Alignments for a candidate for glpK in Methylosarcina fibrata AML-C10

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Methylosarcina fibrata AML-C10

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate WP_232422309.1 A3OW_RS0101585 glycerol kinase GlpK

Query= reanno::WCS417:GFF1099
         (501 letters)



>NCBI__GCF_000372865.1:WP_232422309.1
          Length = 490

 Score =  535 bits (1378), Expect = e-156
 Identities = 268/489 (54%), Positives = 344/489 (70%), Gaps = 6/489 (1%)

Query: 11  IALDQGTTSSRAIIFDRDANVVCTAQREFAQHYPQAGWVEHDPMEIFATQSAVMVEALAQ 70
           +A+DQGT+SSR II+DR AN V  AQ+     YP+ GWVE D  +I+ TQ+  +  AL+Q
Sbjct: 1   MAIDQGTSSSRCIIYDRRANPVAMAQQPLKSCYPEPGWVEQDAEDIWRTQAETIRLALSQ 60

Query: 71  AGLHHDQVAAIGITNQRETTVVWDKVTGRPIYNAIVWQCRRSTEICQQLKRDGHEQYISD 130
             L    + A+GITNQRET VVWD++TG+PI+NAIVWQ RR+ E C++L+  G E  I  
Sbjct: 61  RQLQASDLIAVGITNQRETVVVWDRLTGKPIHNAIVWQDRRTAEECRRLQEAGLEPMIRA 120

Query: 131 TTGLVTDPYFSGTKLKWILDNVEGSRERARNGELLFGTVDSWLIWKFTGGKTHVTDYTNA 190
            TGL+ DPYFS TK++WILD+VEG+RE+A  GEL  GTVDSWL+W  TGG  H+TD +NA
Sbjct: 121 KTGLLIDPYFSATKIRWILDHVEGAREKAGRGELACGTVDSWLVWNLTGGALHITDVSNA 180

Query: 191 SRTMLFNIHTLEWDAKMLEILDIPREMLPEVKSSSEIYGRTK-----SGIAIGGIAGDQQ 245
           +RT+L+NI + +WD ++L + +IP  +LPEVKS++EIYG T      SGI I  +AGDQQ
Sbjct: 181 ARTLLYNIESRQWDEELLNLFEIPSSLLPEVKSTAEIYGTTAHPGIGSGIPIAAVAGDQQ 240

Query: 246 AALFGQMCVEAGQAKNTYGTGCFLLMNTGDKAVKSKHGMLTTIACGPRGEVAYALEGAVF 305
           AALFGQMC++ G AK TYGTG FL+MNTG +   SKH +LTTIA     EVAYALEG+VF
Sbjct: 241 AALFGQMCLDPGMAKCTYGTGSFLMMNTGPERRASKHRLLTTIAWQIGDEVAYALEGSVF 300

Query: 306 NGGSTVQWLRDELKIINDAHDTEYFAGKVKDSNGVYLVPAFTGLGAPYWDPYARGALFGL 365
            GGS +QWLRD L++ +   D E  AG V DS GV  VPA +GLGAP+WDP ARG+LFG+
Sbjct: 301 TGGSVIQWLRDGLRLFDRTADCEALAGSVPDSGGVVFVPALSGLGAPHWDPRARGSLFGI 360

Query: 366 TRGVRVDHIIRAALESIAYQTRDVLDAMQQDSGERLKALRVDGGAVANNFLMQFQADILG 425
           T G    HI RAA+ESI +Q  D+L+A+ +D G  +  LR+DGGA  NN L QFQADI  
Sbjct: 361 TGGTTGAHIARAAIESICFQVNDLLNALSEDGGRPVPQLRIDGGAATNNLLAQFQADISS 420

Query: 426 TQVERPQMRETTALGAAYLAGLACGFWGSLEELRGKAVIEREFEPQLDEAAKEKLYAGWQ 485
            +V RPQ  E+TALGAA LAG+A G W +LEELR +  I+R F   +     ++    W 
Sbjct: 421 LEVVRPQTLESTALGAACLAGIAVGLW-NLEELRKQWAIDRTFHGAMPPEEIDRRTRRWL 479

Query: 486 KAVSRTRDW 494
           KAV R ++W
Sbjct: 480 KAVERAKNW 488


Lambda     K      H
   0.319    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: 706
Number of extensions: 27
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: 501
Length of database: 490
Length adjustment: 34
Effective length of query: 467
Effective length of database: 456
Effective search space:   212952
Effective search space used:   212952
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_232422309.1 A3OW_RS0101585 (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.1462911.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-213  695.0   0.0   2.3e-213  694.9   0.0    1.0  1  NCBI__GCF_000372865.1:WP_232422309.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000372865.1:WP_232422309.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  694.9   0.0  2.3e-213  2.3e-213       4     496 .]       1     488 [.       1     488 [. 0.99

  Alignments for each domain:
  == domain 1  score: 694.9 bits;  conditional E-value: 2.3e-213
                             TIGR01311   4 aaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiGi 76 
                                           +aiDqGt+ssr+i++d++++ va aq+ l++ +p++gwvE+d+++i++++ ++++ al++ + +a++++a+Gi
  NCBI__GCF_000372865.1:WP_232422309.1   1 MAIDQGTSSSRCIIYDRRANPVAMAQQPLKSCYPEPGWVEQDAEDIWRTQAETIRLALSQRQLQASDLIAVGI 73 
                                           69*********************************************************************** PP

                             TIGR01311  77 tnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevr 149
                                           tnqREt+vvWd+ tgkp++naivWqd+rta+ +++l+e++ e ++r+ktGL++++YfsatK+rW+ld+ve++r
  NCBI__GCF_000372865.1:WP_232422309.1  74 TNQRETVVVWDRLTGKPIHNAIVWQDRRTAEECRRLQEAGLEPMIRAKTGLLIDPYFSATKIRWILDHVEGAR 146
                                           ************************************************************************* PP

                             TIGR01311 150 kaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevyg 222
                                           ++a +gel +Gtvd+wl+++Ltgg+ h+tdv+NA+Rtll+n+e+++wdeell+lf+ip++llPe++s++e+yg
  NCBI__GCF_000372865.1:WP_232422309.1 147 EKAGRGELACGTVDSWLVWNLTGGALHITDVSNAARTLLYNIESRQWDEELLNLFEIPSSLLPEVKSTAEIYG 219
                                           ************************************************************************* PP

                             TIGR01311 223 eieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkk 295
                                           ++++   +++++pi++v+Gdqqaal+gq+cl++g+aK+tYgtG+Fl++ntG +   skh+lLtt+a+++g++ 
  NCBI__GCF_000372865.1:WP_232422309.1 220 TTAHP-GIGSGIPIAAVAGDQQAALFGQMCLDPGMAKCTYGTGSFLMMNTGPERRASKHRLLTTIAWQIGDEV 291
                                           *9998.99**************************************************************988 PP

                             TIGR01311 296 ptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltr 368
                                           +  yalEGsv+++G+++qwlrd l+l+++++++e+la sv+ds+gv+fVPa+sGL+aP+Wd++Arg ++G+t 
  NCBI__GCF_000372865.1:WP_232422309.1 292 A--YALEGSVFTGGSVIQWLRDGLRLFDRTADCEALAGSVPDSGGVVFVPALSGLGAPHWDPRARGSLFGITG 362
                                           6..********************************************************************** PP

                             TIGR01311 369 kttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalG 441
                                           +tt +hiaraa+e+++fq++d+l+a+++d g  v +L++DGg+++nnll q+qadi  ++v+rp++ e talG
  NCBI__GCF_000372865.1:WP_232422309.1 363 GTTGAHIARAAIESICFQVNDLLNALSEDGGRPVPQLRIDGGAATNNLLAQFQADISSLEVVRPQTLESTALG 435
                                           ************************************************************************* PP

                             TIGR01311 442 aAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaverslkw 496
                                           aA++ag+avg+w+ +eel+k+++ + +tf+ +m  ee ++++++w +aver+++w
  NCBI__GCF_000372865.1:WP_232422309.1 436 AACLAGIAVGLWN-LEELRKQWAID-RTFHGAMPPEEIDRRTRRWLKAVERAKNW 488
                                           **********998.7899*****98.**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (490 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.51
//
[ok]

This GapMind analysis is from Apr 09 2024. 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