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_089136140.1 CES79_RS01845 glycerol kinase GlpK

Query= SwissProt::O34153
         (506 letters)



>NCBI__GCF_002217945.1:WP_089136140.1
          Length = 502

 Score =  664 bits (1714), Expect = 0.0
 Identities = 305/495 (61%), Positives = 408/495 (82%)

Query: 4   KNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAG 63
           ++Y++AIDQGT+ +RA++FD +G+K+  S+K FPQY+P +GWVE +ANEIWNSVQSVIA 
Sbjct: 7   EHYILAIDQGTSVTRAMLFDHSGRKVIESEKSFPQYYPHNGWVEVDANEIWNSVQSVIAS 66

Query: 64  AFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTE 123
           A I++G+ PE I GIGI++QRETTV+WDK TGQPI +AI W S+Q++PIA Q+   G+ E
Sbjct: 67  ALIDAGVHPEYIDGIGISSQRETTVIWDKATGQPIYHAIGWLSKQTAPIAKQMVAAGYAE 126

Query: 124 MIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTD 183
           +IHE TGLVID+YFSATKVRWLLD+++GAQ +A+ G+LL GTIDSWLVWKL+DGQ+H+TD
Sbjct: 127 LIHEHTGLVIDSYFSATKVRWLLDHVDGAQARAEKGDLLMGTIDSWLVWKLSDGQLHITD 186

Query: 184 YSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPIAGM 243
           Y+NASRTM++NIH L+WD EIL +LNIP  MLPE+ S SEVYG T++Y FYG EVPI G+
Sbjct: 187 YTNASRTMMFNIHDLKWDDEILKILNIPKQMLPEIHSCSEVYGTTKNYQFYGVEVPICGL 246

Query: 244 AGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYAL 303
            GDQQAAL GQMAF+ G +KNTYG GAFI+MNTG++PQLS++ LLTTI Y + G V YAL
Sbjct: 247 VGDQQAALVGQMAFKPGEVKNTYGDGAFIMMNTGDKPQLSNHKLLTTIAYDLEGHVTYAL 306

Query: 304 EGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARG 363
           EGSIFVAG+A+ WL++ +++I+  PQS ++A ++  D+EVYVVPAF GLGAPYWD +ARG
Sbjct: 307 EGSIFVAGTALNWLQETMKIIDNVPQSRQVAMQSTNDDEVYVVPAFNGLGAPYWDQDARG 366

Query: 364 AVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQ 423
           AVFGLTRGT + DFV+ATLQ++AYQ++D+I+TM++D+ + +  +  DGGA++N  LMQFQ
Sbjct: 367 AVFGLTRGTNRSDFVKATLQSIAYQTRDIIETMRQDTAMPVVEILADGGASRNRYLMQFQ 426

Query: 424 ADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNL 483
           ADILD+ + R+++ +TTALGAA  AGLA+G+WK+L E+  +   G+ F P+M A+ R  L
Sbjct: 427 ADILDLPIVRSSDEDTTALGAAICAGLAIGYWKNLKEVSQIHAAGRTFNPKMAADRRKRL 486

Query: 484 YEGWKQAVAATQTFK 498
           Y+GW+ A+ AT+ FK
Sbjct: 487 YDGWQVAIKATRAFK 501


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: 790
Number of extensions: 29
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: 502
Length adjustment: 34
Effective length of query: 472
Effective length of database: 468
Effective search space:   220896
Effective search space used:   220896
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_089136140.1 CES79_RS01845 (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.3181812.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.6e-209  680.4   1.2   6.3e-209  680.3   1.2    1.0  1  NCBI__GCF_002217945.1:WP_089136140.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002217945.1:WP_089136140.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  680.3   1.2  6.3e-209  6.3e-209       1     494 [.       8     498 ..       8     500 .. 0.99

  Alignments for each domain:
  == domain 1  score: 680.3 bits;  conditional E-value: 6.3e-209
                             TIGR01311   1 kliaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaa 73 
                                           ++i+aiDqGt+ +ra++fd++g++v +++k + q++p++gwvE d++ei++sv++v+a+al  +++++e i  
  NCBI__GCF_002217945.1:WP_089136140.1   8 HYILAIDQGTSVTRAMLFDHSGRKVIESEKSFPQYYPHNGWVEVDANEIWNSVQSVIASALIDAGVHPEYIDG 80 
                                           59*********************************************************************** PP

                             TIGR01311  74 iGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnve 146
                                           iGi+ qREttv+Wdk+tg+p+++ai W +++ta i++++ ++++ e ++e+tGL++++YfsatK+rWlld+v+
  NCBI__GCF_002217945.1:WP_089136140.1  81 IGISSQRETTVIWDKATGQPIYHAIGWLSKQTAPIAKQMVAAGYAELIHEHTGLVIDSYFSATKVRWLLDHVD 153
                                           ************************************************************************* PP

                             TIGR01311 147 evrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirssse 219
                                           +++++ae+g+ll+Gt+d+wl++kL++g+ h+td+tNASRt+++n+++lkwd+e+l++++ipk++lPei+s+se
  NCBI__GCF_002217945.1:WP_089136140.1 154 GAQARAEKGDLLMGTIDSWLVWKLSDGQLHITDYTNASRTMMFNIHDLKWDDEILKILNIPKQMLPEIHSCSE 226
                                           ************************************************************************* PP

                             TIGR01311 220 vygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklg 292
                                           vyg++++ ++++ evpi g++Gdqqaalvgq+++k+ge+KntYg G+F+++ntG+k+++s+h+lLtt+ay l+
  NCBI__GCF_002217945.1:WP_089136140.1 227 VYGTTKNYQFYGVEVPICGLVGDQQAALVGQMAFKPGEVKNTYGDGAFIMMNTGDKPQLSNHKLLTTIAYDLE 299
                                           ************************************************************************* PP

                             TIGR01311 293 gkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivG 365
                                           g+ +  yalEGs++vaG+a++wl++ +k+i++  ++ ++a + +++++vy+VPaf+GL+aPyWd+dArg+++G
  NCBI__GCF_002217945.1:WP_089136140.1 300 GHVT--YALEGSIFVAGTALNWLQETMKIIDNVPQSRQVAMQSTNDDEVYVVPAFNGLGAPYWDQDARGAVFG 370
                                           *986..******************************************************************* PP

                             TIGR01311 366 ltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaett 438
                                           ltr+t+++++++a+l+++a+q+rdi+e+m++d+ + v ++ +DGg+s+n++lmq+qadil+++++r++ ++tt
  NCBI__GCF_002217945.1:WP_089136140.1 371 LTRGTNRSDFVKATLQSIAYQTRDIIETMRQDTAMPVVEILADGGASRNRYLMQFQADILDLPIVRSSDEDTT 443
                                           ************************************************************************* PP

                             TIGR01311 439 alGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaversl 494
                                           alGaA++agla+g+wk+++e+++ ++a  +tf+p+m +++r++ y  w+ a++ ++
  NCBI__GCF_002217945.1:WP_089136140.1 444 ALGAAICAGLAIGYWKNLKEVSQIHAAG-RTFNPKMAADRRKRLYDGWQVAIKATR 498
                                           ********************99998886.***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (502 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 34.64
//
[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