Alignments for a candidate for glpK in Geobacter lovleyi SZ

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Geobacter lovleyi SZ

Align glycerol kinase; EC 2.7.1.30 (characterized)
to candidate WP_012470731.1 GLOV_RS13310 glycerol kinase

Query= CharProtDB::CH_121461
         (502 letters)



>NCBI__GCF_000020385.1:WP_012470731.1
          Length = 496

 Score =  604 bits (1557), Expect = e-177
 Identities = 295/494 (59%), Positives = 368/494 (74%), Gaps = 1/494 (0%)

Query: 6   YIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLVEVL 65
           +I+ALDQGTTSSRA+V DHD  +  ++Q+EF QI+P+PG VEHD  EIWA+Q    VE +
Sbjct: 3   FILALDQGTTSSRALVFDHDGTVRGLAQKEFRQIFPEPGLVEHDAEEIWASQLGVAVEAV 62

Query: 66  AKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDYI 125
           A+A +S+  IAAIGITNQRETT+VW++ TGKPI+NAIVWQ RRTA  C+ LKR GLE   
Sbjct: 63  ARAGLSAADIAAIGITNQRETTVVWDRRTGKPIHNAIVWQDRRTAAECDRLKRLGLEATF 122

Query: 126 RSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDYT 185
           R+ TGLV+DPYFSGTK+ W+LDH+ G+R++A RGEL FGT+D+WL+W +T G  H+TD +
Sbjct: 123 RARTGLVLDPYFSGTKLAWLLDHLPGARDKAERGELAFGTIDSWLVWNLTGGERHLTDAS 182

Query: 186 NASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISGIAG 245
           NASRT+LFNIH  +WD ++L++L IP  +LPEV  SS+VYG+T        R+PISGIAG
Sbjct: 183 NASRTLLFNIHEGNWDQELLQLLRIPPAILPEVVPSSQVYGET-AARFFAARVPISGIAG 241

Query: 246 DQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALEG 305
           DQQAALFGQLC + GM KNTYGTGCFMLM TGE+ V SE  LLTT+AC       YALEG
Sbjct: 242 DQQAALFGQLCDRPGMVKNTYGTGCFMLMQTGERPVLSERNLLTTVACRLGERTEYALEG 301

Query: 306 AVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGAI 365
           +VF AGA++QWLRD + +I  + + E  A  V +  GVY+VPAF GLGAP+WDPYARG +
Sbjct: 302 SVFAAGAAVQWLRDGLGIIRSSEEVETLAATVPDNGGVYLVPAFAGLGAPHWDPYARGTL 361

Query: 366 FGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSD 425
            G+TRG  A HI RATLESIA+QT D+LEAM+AD+   L  LRVDGGA ANN LMQFQ+D
Sbjct: 362 LGITRGSTAGHIARATLESIAFQTADLLEAMEADAATPLTELRVDGGATANNLLMQFQAD 421

Query: 426 ILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYA 485
           +LG  V RP VRE TALGAAYLAGLA+G+WQ+  EL      E+ F P +E         
Sbjct: 422 LLGVPVVRPRVRETTALGAAYLAGLAIGYWQDRKELSRLWQAEQAFAPVLERERMAELRY 481

Query: 486 GWKKAVKRAMAWEE 499
            W +AV+R+  W +
Sbjct: 482 NWNRAVERSKGWAQ 495


Lambda     K      H
   0.318    0.134    0.404 

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: 732
Number of extensions: 20
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: 502
Length of database: 496
Length adjustment: 34
Effective length of query: 468
Effective length of database: 462
Effective search space:   216216
Effective search space used:   216216
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_012470731.1 GLOV_RS13310 (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.5566.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-222  725.3   0.0   1.5e-222  725.2   0.0    1.0  1  lcl|NCBI__GCF_000020385.1:WP_012470731.1  GLOV_RS13310 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020385.1:WP_012470731.1  GLOV_RS13310 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  725.2   0.0  1.5e-222  1.5e-222       2     496 .]       3     493 ..       2     493 .. 0.99

  Alignments for each domain:
  == domain 1  score: 725.2 bits;  conditional E-value: 1.5e-222
                                 TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaee 70 
                                               +i+a+DqGttssra+vfd++g++ + aqke++qifp++g vEhd++ei++s++ v+ ea+++++ +a++
  lcl|NCBI__GCF_000020385.1:WP_012470731.1   3 FILALDQGTTSSRALVFDHDGTVRGLAQKEFRQIFPEPGLVEHDAEEIWASQLGVAVEAVARAGLSAAD 71 
                                               89******************************************************************* PP

                                 TIGR01311  71 iaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlr 139
                                               iaaiGitnqREttvvWd++tgkp++naivWqd+rta  +++lk+ + e ++r++tGL+l++Yfs+tKl+
  lcl|NCBI__GCF_000020385.1:WP_012470731.1  72 IAAIGITNQRETTVVWDRRTGKPIHNAIVWQDRRTAAECDRLKRLGLEATFRARTGLVLDPYFSGTKLA 140
                                               ********************************************************************* PP

                                 TIGR01311 140 WlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipk 208
                                               Wlld+ +++r++ae+gel fGt+d+wl+++Ltgg+ h+td++NASRtll+n+++ +wd+ell+l++ip 
  lcl|NCBI__GCF_000020385.1:WP_012470731.1 141 WLLDHLPGARDKAERGELAFGTIDSWLVWNLTGGERHLTDASNASRTLLFNIHEGNWDQELLQLLRIPP 209
                                               ********************************************************************* PP

                                 TIGR01311 209 ellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkv 277
                                               ++lPe+++ss+vyge++++ ++ ++vpi+g++Gdqqaal+gqlc ++g++KntYgtGcF+l++tGe++v
  lcl|NCBI__GCF_000020385.1:WP_012470731.1 210 AILPEVVPSSQVYGETAAR-FFAARVPISGIAGDQQAALFGQLCDRPGMVKNTYGTGCFMLMQTGERPV 277
                                               *****************99.************************************************* PP

                                 TIGR01311 278 iskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPa 346
                                               +s+ +lLttva++lg+++  +yalEGsv+ aGaavqwlrd l++i+++eeve+la +v+d++gvy+VPa
  lcl|NCBI__GCF_000020385.1:WP_012470731.1 278 LSERNLLTTVACRLGERT--EYALEGSVFAAGAAVQWLRDGLGIIRSSEEVETLAATVPDNGGVYLVPA 344
                                               ***************877..5************************************************ PP

                                 TIGR01311 347 fsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknn 415
                                               f+GL+aP+Wd+ Argt++G+tr++t+ hiara+le++afq+ d+leame+da + +++L+vDGg+++nn
  lcl|NCBI__GCF_000020385.1:WP_012470731.1 345 FAGLGAPHWDPYARGTLLGITRGSTAGHIARATLESIAFQTADLLEAMEADAATPLTELRVDGGATANN 413
                                               ********************************************************************* PP

                                 TIGR01311 416 llmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkyk 484
                                               llmq+qad+lgv+v+rp+v ettalGaA++agla+g+w++ +el++ ++ae ++f+p  ++e+ ++   
  lcl|NCBI__GCF_000020385.1:WP_012470731.1 414 LLMQFQADLLGVPVVRPRVRETTALGAAYLAGLAIGYWQDRKELSRLWQAE-QAFAPVLERERMAELRY 481
                                               **************************************************7.**********9999999 PP

                                 TIGR01311 485 kwkeaverslkw 496
                                               +w++avers++w
  lcl|NCBI__GCF_000020385.1:WP_012470731.1 482 NWNRAVERSKGW 493
                                               **********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (496 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: 10.85
//
[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