Alignments for a candidate for glpK in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Beijerinckia indica ATCC 9039

Align glycerol kinase (EC 2.7.1.30) (characterized)
to candidate WP_012383391.1 BIND_RS01930 glycerol kinase

Query= BRENDA::D0VZG4
         (505 letters)



>NCBI__GCF_000019845.1:WP_012383391.1
          Length = 507

 Score =  622 bits (1603), Expect = 0.0
 Identities = 300/505 (59%), Positives = 376/505 (74%), Gaps = 4/505 (0%)

Query: 1   MADYVLAIDQGTTSSRAIVFNHSGEIYSTGQLEHDQIFPRAGWVEHNPEQIWNNVREVVG 60
           M  YV  IDQGTTS+R +VFN  GEI +  QLEH+QI P+AGWVEH+P +IW   ++V+ 
Sbjct: 1   MTKYVAVIDQGTTSTRCMVFNKQGEIVAQHQLEHEQICPQAGWVEHDPLEIWERTKDVIH 60

Query: 61  LALTRGNLTHEDIAAVGITNQRETAVVWDKTTGKPVYNAIVWQDTRTQKIVDELGGDEGA 120
            ++ +  L   DIAA+GITNQRET ++W++ TG+P  NAIVWQDTRT  + +++  + G 
Sbjct: 61  GSVAKAGLVAADIAAIGITNQRETTMIWNRKTGQPYGNAIVWQDTRTDIVCNQMSAEGGQ 120

Query: 121 EKYKSIVGLPLATYFSGPKIKWILDNVEGAREKAEKGDLLFGNTDTWVLWNMTGGT-EGG 179
            ++++  GLPLATYFSGPKI+W+LD+  G R+ AEKG+ LFGN D+W++W +TGG     
Sbjct: 121 NRFQAKTGLPLATYFSGPKIRWMLDHYPGLRQDAEKGEALFGNMDSWLIWKLTGGPGPAA 180

Query: 180 VHVTDVTNASRTMLMDLDTLSWREDIAADMGIPLSMLPDIRSSS--EVYGHGRPRGLVPG 237
           VHVTDVTNASRTMLM+L TL W E++ +   IP +MLP IR SS  E YG  R  G   G
Sbjct: 181 VHVTDVTNASRTMLMNLKTLDWDEELLSAFAIPRAMLPSIRPSSDPEFYGFTRQDGPFGG 240

Query: 238 -VPIAGILGDQQAATFGQACFEVGQAKNTYGTGNFLLLNTGTEKVMSKNGLLTTVCYKIG 296
            +PI G LGDQQAAT GQ CF+ G+AKNTYGTG F+L+NTGTE V S +GLLTTVCY+ G
Sbjct: 241 EIPICGDLGDQQAATVGQVCFDAGEAKNTYGTGCFMLMNTGTEMVHSNHGLLTTVCYQFG 300

Query: 297 DAPAVYALEGSIAVTGSLVQWLRDNLGMFEDAPDVEWLAGKVQDNGGAYFVPAFSGLFAP 356
                YALEGS+A+ G+LVQWLRD + +   A D+E LA  V DNGG YFVPAFSGLFAP
Sbjct: 301 HEKPHYALEGSVAIAGALVQWLRDRMRVINTAADIENLAKLVPDNGGMYFVPAFSGLFAP 360

Query: 357 YWRPDARGALVGLTRYVNRNHIARAALEATAFQSREVVDAMNADSGVDLTELRVDGGMVA 416
           YWR +ARG ++G+TR++NR H ARA+LEA A+Q+REVVDAM ADS V L  L+VDGGM A
Sbjct: 361 YWRSEARGLIIGMTRFINRGHFARASLEAAAYQTREVVDAMQADSNVSLKVLKVDGGMTA 420

Query: 417 NELLMQFQADQLGVDVVRPKVAETTALGAAYAAGIAVGFWKGEQDVIDNWAEDKRWSPSM 476
           N+LLMQ QAD LGV VVRPKVAE+TALGAAYAAG+A+G+WK   D+  NW  DK W PS 
Sbjct: 421 NDLLMQIQADVLGVPVVRPKVAESTALGAAYAAGLAIGYWKNSDDLCQNWGVDKSWKPSG 480

Query: 477 ESGERERLYRNWKKAVTKTMEWVDE 501
           +   R + Y  WKKAVT+T +W+DE
Sbjct: 481 DDTLRTKNYAMWKKAVTRTFDWLDE 505


Lambda     K      H
   0.316    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: 931
Number of extensions: 35
Number of successful extensions: 3
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: 505
Length of database: 507
Length adjustment: 34
Effective length of query: 471
Effective length of database: 473
Effective search space:   222783
Effective search space used:   222783
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_012383391.1 BIND_RS01930 (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.13416.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.8e-229  747.4   0.1   3.2e-229  747.2   0.1    1.0  1  lcl|NCBI__GCF_000019845.1:WP_012383391.1  BIND_RS01930 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012383391.1  BIND_RS01930 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  747.2   0.1  3.2e-229  3.2e-229       1     496 []       3     502 ..       3     502 .. 0.99

  Alignments for each domain:
  == domain 1  score: 747.2 bits;  conditional E-value: 3.2e-229
                                 TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikae 69 
                                               k++a iDqGtts+r++vf+k+ge+va++q e++qi p++gwvEhdplei+e+++ v++ +++k++  a+
  lcl|NCBI__GCF_000019845.1:WP_012383391.1   3 KYVAVIDQGTTSTRCMVFNKQGEIVAQHQLEHEQICPQAGWVEHDPLEIWERTKDVIHGSVAKAGLVAA 71 
                                               69******************************************************************* PP

                                 TIGR01311  70 eiaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKl 138
                                               +iaaiGitnqREtt++W+++tg+p  naivWqdtrt  +++++++e+ ++++++ktGLpl tYfs+ K+
  lcl|NCBI__GCF_000019845.1:WP_012383391.1  72 DIAAIGITNQRETTMIWNRKTGQPYGNAIVWQDTRTDIVCNQMSAEGGQNRFQAKTGLPLATYFSGPKI 140
                                               ********************************************************************* PP

                                 TIGR01311 139 rWlldnveevrkaaeegellfGtvdtwliykLtgg....kvhvtdvtNASRtlllnletlkwdeellel 203
                                               rW+ld+ +++r+ ae+ge+lfG +d+wli+kLtgg    +vhvtdvtNASRt+l+nl+tl+wdeell++
  lcl|NCBI__GCF_000019845.1:WP_012383391.1 141 RWMLDHYPGLRQDAEKGEALFGNMDSWLIWKLTGGpgpaAVHVTDVTNASRTMLMNLKTLDWDEELLSA 209
                                               ***********************************99*99***************************** PP

                                 TIGR01311 204 fkipkellPeirssse..vygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlll 270
                                               f ip+++lP ir+ss+   yg ++++  ++ e+pi g lGdqqaa vgq+c+++geaKntYgtGcF+l+
  lcl|NCBI__GCF_000019845.1:WP_012383391.1 210 FAIPRAMLPSIRPSSDpeFYGFTRQDGPFGGEIPICGDLGDQQAATVGQVCFDAGEAKNTYGTGCFMLM 278
                                               **************96659************************************************** PP

                                 TIGR01311 271 ntGekkviskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedse 339
                                               ntG+++v+s+hglLttv+y++g++kp +yalEGsva+aGa+vqwlrd++++i++a+++e+lak v+d++
  lcl|NCBI__GCF_000019845.1:WP_012383391.1 279 NTGTEMVHSNHGLLTTVCYQFGHEKP-HYALEGSVAIAGALVQWLRDRMRVINTAADIENLAKLVPDNG 346
                                               *************************8.****************************************** PP

                                 TIGR01311 340 gvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevkvLkvD 408
                                               g+yfVPafsGLfaPyW+s+Arg i+G+tr+ ++ h+ara+lea a+q+r++++am++d++v++kvLkvD
  lcl|NCBI__GCF_000019845.1:WP_012383391.1 347 GMYFVPAFSGLFAPYWRSEARGLIIGMTRFINRGHFARASLEAAAYQTREVVDAMQADSNVSLKVLKVD 415
                                               ********************************************************************* PP

                                 TIGR01311 409 GglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdee 477
                                               Gg+++n+llmqiqad+lgv+v+rpkvae talGaA+aagla+g+wk++++l +++ ++ k+++p+ d++
  lcl|NCBI__GCF_000019845.1:WP_012383391.1 416 GGMTANDLLMQIQADVLGVPVVRPKVAESTALGAAYAAGLAIGYWKNSDDLCQNWGVD-KSWKPSGDDT 483
                                               *********************************************************8.********** PP

                                 TIGR01311 478 erekkykkwkeaverslkw 496
                                                r+k+y+ wk+av+r+ +w
  lcl|NCBI__GCF_000019845.1:WP_012383391.1 484 LRTKNYAMWKKAVTRTFDW 502
                                               ****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (507 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.98
//
[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