Alignments for a candidate for glpK in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Pseudomonas benzenivorans DSM 8628

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate WP_090447981.1 BLS63_RS22215 glycerol kinase

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



>NCBI__GCF_900100495.1:WP_090447981.1
          Length = 495

 Score =  627 bits (1618), Expect = 0.0
 Identities = 307/492 (62%), Positives = 377/492 (76%), Gaps = 3/492 (0%)

Query: 26  HVLAIDQGTTSSRAIVFDADMNIVSIAQEEFAQHYPDSGWVEHDPEDLWDTVLRTCRNVL 85
           ++LAIDQGTTSSRAIVF A    V+ AQ+EF Q++P  GWVEHD E++W + L  CR  L
Sbjct: 4   YLLAIDQGTTSSRAIVFSAQGLPVARAQQEFKQYFPQDGWVEHDGEEIWRSTLEVCRQAL 63

Query: 86  ERTGLAATDLAGIGITNQRETTVVWDKSTGKPIHNAIVWQDRRTAPFCAELRKAGHDALI 145
            ++GL A+ +A IGITNQRETT+VWD  TG PIH AIVWQDRRTA +CA L+ AG +A++
Sbjct: 64  AQSGLPASQIAAIGITNQRETTLVWDALTGAPIHPAIVWQDRRTADYCAALKAAGFEAMV 123

Query: 146 TAQTGLLADPYFSGTKLKYILDTVEGARDRAKAGELLFGTVDSFLIWRLTNGAAHVTDAT 205
           +A+TGLL DPYFSGTKL++ILD V GAR+RA  GEL FGTVDSFL+WRLT G +H TDAT
Sbjct: 124 SAKTGLLIDPYFSGTKLRWILDNVAGARERAARGELRFGTVDSFLLWRLTGGKSHKTDAT 183

Query: 206 NAARTMLYDIHKGAWSAEICTLFDIPLGMLPQVHDCDAEFGTCTPEHLGGAVPILGVAGD 265
           NA+RT+L++IH   W AE+  L +IP  +LPQV DC AEFGTC  E LG  +P+LG+AGD
Sbjct: 184 NASRTLLFNIHTQQWDAELLELLEIPASLLPQVLDCAAEFGTCAAELLGAPIPVLGMAGD 243

Query: 266 QQAATIGQACFEPGMLKSTYGTGCFALLNTGEAPVTSTNRLLTTIAYQLDGKPTYALEGS 325
           QQAA IGQACF+PGM+KSTYGTGCF + NTG +PV+S NRLLTT+ Y+LDG+ TYA+EGS
Sbjct: 244 QQAALIGQACFQPGMVKSTYGTGCFMIQNTGASPVSSKNRLLTTVGYRLDGQVTYAVEGS 303

Query: 326 IFVAGAVVQWLRDGLKLIANASETQPLAEAADPHDPVILVPAFTGLGAPYWNAECRGAVF 385
           IFVAGA VQWLRDG+KLI++AS+T+ LAE       V LVPAFTGLGAPYW+ + RGA+F
Sbjct: 304 IFVAGAAVQWLRDGIKLISHASDTEALAEQTGDTCGVYLVPAFTGLGAPYWDPKARGAIF 363

Query: 386 GLSRGSGPEEFARAALESVGYQTRDLLEAMHKDWSDAREGQPTLRVDGGMTASDWTMQFL 445
           GL+R +G +E   A L+SV YQTRDLLEAM +D + A      LRVDGGM  ++W MQFL
Sbjct: 364 GLTRDTGIKEIVTAGLQSVCYQTRDLLEAMRQDGAAA---PSALRVDGGMVVNNWLMQFL 420

Query: 446 ADIIDAPVDRPKITETTALGVAWLAGQKAGLYPDRAGFAANWALDQRFEPKMDATTRDTK 505
           ADI+  PV+RP++TETTALGVA+LAG KAG+Y D A  A +W   QRFEP+M    R   
Sbjct: 421 ADILGVPVERPEVTETTALGVAYLAGLKAGIYRDLAEIAGHWQRQQRFEPRMADAQRGKL 480

Query: 506 YAAWKRAVAAVQ 517
           Y  W  AV  V+
Sbjct: 481 YRGWLNAVQRVR 492


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: 824
Number of extensions: 31
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: 495
Length adjustment: 34
Effective length of query: 485
Effective length of database: 461
Effective search space:   223585
Effective search space used:   223585
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_090447981.1 BLS63_RS22215 (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.452099.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-221  720.4   0.0   4.7e-221  720.3   0.0    1.0  1  NCBI__GCF_900100495.1:WP_090447981.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100495.1:WP_090447981.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  720.3   0.0  4.7e-221  4.7e-221       2     494 ..       4     492 ..       3     494 .. 0.99

  Alignments for each domain:
  == domain 1  score: 720.3 bits;  conditional E-value: 4.7e-221
                             TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaai 74 
                                           +++aiDqGttssraivf+++g  va+aq+e++q+fp++gwvEhd +ei++s+++v+++al++++  a++iaai
  NCBI__GCF_900100495.1:WP_090447981.1   4 YLLAIDQGTTSSRAIVFSAQGLPVARAQQEFKQYFPQDGWVEHDGEEIWRSTLEVCRQALAQSGLPASQIAAI 76 
                                           99*********************************************************************** PP

                             TIGR01311  75 GitnqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnvee 147
                                           GitnqREtt+vWd+ tg p+++aivWqd+rta+++++lk+++ e ++++ktGL++++Yfs+tKlrW+ldnv +
  NCBI__GCF_900100495.1:WP_090447981.1  77 GITNQRETTLVWDALTGAPIHPAIVWQDRRTADYCAALKAAGFEAMVSAKTGLLIDPYFSGTKLRWILDNVAG 149
                                           ************************************************************************* PP

                             TIGR01311 148 vrkaaeegellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssev 220
                                           +r++a +gel fGtvd++l+++Ltggk h td+tNASRtll+n++t++wd ellel++ip++llP++ ++++ 
  NCBI__GCF_900100495.1:WP_090447981.1 150 ARERAARGELRFGTVDSFLLWRLTGGKSHKTDATNASRTLLFNIHTQQWDAELLELLEIPASLLPQVLDCAAE 222
                                           ************************************************************************* PP

                             TIGR01311 221 ygeieekellkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklgg 293
                                           +g+++++ ll++ +p+ g++Gdqqaal+gq+c+++g++K+tYgtGcF++ ntG ++v sk++lLttv+y+l+g
  NCBI__GCF_900100495.1:WP_090447981.1 223 FGTCAAE-LLGAPIPVLGMAGDQQAALIGQACFQPGMVKSTYGTGCFMIQNTGASPVSSKNRLLTTVGYRLDG 294
                                           ****999.***************************************************************** PP

                             TIGR01311 294 kkptkyalEGsvavaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGl 366
                                           + +  ya+EGs++vaGaavqwlrd +kli++a+++e+la++  d+ gvy+VPaf+GL+aPyWd++Arg+i+Gl
  NCBI__GCF_900100495.1:WP_090447981.1 295 QVT--YAVEGSIFVAGAAVQWLRDGIKLISHASDTEALAEQTGDTCGVYLVPAFTGLGAPYWDPKARGAIFGL 365
                                           996..******************************************************************** PP

                             TIGR01311 367 trkttkehiaraaleavafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaetta 439
                                           tr+t  ++i++a l++v++q+rd+leam++d  +  ++L+vDGg++ nn+lmq+ adilgv+verp+v+etta
  NCBI__GCF_900100495.1:WP_090447981.1 366 TRDTGIKEIVTAGLQSVCYQTRDLLEAMRQDGAAAPSALRVDGGMVVNNWLMQFLADILGVPVERPEVTETTA 438
                                           ************************************************************************* PP

                             TIGR01311 440 lGaAlaaglavgvwkseeeleksaeaeektfepemdeeerekkykkwkeaversl 494
                                           lG+A++agl++g+++++ e++ +++++ ++fep+m +++r k y+ w +av+r +
  NCBI__GCF_900100495.1:WP_090447981.1 439 LGVAYLAGLKAGIYRDLAEIAGHWQRQ-QRFEPRMADAQRGKLYRGWLNAVQRVR 492
                                           *************************97.************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (495 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 34.13
//
[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