Alignments for a candidate for glpK in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Trichormus variabilis ATCC 29413

Align Glycerol kinase; ATP:glycerol 3-phosphotransferase; Glycerokinase; GK; EC 2.7.1.30 (characterized)
to candidate WP_011321475.1 AVA_RS24445 glycerol kinase

Query= SwissProt::O66131
         (496 letters)



>NCBI__GCF_000204075.1:WP_011321475.1
          Length = 500

 Score =  506 bits (1303), Expect = e-148
 Identities = 240/495 (48%), Positives = 337/495 (68%), Gaps = 10/495 (2%)

Query: 4   YMLAIDQGTTSSRAILFNQKGEIVHMAQKEFTQYFPQPGWVEHNANEIWGSVLAVIASVL 63
           Y+LA+D GTT +RA +FN  G+IV  A KE TQ++PQPGW+EH+A EIW     V+ + +
Sbjct: 8   YILALDLGTTGNRAFIFNNAGKIVAQAYKELTQHYPQPGWLEHDAEEIWQDTCWVMKTAI 67

Query: 64  SEAQVKPEQVAGIGITNQRETTVVWEKDTGNPIYNAIVWQSRQTAGICDELKAKGYDPLF 123
           + AQ+ P ++A IG+T QRET ++W+K TG P++ AIVWQ R+TA +C +L+ KGY    
Sbjct: 68  ANAQISPSEIAAIGLTVQRETCLLWDKTTGKPLHKAIVWQDRRTAPLCHQLQEKGYAQEI 127

Query: 124 RKKTGLLIDAYFSGTKVKWILDHVDGARERAERGELLFGTIDTWLIWKLSGGRVHVTDYS 183
             +TGL++DAYFS TK++W+LD++ G     +   +L GTIDTW++WKL+GG+VH TD+S
Sbjct: 128 YSRTGLVVDAYFSATKLRWLLDYITGV----DLKNVLAGTIDTWILWKLTGGKVHATDHS 183

Query: 184 NASRTLMFNIHTLEWDDELLDILGVPKAMLPEVRPSSEVYAKTAPYHFFGVEVPIAGAAG 243
           NASRT++ N+ T EWD++LL+IL +P  +LP+++PS   +  T         +PI    G
Sbjct: 184 NASRTMLMNLKTGEWDEQLLEILQIPAHILPQIQPSLGKFGLTDT-SLLDTAIPITAILG 242

Query: 244 DQQAALFGQACFTEGMAKNTYGTGCFMLMNTGEKAVASKHGLLTTIAWGIDGKVE----- 298
           DQQAALFG  C   G+ K TYGTG F++ +TG   V S+H L++TIAW      E     
Sbjct: 243 DQQAALFGHGCDRPGLMKCTYGTGSFLVAHTGSNIVRSQHQLISTIAWTQYNSQENINIG 302

Query: 299 YALEGSIFVAGSAIQWLRDGLRMIKTAADSETYAEKVESTDGVYVVPAFIGLGTPYWDSE 358
           YALEGS+F +G+ IQWLRDG+++IKTAA++ET A +V+   GVY VPAF GLG PYWD  
Sbjct: 303 YALEGSMFTSGACIQWLRDGIKLIKTAAETETMANQVDDNGGVYFVPAFSGLGAPYWDMN 362

Query: 359 VRGAVFGLTRGTTKEHFIRATLESLAYQTKDVLAVMEADSGISLTTLRVDGGAVKNNFLM 418
            RGA FG+T     +H +RA LE++AYQ  +V+  + A     +  L VDGGA +NNFLM
Sbjct: 363 ARGAFFGITASVQPQHLVRAVLEAIAYQVLEVVQAINASCSSPMQRLIVDGGACENNFLM 422

Query: 419 QFQSDLLAVPVERPVVNETTALGAAYLAGLAVGYWNSRDDIAAQWQLERRFEPKMDDDKR 478
           QFQ+D+L +PVERP + +TT  GAA+ AGLAVG+W+S   +  Q Q++R FEP       
Sbjct: 423 QFQADVLGIPVERPTMRDTTVQGAAFAAGLAVGFWDSYTALVNQRQIDRIFEPGEGSQNA 482

Query: 479 TMLYDGWKKAVRAAM 493
              +  W+KAV+ ++
Sbjct: 483 IYNFATWQKAVKRSL 497


Lambda     K      H
   0.319    0.134    0.406 

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: 699
Number of extensions: 28
Number of successful extensions: 4
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: 496
Length of database: 500
Length adjustment: 34
Effective length of query: 462
Effective length of database: 466
Effective search space:   215292
Effective search space used:   215292
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_011321475.1 AVA_RS24445 (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.10212.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.1e-205  666.5   2.3     1e-204  666.4   2.3    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011321475.1  AVA_RS24445 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011321475.1  AVA_RS24445 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  666.4   2.3    1e-204    1e-204       2     496 .]       8     499 ..       7     499 .. 0.98

  Alignments for each domain:
  == domain 1  score: 666.4 bits;  conditional E-value: 1e-204
                                 TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaee 70 
                                               +i+a+D Gtt++ra +f++ g++va+a+kel+q++p++gw+Ehd++ei+++++ v+++a+++++i+++e
  lcl|NCBI__GCF_000204075.1:WP_011321475.1   8 YILALDLGTTGNRAFIFNNAGKIVAQAYKELTQHYPQPGWLEHDAEEIWQDTCWVMKTAIANAQISPSE 76 
                                               9******************************************************************** PP

                                 TIGR01311  71 iaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlr 139
                                               iaaiG+t qREt+++Wdk+tgkpl++aivWqd+rta ++++l+e+++ +e+ ++tGL++++YfsatKlr
  lcl|NCBI__GCF_000204075.1:WP_011321475.1  77 IAAIGLTVQRETCLLWDKTTGKPLHKAIVWQDRRTAPLCHQLQEKGYAQEIYSRTGLVVDAYFSATKLR 145
                                               ********************************************************************* PP

                                 TIGR01311 140 WlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipk 208
                                               Wlld + +v      +++l+Gt+dtw+++kLtggkvh+td++NASRt+l+nl+t +wde+lle+++ip+
  lcl|NCBI__GCF_000204075.1:WP_011321475.1 146 WLLDYITGVDL----KNVLAGTIDTWILWKLTGGKVHATDHSNASRTMLMNLKTGEWDEQLLEILQIPA 210
                                               ******99865....89**************************************************** PP

                                 TIGR01311 209 ellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkv 277
                                               ++lP+i++s   +g ++++ ll +++pit++lGdqqaal+g+ c ++g +K+tYgtG+Fl+++tG+++v
  lcl|NCBI__GCF_000204075.1:WP_011321475.1 211 HILPQIQPSLGKFGLTDTS-LLDTAIPITAILGDQQAALFGHGCDRPGLMKCTYGTGSFLVAHTGSNIV 278
                                               *****************99.9************************************************ PP

                                 TIGR01311 278 iskhglLttvaykl.ggkkp..tkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyf 343
                                                s+h+l++t+a++  +++++    yalEGs++++Ga++qwlrd +klik+a+e+e++a++v+d++gvyf
  lcl|NCBI__GCF_000204075.1:WP_011321475.1 279 RSQHQLISTIAWTQyNSQENinIGYALEGSMFTSGACIQWLRDGIKLIKTAAETETMANQVDDNGGVYF 347
                                               ************985333335589********************************************* PP

                                 TIGR01311 344 VPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevkvLkvDGgls 412
                                               VPafsGL+aPyWd++Arg+++G+t+ ++ +h++ra+lea+a+q+ ++++a+++ + + ++ L vDGg++
  lcl|NCBI__GCF_000204075.1:WP_011321475.1 348 VPAFSGLGAPYWDMNARGAFFGITASVQPQHLVRAVLEAIAYQVLEVVQAINASCSSPMQRLIVDGGAC 416
                                               ********************************************************************* PP

                                 TIGR01311 413 knnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerek 481
                                               +nn+lmq+qad+lg++verp++ +tt  GaA+aaglavg+w+s + l ++ + + ++fep   +++   
  lcl|NCBI__GCF_000204075.1:WP_011321475.1 417 ENNFLMQFQADVLGIPVERPTMRDTTVQGAAFAAGLAVGFWDSYTALVNQRQID-RIFEPGEGSQNAIY 484
                                               ***********************************************9999997.************** PP

                                 TIGR01311 482 kykkwkeaverslkw 496
                                               ++++w++av+rsl+w
  lcl|NCBI__GCF_000204075.1:WP_011321475.1 485 NFATWQKAVKRSLDW 499
                                               ************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (500 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: 7.33
//
[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 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