDPVMLEALDIPREMLPEVRSSSEIYGHAYIGSGQSTGIPIA 243

Query: 239 GIAGDQQAALFGQMCVEAGQAKNTYGTGCFLLMNTGDKAVKSKHGMLTTIACGPRGEVAY 298
           GIAGDQQAALFGQMCVE GQAKNTYGTGCFLLMNTG KAV+S+HG+LTTIACGPRGEV Y
Sbjct: 244 GIAGDQQAALFGQMCVELGQAKNTYGTGCFLLMNTGTKAVQSEHGLLTTIACGPRGEVNY 303

Query: 299 ALEGAVFNGGSTVQWLRDELKIINDAHDTEYFAGKVKDSNGVYLVPAFTGLGAPYWDPYA 358
           ALEGA+FNGGSTVQWLRDELK++N++ D+EYFA KV DSNG+YLVPAFTGLGAPYWDP A
Sbjct: 304 ALEGAIFNGGSTVQWLRDELKVLNESLDSEYFATKVPDSNGIYLVPAFTGLGAPYWDPRA 363

Query: 359 RGALFGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQ 418
           RGALFGLTRGV+VDH+IRAALESIAYQTRDVLDAMQQD+GERL+ALRVDGGAVANNFLMQ
Sbjct: 364 RGALFGLTRGVKVDHLIRAALESIAYQTRDVLDAMQQDAGERLRALRVDGGAVANNFLMQ 423

Query: 419 FQADILGTQVERPQMRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDEAAKE 478
           FQAD+LGTQVERPQM+ETTALGAAYLAGLA GFW  L+ELR K+ IER FEP      +E
Sbjct: 424 FQADLLGTQVERPQMKETTALGAAYLAGLATGFWSDLDELRSKSSIERVFEPACGSEQRE 483

Query: 479 KLYAGWQKAVSRTRDW 494
            LY GWQKAV RTR+W
Sbjct: 484 ALYRGWQKAVDRTRNW 499


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: 825
Number of extensions: 28
Number of successful extensions: 2
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: 502
Length adjustment: 34
Effective length of query: 467
Effective length of database: 468
Effective search space:   218556
Effective search space used:   218556
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 GFF2719 Psest_2773 (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.20635.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   9.8e-226  735.7   0.1   1.1e-225  735.5   0.1    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2719  Psest_2773 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2719  Psest_2773 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  735.5   0.1  1.1e-225  1.1e-225       1     496 []       7     499 ..       7     499 .. 0.99

  Alignments for each domain:
  == domain 1  score: 735.5 bits;  conditional E-value: 1.1e-225
                           TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiG 75 
                                         ++i+a+DqGttssraiv+d+++++v++aq+e+ qi+p+++wvEhdp+ei++++  v  eal++++i+ e++aaiG
  lcl|FitnessBrowser__psRCH2:GFF2719   7 QFIVALDQGTTSSRAIVLDRNANVVTIAQREFAQIYPQPSWVEHDPMEIWATQSGVFVEALAQAGITNEQVAAIG 81 
                                         69************************************************************************* PP

                           TIGR01311  76 itnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevrk 150
                                         itnqREt++vWdk tg+p++naivWq+++ + i+++lk+++ ee++r++tGL++++Yfs+tK++W+ld+ve+ r+
  lcl|FitnessBrowser__psRCH2:GFF2719  82 ITNQRETAIVWDKITGRPIYNAIVWQSRQSTPICDQLKRDGMEEHIRKTTGLVIDPYFSGTKIKWILDHVEGSRE 156
                                         *************************************************************************** PP

                           TIGR01311 151 aaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevygeie 225
                                         +a++gellfGtvd+wli+k+t+gk+hvtd+tNASRtll+++++l+wd  +le+++ip+e+lPe+rssse+yg+  
  lcl|FitnessBrowser__psRCH2:GFF2719 157 RARRGELLFGTVDCWLIWKMTQGKAHVTDYTNASRTLLFDIHKLDWDPVMLEALDIPREMLPEVRSSSEIYGHAY 231
                                         *************************************************************************99 PP

                           TIGR01311 226 ekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkya 300
                                           +   +++pi+g++Gdqqaal+gq+c++ g+aKntYgtGcFll+ntG+k+v s+hglLtt+a+   g+   +ya
  lcl|FitnessBrowser__psRCH2:GFF2719 232 IGSGQSTGIPIAGIAGDQQAALFGQMCVELGQAKNTYGTGCFLLMNTGTKAVQSEHGLLTTIACGPRGEV--NYA 304
                                         99999***********************************************************999877..6** PP

                           TIGR01311 301 lEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehi 375
                                         lEG+++ +G++vqwlrd+lk+++++ ++e +a++v+ds+g+y+VPaf+GL+aPyWd++Arg+++Gltr+++  h+
  lcl|FitnessBrowser__psRCH2:GFF2719 305 LEGAIFNGGSTVQWLRDELKVLNESLDSEYFATKVPDSNGIYLVPAFTGLGAPYWDPRARGALFGLTRGVKVDHL 379
                                         *************************************************************************** PP

                           TIGR01311 376 araaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglav 450
                                         +raale++a+q+rd+l+am++dag ++++L+vDGg+++nn+lmq+qad+lg++verp+++ettalGaA++agla+
  lcl|FitnessBrowser__psRCH2:GFF2719 380 IRAALESIAYQTRDVLDAMQQDAGERLRALRVDGGAVANNFLMQFQADLLGTQVERPQMKETTALGAAYLAGLAT 454
                                         *************************************************************************** PP

                           TIGR01311 451 gvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                         g+w++++el+++++ e ++fep+  +e+re+ y+ w++av+r+++w
  lcl|FitnessBrowser__psRCH2:GFF2719 455 GFWSDLDELRSKSSIE-RVFEPACGSEQREALYRGWQKAVDRTRNW 499
                                         **************97.**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (502 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: 7.89
//
[ok]

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

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Protein sequences (fasta format)
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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