Alignments for a candidate for glpK in Collinsella tanakaei YIT 12063

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Collinsella tanakaei YIT 12063

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate WP_009141774.1 HMPREF9452_RS08720 glycerol kinase GlpK

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



>NCBI__GCF_000225705.1:WP_009141774.1
          Length = 514

 Score =  563 bits (1452), Expect = e-165
 Identities = 280/490 (57%), Positives = 353/490 (72%), Gaps = 5/490 (1%)

Query: 8   NYIIALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQSAVMVEA 67
           +YI+ALD GTTS RAII D    +V  A R  +  YPQ GWVE DPMEI A+Q AVM+E 
Sbjct: 21  SYIMALDSGTTSVRAIIVDEYDCIVAQASRAISTTYPQPGWVEQDPMEILASQIAVMMEV 80

Query: 68  LAQAGLHHDQVAAIGITNQRETTVVWDKVTGRPIYNAIVWQCRRSTEICQQLKRDGHEQY 127
             ++G+H D +AAIGITNQRETTVVWD+ +G+PIYNAI WQCRR+  I   L  +G +Q 
Sbjct: 81  QFKSGIHSDSIAAIGITNQRETTVVWDRDSGQPIYNAIGWQCRRTAPIADALVHEGMDQT 140

Query: 128 ISDTTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGGKTHVTDY 187
           I + TGL  D YFSGTK+KWILDNV G+RE A  G+L+FGT+D+WLI+  TGG  + TDY
Sbjct: 141 IREKTGLKPDAYFSGTKVKWILDNVSGAREAAAAGQLMFGTIDTWLIYNLTGGMVYATDY 200

Query: 188 TNASRTMLFNIHTLEWDAKMLEILDIPREMLPEVKSSSEIYGRTKSGI-----AIGGIAG 242
           TNASRTMLFNIHTLEWD ++LE LDIPR MLPEV+ SS  +GR  S I      I G+AG
Sbjct: 201 TNASRTMLFNIHTLEWDDELLEALDIPRSMLPEVRWSSGDFGRVSSEIMTHTPPITGVAG 260

Query: 243 DQQAALFGQMCVEAGQAKNTYGTGCFLLMNTGDKAVKSKHGMLTTIACGPRGEVAYALEG 302
           DQQA+ FG  C E GQ KNTYGTGCF+LMNTGD+ V SK+G+L+TI     G+++YALEG
Sbjct: 261 DQQASFFGHCCFEPGQTKNTYGTGCFMLMNTGDEVVHSKNGLLSTIGIAENGKISYALEG 320

Query: 303 AVFNGGSTVQWLRDELKIINDAHDTEYFAGKVKDSNGVYLVPAFTGLGAPYWDPYARGAL 362
           ++F+ GST+QWLRD+L II DA +T   A  +  +NG YLVPAF+GLGAP+WDP +RG +
Sbjct: 321 SIFHAGSTIQWLRDKLGIIADAGETAAIARSLSSNNGCYLVPAFSGLGAPWWDPDSRGLI 380

Query: 363 FGLTRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQAD 422
            GLT G     ++RAA ES+AYQT DVL +M+ D+G +L  L VDG A  N F+MQFQAD
Sbjct: 381 CGLTAGSDRATLVRAACESMAYQTYDVLRSMEADAGRKLSGLSVDGAASRNEFIMQFQAD 440

Query: 423 ILGTQVERPQMRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDEAAKEKLYA 482
           +LG  + + +  ETTALGAAYLAGLA G+W   +EL     + + FEP  +     ++ +
Sbjct: 441 LLGIPITQSESIETTALGAAYLAGLAVGYWEDRDELVQNRNLGKCFEPAGNPVELARVLS 500

Query: 483 GWQKAVSRTR 492
           GW  AV+R+R
Sbjct: 501 GWHDAVARSR 510


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: 670
Number of extensions: 13
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: 514
Length adjustment: 34
Effective length of query: 467
Effective length of database: 480
Effective search space:   224160
Effective search space used:   224160
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 WP_009141774.1 HMPREF9452_RS08720 (glycerol kinase GlpK)
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.1104565.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-205  668.7   0.1   2.2e-205  668.6   0.1    1.0  1  NCBI__GCF_000225705.1:WP_009141774.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000225705.1:WP_009141774.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  668.6   0.1  2.2e-205  2.2e-205       2     494 ..      22     510 ..      21     512 .. 0.99

  Alignments for each domain:
  == domain 1  score: 668.6 bits;  conditional E-value: 2.2e-205
                             TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaai 74 
                                           +i+a+D Gtts rai+ d+   +va+a++ +s+++p++gwvE+dp+eil+s+ +v+ e+  k++i+++ iaai
  NCBI__GCF_000225705.1:WP_009141774.1  22 YIMALDSGTTSVRAIIVDEYDCIVAQASRAISTTYPQPGWVEQDPMEILASQIAVMMEVQFKSGIHSDSIAAI 94 
                                           9************************************************************************ PP

                             TIGR01311  75 GitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnvee 147
                                           GitnqREttvvWd+++g+p++nai Wq++rta i+++l +e+ ++++rektGL  ++Yfs+tK++W+ldnv +
  NCBI__GCF_000225705.1:WP_009141774.1  95 GITNQRETTVVWDRDSGQPIYNAIGWQCRRTAPIADALVHEGMDQTIREKTGLKPDAYFSGTKVKWILDNVSG 167
                                           ************************************************************************* PP

                             TIGR01311 148 vrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssev 220
                                           +r+aa +g+l+fGt+dtwliy+Ltgg v++td+tNASRt+l+n++tl+wd+elle+++ip+++lPe+r ss  
  NCBI__GCF_000225705.1:WP_009141774.1 168 AREAAAAGQLMFGTIDTWLIYNLTGGMVYATDYTNASRTMLFNIHTLEWDDELLEALDIPRSMLPEVRWSSGD 240
                                           ************************************************************************* PP

                             TIGR01311 221 ygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklgg 293
                                           +g ++++ +++++ pitgv+Gdqqa+++g+ c+++g++KntYgtGcF+l+ntG+++v+sk+glL+t++   +g
  NCBI__GCF_000225705.1:WP_009141774.1 241 FGRVSSE-IMTHTPPITGVAGDQQASFFGHCCFEPGQTKNTYGTGCFMLMNTGDEVVHSKNGLLSTIGIAENG 312
                                           *****99.9999**********************************************************999 PP

                             TIGR01311 294 kkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGl 366
                                           k +  yalEGs++ aG+++qwlrd+l++i +a e+ ++a+s ++++g+y+VPafsGL+aP+Wd+d rg i+Gl
  NCBI__GCF_000225705.1:WP_009141774.1 313 KIS--YALEGSIFHAGSTIQWLRDKLGIIADAGETAAIARSLSSNNGCYLVPAFSGLGAPWWDPDSRGLICGL 383
                                           886..******************************************************************** PP

                             TIGR01311 367 trkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaetta 439
                                           t+++ ++ ++raa e++a+q+ d+l++me+dag +++ L vDG++s+n+++mq+qad+lg+++++++  etta
  NCBI__GCF_000225705.1:WP_009141774.1 384 TAGSDRATLVRAACESMAYQTYDVLRSMEADAGRKLSGLSVDGAASRNEFIMQFQADLLGIPITQSESIETTA 456
                                           ************************************************************************* PP

                             TIGR01311 440 lGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaversl 494
                                           lGaA++aglavg+w++ +el ++ +   k fep+ +  e ++ ++ w++av+rs+
  NCBI__GCF_000225705.1:WP_009141774.1 457 LGAAYLAGLAVGYWEDRDELVQNRNLG-KCFEPAGNPVELARVLSGWHDAVARSR 510
                                           ********************9999997.*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (514 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: 0.00u 0.02s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.18
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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