Alignments for a candidate for glpK in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Phaeobacter inhibens BS107

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate GFF3152 PGA1_c32030 glycerol kinase GlpK

Query= reanno::Dino:3610039
         (519 letters)



>FitnessBrowser__Phaeo:GFF3152
          Length = 494

 Score =  713 bits (1841), Expect = 0.0
 Identities = 344/491 (70%), Positives = 395/491 (80%), Gaps = 2/491 (0%)

Query: 26  HVLAIDQGTTSSRAIVFDADMNIVSIAQEEFAQHYPDSGWVEHDPEDLWDTVLRTCRNVL 85
           ++LAIDQGTTS+RAI+FD  M     AQ+EF QH+P +GWVEHDPE+LW T L  CR V+
Sbjct: 3   YILAIDQGTTSTRAILFDDRMQAQGSAQQEFTQHFPQAGWVEHDPENLWSTTLDVCRKVM 62

Query: 86  ERTGLAATDLAGIGITNQRETTVVWDKSTGKPIHNAIVWQDRRTAPFCAELRKAGHDALI 145
              G+ A ++AGIGITNQRETTVVWD+ +GKPIHNAIVWQDRRT+P C ELR AGH+  +
Sbjct: 63  AEQGVTAAEIAGIGITNQRETTVVWDRHSGKPIHNAIVWQDRRTSPICEELRAAGHEDSV 122

Query: 146 TAQTGLLADPYFSGTKLKYILDTVEGARDRAKAGELLFGTVDSFLIWRLTNGAAHVTDAT 205
             +TGLL DPYFSGTKLK+ILDTV  AR RA+AG+LLFGTVDSFLIWRLT GA+HVTDAT
Sbjct: 123 RQKTGLLLDPYFSGTKLKWILDTVPEARARAEAGDLLFGTVDSFLIWRLTGGASHVTDAT 182

Query: 206 NAARTMLYDIHKGAWSAEICTLFDIPLGMLPQVHDCDAEFGTCTPEHLGGAVPILGVAGD 265
           NAART++YDI KG WS+EIC    +P  MLP+V DC A+FGT   E LGG + ILGVAGD
Sbjct: 183 NAARTLMYDIRKGRWSSEICGFLGVPRDMLPEVKDCAADFGTTKAEFLGGEIAILGVAGD 242

Query: 266 QQAATIGQACFEPGMLKSTYGTGCFALLNTGEAPVTSTNRLLTTIAYQLDGKPTYALEGS 325
           QQAATIGQACF+PGM+KSTYGTGCFALLNTG+ PV S NR+LTTIAYQLDG PTYALEGS
Sbjct: 243 QQAATIGQACFQPGMMKSTYGTGCFALLNTGDTPVVSQNRMLTTIAYQLDGAPTYALEGS 302

Query: 326 IFVAGAVVQWLRDGLKLIANASETQPLAEAADPHDPVILVPAFTGLGAPYWNAECRGAVF 385
           IF+AGA VQWLRDGL +I +A E+  LA  ADP   VILVPAFTGLGAPYW  +CRG +F
Sbjct: 303 IFIAGAAVQWLRDGLGIIGSAQESGALARNADPGQDVILVPAFTGLGAPYWKPDCRGGMF 362

Query: 386 GLSRGSGPEEFARAALESVGYQTRDLLEAMHKDWSDAREGQPTLRVDGGMTASDWTMQFL 445
           GL+R SGP EFARAAL+SV YQTRDL EAM  DW    E   TLRVDGGM+AS+WTMQ L
Sbjct: 363 GLTRNSGPAEFARAALQSVAYQTRDLWEAMRADWDG--ESLVTLRVDGGMSASNWTMQSL 420

Query: 446 ADIIDAPVDRPKITETTALGVAWLAGQKAGLYPDRAGFAANWALDQRFEPKMDATTRDTK 505
           AD++ A VDRP + ETTALG AWLAG +AG+YPD+AGFAA WALDQ+F P+MD   R   
Sbjct: 421 ADLLGAAVDRPVMQETTALGAAWLAGMRAGVYPDQAGFAATWALDQQFTPEMDEDRRSAA 480

Query: 506 YAAWKRAVAAV 516
           YA WKRAV AV
Sbjct: 481 YARWKRAVEAV 491


Lambda     K      H
   0.319    0.134    0.416 

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: 930
Number of extensions: 34
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: 519
Length of database: 494
Length adjustment: 34
Effective length of query: 485
Effective length of database: 460
Effective search space:   223100
Effective search space used:   223100
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 GFF3152 PGA1_c32030 (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.14348.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   6.2e-211  686.9   0.3     7e-211  686.7   0.3    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3152  PGA1_c32030 glycerol kinase GlpK


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3152  PGA1_c32030 glycerol kinase GlpK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  686.7   0.3    7e-211    7e-211       2     493 ..       3     491 ..       2     494 .] 0.99

  Alignments for each domain:
  == domain 1  score: 686.7 bits;  conditional E-value: 7e-211
                          TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiGit 77 
                                        +i+aiDqGtts+rai+fd++ +  ++aq+e++q+fp++gwvEhdp++++++++ v+++++++ +++a+eia iGit
  lcl|FitnessBrowser__Phaeo:GFF3152   3 YILAIDQGTTSTRAILFDDRMQAQGSAQQEFTQHFPQAGWVEHDPENLWSTTLDVCRKVMAEQGVTAAEIAGIGIT 78 
                                        9*************************************************************************** PP

                          TIGR01311  78 nqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevrkaae 153
                                        nqREttvvWd+++gkp++naivWqd+rt+ i+eel+++++e+ +r+ktGL+l++Yfs+tKl+W+ld v+e+r++ae
  lcl|FitnessBrowser__Phaeo:GFF3152  79 NQRETTVVWDRHSGKPIHNAIVWQDRRTSPICEELRAAGHEDSVRQKTGLLLDPYFSGTKLKWILDTVPEARARAE 154
                                        **************************************************************************** PP

                          TIGR01311 154 egellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevygeieekel 229
                                        +g+llfGtvd++li++Ltgg+ hvtd+tNA+Rtl++++++ +w++e++ ++++p+++lPe++++++ +g+++++ +
  lcl|FitnessBrowser__Phaeo:GFF3152 155 AGDLLFGTVDSFLIWRLTGGASHVTDATNAARTLMYDIRKGRWSSEICGFLGVPRDMLPEVKDCAADFGTTKAE-F 229
                                        ************************************************************************99.* PP

                          TIGR01311 230 lkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkyalEGsv 305
                                        l+ e+ i gv+Gdqqaa +gq+c+++g++K+tYgtGcF llntG+++v+s++++Ltt+ay+l+g    +yalEGs+
  lcl|FitnessBrowser__Phaeo:GFF3152 230 LGGEIAILGVAGDQQAATIGQACFQPGMMKSTYGTGCFALLNTGDTPVVSQNRMLTTIAYQLDGAP--TYALEGSI 303
                                        ***************************************************************976..5******* PP

                          TIGR01311 306 avaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraale 381
                                        ++aGaavqwlrd l++i +a+e+++la++++  ++v +VPaf+GL+aPyW++d rg ++Gltr++  +++araal+
  lcl|FitnessBrowser__Phaeo:GFF3152 304 FIAGAAVQWLRDGLGIIGSAQESGALARNADPGQDVILVPAFTGLGAPYWKPDCRGGMFGLTRNSGPAEFARAALQ 379
                                        **************************************************************************** PP

                          TIGR01311 382 avafqardileamekdag.vevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkse 456
                                        +va+q+rd+ eam++d    ++ +L+vDGg+s++n+ mq  ad+lg  v rp ++ettalGaA++ag+ +gv+ ++
  lcl|FitnessBrowser__Phaeo:GFF3152 380 SVAYQTRDLWEAMRADWDgESLVTLRVDGGMSASNWTMQSLADLLGAAVDRPVMQETTALGAAWLAGMRAGVYPDQ 455
                                        ****************9747889***************************************************** PP

                          TIGR01311 457 eeleksaeaeektfepemdeeerekkykkwkeavers 493
                                          ++++++ + ++f+pemde++r++ y++wk+ave  
  lcl|FitnessBrowser__Phaeo:GFF3152 456 AGFAATWALD-QQFTPEMDEDRRSAAYARWKRAVEAV 491
                                        *********8.***********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (494 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.53
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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