Alignments for a candidate for glpK in Lactobacillus silagei IWT126

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Lactobacillus silagei IWT126

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate WP_089136568.1 CES79_RS05570 glycerol kinase GlpK

Query= SwissProt::O34153
         (506 letters)



>NCBI__GCF_002217945.1:WP_089136568.1
          Length = 503

 Score =  719 bits (1856), Expect = 0.0
 Identities = 333/500 (66%), Positives = 426/500 (85%)

Query: 1   MAEKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSV 60
           M ++ Y+MAID+GTTS+RAI+F+R+G+ +G +Q+EF Q+FPK GWVEH+ANEIW++VQSV
Sbjct: 1   MNDEQYIMAIDEGTTSTRAILFNRDGQIVGQAQREFTQHFPKPGWVEHDANEIWSAVQSV 60

Query: 61  IAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDG 120
           I+ A I++ I+P  + GIGITNQRETT++WDK TG+P+ +A+VWQS+Q+S IAD+LK  G
Sbjct: 61  ISDAVIDAKIQPYKVRGIGITNQRETTIIWDKNTGEPVYHAVVWQSKQTSQIADELKAKG 120

Query: 121 HTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVH 180
           + ++IH+KTGLVID+YFSATK+ W+LDN+ G +E+A+ GELLFGTID+W++WKLT G+VH
Sbjct: 121 YADLIHKKTGLVIDSYFSATKIMWILDNVPGVRERAEKGELLFGTIDTWILWKLTGGRVH 180

Query: 181 VTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPI 240
            TDY+NASRTML+NIH L+WD+EIL+LLNIP+S+LPEV  +S  +G+T  + F+G +VPI
Sbjct: 181 ATDYTNASRTMLFNIHDLKWDKEILNLLNIPASLLPEVHPSSYTFGYTAGFTFFGLQVPI 240

Query: 241 AGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVY 300
           AG+AGDQQAALFGQ AFEKG +KNTYGTGAFIVMNTG EP LSD  LLTTI YGIN +V 
Sbjct: 241 AGIAGDQQAALFGQTAFEKGSVKNTYGTGAFIVMNTGTEPTLSDKGLLTTIAYGINNEVT 300

Query: 301 YALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSE 360
           YALEGSIFVAGSA+QWLRDG+R+ + + +SE++A +AK  N+VYVVPAFTGLGAPYWD E
Sbjct: 301 YALEGSIFVAGSAVQWLRDGMRLFKHASESEKMAVEAKTTNDVYVVPAFTGLGAPYWDQE 360

Query: 361 ARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLM 420
            RGAVFGLTRGTT+E F+RATL+A+AYQ++DV+DTM  D+GIDI  L VDGGAA N+ LM
Sbjct: 361 VRGAVFGLTRGTTREQFIRATLEAIAYQTRDVVDTMAADTGIDIKTLSVDGGAANNNFLM 420

Query: 421 QFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEER 480
           QFQADIL+  +QRAA  ETTALGA+YLAGLA GFW+D+DE+K M + G+ F P+M A++R
Sbjct: 421 QFQADILNTHIQRAAIAETTALGASYLAGLATGFWQDMDEIKKMHKAGEEFDPQMSAKDR 480

Query: 481 DNLYEGWKQAVAATQTFKFK 500
           +N Y GW+QAV ATQ FK K
Sbjct: 481 ENCYSGWQQAVKATQLFKPK 500


Lambda     K      H
   0.315    0.132    0.386 

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: 838
Number of extensions: 25
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: 506
Length of database: 503
Length adjustment: 34
Effective length of query: 472
Effective length of database: 469
Effective search space:   221368
Effective search space used:   221368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate WP_089136568.1 CES79_RS05570 (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.3809279.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.8e-225  732.9   6.2   7.7e-225  732.7   6.2    1.0  1  NCBI__GCF_002217945.1:WP_089136568.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002217945.1:WP_089136568.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  732.7   6.2  7.7e-225  7.7e-225       1     494 [.       5     495 ..       5     497 .. 0.99

  Alignments for each domain:
  == domain 1  score: 732.7 bits;  conditional E-value: 7.7e-225
                             TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaa 73 
                                           ++i+aiD+Gtts+rai+f+++g++v++aq+e++q+fpk+gwvEhd++ei+++v++v+++a+  ++i+++++  
  NCBI__GCF_002217945.1:WP_089136568.1   5 QYIMAIDEGTTSTRAILFNRDGQIVGQAQREFTQHFPKPGWVEHDANEIWSAVQSVISDAVIDAKIQPYKVRG 77 
                                           69*********************************************************************** PP

                             TIGR01311  74 iGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnve 146
                                           iGitnqREtt++Wdk+tg+p+++a+vWq+++t++i++elk++++ + +++ktGL++++YfsatK+ W+ldnv+
  NCBI__GCF_002217945.1:WP_089136568.1  78 IGITNQRETTIIWDKNTGEPVYHAVVWQSKQTSQIADELKAKGYADLIHKKTGLVIDSYFSATKIMWILDNVP 150
                                           ************************************************************************* PP

                             TIGR01311 147 evrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirssse 219
                                           +vr++ae+gellfGt+dtw+++kLtgg+vh+td+tNASRt+l+n+++lkwd+e+l+l++ip++llPe+++ss 
  NCBI__GCF_002217945.1:WP_089136568.1 151 GVRERAEKGELLFGTIDTWILWKLTGGRVHATDYTNASRTMLFNIHDLKWDKEILNLLNIPASLLPEVHPSSY 223
                                           ************************************************************************* PP

                             TIGR01311 220 vygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklg 292
                                           ++g+++  ++++ +vpi+g++Gdqqaal+gq++++kg++KntYgtG+F+++ntG+++++s++glLtt+ay ++
  NCBI__GCF_002217945.1:WP_089136568.1 224 TFGYTAGFTFFGLQVPIAGIAGDQQAALFGQTAFEKGSVKNTYGTGAFIVMNTGTEPTLSDKGLLTTIAYGIN 296
                                           ************************************************************************* PP

                             TIGR01311 293 gkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivG 365
                                           ++ +  yalEGs++vaG+avqwlrd ++l+k+a+e+ek+a +++++++vy+VPaf+GL+aPyWd++ rg+++G
  NCBI__GCF_002217945.1:WP_089136568.1 297 NEVT--YALEGSIFVAGSAVQWLRDGMRLFKHASESEKMAVEAKTTNDVYVVPAFTGLGAPYWDQEVRGAVFG 367
                                           9886..******************************************************************* PP

                             TIGR01311 366 ltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaett 438
                                           ltr+tt+e+++ra+lea+a+q+rd++++m++d+g+++k+L vDGg+++nn+lmq+qadil+++++r+ +aett
  NCBI__GCF_002217945.1:WP_089136568.1 368 LTRGTTREQFIRATLEAIAYQTRDVVDTMAADTGIDIKTLSVDGGAANNNFLMQFQADILNTHIQRAAIAETT 440
                                           ************************************************************************* PP

                             TIGR01311 439 alGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaversl 494
                                           alGa ++agla+g+w++ +e++k ++a  ++f p+m+++ re+ y+ w++av+ ++
  NCBI__GCF_002217945.1:WP_089136568.1 441 ALGASYLAGLATGFWQDMDEIKKMHKAG-EEFDPQMSAKDRENCYSGWQQAVKATQ 495
                                           ***********************99997.***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (503 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 22.66
//
[ok]

This GapMind analysis is from Sep 24 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 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