Alignments for a candidate for glpK in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Halomonas desiderata SP1

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate WP_086509598.1 BZY95_RS08930 glycerol kinase

Query= reanno::Smeli:SM_b21009
         (497 letters)



>NCBI__GCF_002151265.1:WP_086509598.1
          Length = 493

 Score =  612 bits (1579), Expect = e-180
 Identities = 297/492 (60%), Positives = 368/492 (74%), Gaps = 2/492 (0%)

Query: 1   MGGYILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVK 60
           M  Y+LAIDQGTTS+RAI+FD +  +  V Q+EF QHFP  GWVEHDPE+IW TV+ST +
Sbjct: 1   MADYLLAIDQGTTSSRAILFDRDGHVIRVAQREFPQHFPHDGWVEHDPEDIWDTVLSTCR 60

Query: 61  EAIEKSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLE 120
           EA+E SG+  ++IA +GITNQRET ++WDR TGKP++NAIVWQDRRTA FC +L+++G  
Sbjct: 61  EAVETSGVALDEIAGVGITNQRETTLLWDRATGKPLYNAIVWQDRRTADFCRELQERGHA 120

Query: 121 KTFVKKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGECFCT 180
           +     TGLL+DPYFS TKL WLL NV+GA+ RA +GEL FGT+DTFL+WRLTGG    T
Sbjct: 121 ELVQSHTGLLIDPYFSATKLAWLLDNVEGARERAERGELAFGTVDTFLLWRLTGGRVHAT 180

Query: 181 DATNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIPILGV 240
           DATNASRT+L++I    WDDEL ++  +P  +LPEV+D +ADFG  +    GA +PI GV
Sbjct: 181 DATNASRTMLFDINAQQWDDELLKLFEIPSGLLPEVRDSSADFGTVEARWLGAELPIGGV 240

Query: 241 AGDQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETTYAL 300
            GDQQAA +GQACF+PGM KSTYGTGCF ++NTG    RS+NRLL+T+AYRL+G+TTYA+
Sbjct: 241 VGDQQAALVGQACFEPGMGKSTYGTGCFMIVNTGDRPARSRNRLLSTVAYRLNGKTTYAM 300

Query: 301 EGSIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARG 360
           EGSIFVAGAAVQWLRDGLK+ K A +T +LA+       VYLVPAFTGLGAPHWDP ARG
Sbjct: 301 EGSIFVAGAAVQWLRDGLKLFKDAAETEALAKQTRAGHSVYLVPAFTGLGAPHWDPKARG 360

Query: 361 AIFGMTRNTGPAEFARAALEAVCYQTRDLLEAMHKDWRRNGNDTVLRVDGGMVASDWTMQ 420
           AIFG+TR+TG AE   A L+AVCYQTRDL   M  D         LRVDGGMVA+ W +Q
Sbjct: 361 AIFGLTRDTGIAEIVAAGLQAVCYQTRDLQACMSDD--MGVPPGTLRVDGGMVANSWLVQ 418

Query: 421 RLSDLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDEATRK 480
            L+D+L   VDRP +LETTALG A++AG R G + + E  A+ W  +R F P M E  R+
Sbjct: 419 FLADMLGVQVDRPTVLETTALGAAYMAGLRFGWYRDLEEIAELWRCERSFMPSMPETERE 478

Query: 481 VKLKGWRSAVKR 492
              +GW  AV+R
Sbjct: 479 RLYRGWLEAVER 490


Lambda     K      H
   0.319    0.134    0.415 

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: 797
Number of extensions: 32
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: 497
Length of database: 493
Length adjustment: 34
Effective length of query: 463
Effective length of database: 459
Effective search space:   212517
Effective search space used:   212517
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_086509598.1 BZY95_RS08930 (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.7629.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.5e-222  722.7   0.0   9.6e-222  722.5   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509598.1  BZY95_RS08930 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509598.1  BZY95_RS08930 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  722.5   0.0  9.6e-222  9.6e-222       2     494 ..       4     492 ..       3     493 .] 0.99

  Alignments for each domain:
  == domain 1  score: 722.5 bits;  conditional E-value: 9.6e-222
                                 TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaee 70 
                                               +++aiDqGttssrai+fd++g+++  aq+e+ q+fp++gwvEhdp++i+++v+++++ea+e +++  +e
  lcl|NCBI__GCF_002151265.1:WP_086509598.1   4 YLLAIDQGTTSSRAILFDRDGHVIRVAQREFPQHFPHDGWVEHDPEDIWDTVLSTCREAVETSGVALDE 72 
                                               99******************************************************************* PP

                                 TIGR01311  71 iaaiGitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlr 139
                                               ia +GitnqREtt++Wd++tgkpl+naivWqd+rta++++el+e+++ e ++++tGL++++YfsatKl+
  lcl|NCBI__GCF_002151265.1:WP_086509598.1  73 IAGVGITNQRETTLLWDRATGKPLYNAIVWQDRRTADFCRELQERGHAELVQSHTGLLIDPYFSATKLA 141
                                               ********************************************************************* PP

                                 TIGR01311 140 WlldnveevrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipk 208
                                               Wlldnve++r++ae+gel fGtvdt+l+++Ltgg+vh+td+tNASRt+l++++ ++wd+ell+lf+ip+
  lcl|NCBI__GCF_002151265.1:WP_086509598.1 142 WLLDNVEGARERAERGELAFGTVDTFLLWRLTGGRVHATDATNASRTMLFDINAQQWDDELLKLFEIPS 210
                                               ********************************************************************* PP

                                 TIGR01311 209 ellPeirsssevygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkv 277
                                                llPe+r+ss+ +g++e++ +l++e+pi gv+Gdqqaalvgq+c+++g+ K+tYgtGcF+++ntG++++
  lcl|NCBI__GCF_002151265.1:WP_086509598.1 211 GLLPEVRDSSADFGTVEAR-WLGAELPIGGVVGDQQAALVGQACFEPGMGKSTYGTGCFMIVNTGDRPA 278
                                               ****************999.************************************************* PP

                                 TIGR01311 278 iskhglLttvayklggkkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPa 346
                                                s+++lL+tvay+l+gk++  ya+EGs++vaGaavqwlrd lkl+k+a+e+e+lak+    + vy+VPa
  lcl|NCBI__GCF_002151265.1:WP_086509598.1 279 RSRNRLLSTVAYRLNGKTT--YAMEGSIFVAGAAVQWLRDGLKLFKDAAETEALAKQTRAGHSVYLVPA 345
                                               ****************996..************************************************ PP

                                 TIGR01311 347 fsGLfaPyWdsdArgtivGltrkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknn 415
                                               f+GL+aP+Wd++Arg+i+Gltr+t  ++i+ a l+av++q+rd+ ++m+ d+gv   +L+vDGg+++n 
  lcl|NCBI__GCF_002151265.1:WP_086509598.1 346 FTGLGAPHWDPKARGAIFGLTRDTGIAEIVAAGLQAVCYQTRDLQACMSDDMGVPPGTLRVDGGMVANS 414
                                               ********************************************************************* PP

                                 TIGR01311 416 llmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkyk 484
                                               +l+q+ ad+lgv+v rp+v ettalGaA++agl +g ++++ee+++ ++ e ++f p+m e+ere+ y+
  lcl|NCBI__GCF_002151265.1:WP_086509598.1 415 WLVQFLADMLGVQVDRPTVLETTALGAAYMAGLRFGWYRDLEEIAELWRCE-RSFMPSMPETERERLYR 482
                                               **************************************************7.***************** PP

                                 TIGR01311 485 kwkeaversl 494
                                                w eaver +
  lcl|NCBI__GCF_002151265.1:WP_086509598.1 483 GWLEAVERVK 492
                                               *******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (493 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: 00:00:00.05
# Mc/sec: 4.22
//
[ok]

This GapMind analysis is from Sep 24 2021. 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 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