Alignments for a candidate for glpK in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Dinoroseobacter shibae DFL-12

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate 3610039 Dshi_3420 glycerol kinase (RefSeq)

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



>FitnessBrowser__Dino:3610039
          Length = 519

 Score = 1058 bits (2736), Expect = 0.0
 Identities = 519/519 (100%), Positives = 519/519 (100%)

Query: 1   MDRQRGQFLLNLRALKPRPGEGTVRHVLAIDQGTTSSRAIVFDADMNIVSIAQEEFAQHY 60
           MDRQRGQFLLNLRALKPRPGEGTVRHVLAIDQGTTSSRAIVFDADMNIVSIAQEEFAQHY
Sbjct: 1   MDRQRGQFLLNLRALKPRPGEGTVRHVLAIDQGTTSSRAIVFDADMNIVSIAQEEFAQHY 60

Query: 61  PDSGWVEHDPEDLWDTVLRTCRNVLERTGLAATDLAGIGITNQRETTVVWDKSTGKPIHN 120
           PDSGWVEHDPEDLWDTVLRTCRNVLERTGLAATDLAGIGITNQRETTVVWDKSTGKPIHN
Sbjct: 61  PDSGWVEHDPEDLWDTVLRTCRNVLERTGLAATDLAGIGITNQRETTVVWDKSTGKPIHN 120

Query: 121 AIVWQDRRTAPFCAELRKAGHDALITAQTGLLADPYFSGTKLKYILDTVEGARDRAKAGE 180
           AIVWQDRRTAPFCAELRKAGHDALITAQTGLLADPYFSGTKLKYILDTVEGARDRAKAGE
Sbjct: 121 AIVWQDRRTAPFCAELRKAGHDALITAQTGLLADPYFSGTKLKYILDTVEGARDRAKAGE 180

Query: 181 LLFGTVDSFLIWRLTNGAAHVTDATNAARTMLYDIHKGAWSAEICTLFDIPLGMLPQVHD 240
           LLFGTVDSFLIWRLTNGAAHVTDATNAARTMLYDIHKGAWSAEICTLFDIPLGMLPQVHD
Sbjct: 181 LLFGTVDSFLIWRLTNGAAHVTDATNAARTMLYDIHKGAWSAEICTLFDIPLGMLPQVHD 240

Query: 241 CDAEFGTCTPEHLGGAVPILGVAGDQQAATIGQACFEPGMLKSTYGTGCFALLNTGEAPV 300
           CDAEFGTCTPEHLGGAVPILGVAGDQQAATIGQACFEPGMLKSTYGTGCFALLNTGEAPV
Sbjct: 241 CDAEFGTCTPEHLGGAVPILGVAGDQQAATIGQACFEPGMLKSTYGTGCFALLNTGEAPV 300

Query: 301 TSTNRLLTTIAYQLDGKPTYALEGSIFVAGAVVQWLRDGLKLIANASETQPLAEAADPHD 360
           TSTNRLLTTIAYQLDGKPTYALEGSIFVAGAVVQWLRDGLKLIANASETQPLAEAADPHD
Sbjct: 301 TSTNRLLTTIAYQLDGKPTYALEGSIFVAGAVVQWLRDGLKLIANASETQPLAEAADPHD 360

Query: 361 PVILVPAFTGLGAPYWNAECRGAVFGLSRGSGPEEFARAALESVGYQTRDLLEAMHKDWS 420
           PVILVPAFTGLGAPYWNAECRGAVFGLSRGSGPEEFARAALESVGYQTRDLLEAMHKDWS
Sbjct: 361 PVILVPAFTGLGAPYWNAECRGAVFGLSRGSGPEEFARAALESVGYQTRDLLEAMHKDWS 420

Query: 421 DAREGQPTLRVDGGMTASDWTMQFLADIIDAPVDRPKITETTALGVAWLAGQKAGLYPDR 480
           DAREGQPTLRVDGGMTASDWTMQFLADIIDAPVDRPKITETTALGVAWLAGQKAGLYPDR
Sbjct: 421 DAREGQPTLRVDGGMTASDWTMQFLADIIDAPVDRPKITETTALGVAWLAGQKAGLYPDR 480

Query: 481 AGFAANWALDQRFEPKMDATTRDTKYAAWKRAVAAVQQA 519
           AGFAANWALDQRFEPKMDATTRDTKYAAWKRAVAAVQQA
Sbjct: 481 AGFAANWALDQRFEPKMDATTRDTKYAAWKRAVAAVQQA 519


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: 1147
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: 519
Length of database: 519
Length adjustment: 35
Effective length of query: 484
Effective length of database: 484
Effective search space:   234256
Effective search space used:   234256
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 3610039 Dshi_3420 (glycerol kinase (RefSeq))
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.31738.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.4e-206  672.5   0.0   1.5e-206  672.4   0.0    1.0  1  lcl|FitnessBrowser__Dino:3610039  Dshi_3420 glycerol kinase (RefSe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3610039  Dshi_3420 glycerol kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  672.4   0.0  1.5e-206  1.5e-206       2     494 ..      26     517 ..      25     519 .] 0.98

  Alignments for each domain:
  == domain 1  score: 672.4 bits;  conditional E-value: 1.5e-206
                         TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiGitn 78 
                                        ++aiDqGttssraivfd++ ++v++aq+e+ q++p +gwvEhdp++++++v+++++++le+++  a+++a iGitn
  lcl|FitnessBrowser__Dino:3610039  26 HVLAIDQGTTSSRAIVFDADMNIVSIAQEEFAQHYPDSGWVEHDPEDLWDTVLRTCRNVLERTGLAATDLAGIGITN 102
                                       589************************************************************************** PP

                         TIGR01311  79 qREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevrkaaeeg 155
                                       qREttvvWdk+tgkp++naivWqd+rta +++el++++++  ++++tGL+ ++Yfs+tKl+++ld ve++r++a++g
  lcl|FitnessBrowser__Dino:3610039 103 QRETTVVWDKSTGKPIHNAIVWQDRRTAPFCAELRKAGHDALITAQTGLLADPYFSGTKLKYILDTVEGARDRAKAG 179
                                       ***************************************************************************** PP

                         TIGR01311 156 ellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevygeieekellke 232
                                       ellfGtvd++li++Lt+g++hvtd+tNA+Rt+l+++++ +w+ e++ lf+ip  +lP+++++ + +g+++++ +l+ 
  lcl|FitnessBrowser__Dino:3610039 180 ELLFGTVDSFLIWRLTNGAAHVTDATNAARTMLYDIHKGAWSAEICTLFDIPLGMLPQVHDCDAEFGTCTPE-HLGG 255
                                       **********************************************************************99.99** PP

                         TIGR01311 233 evpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkyalEGsvavaG 309
                                       +vpi gv+Gdqqaa +gq+c+++g+ K+tYgtGcF llntGe +v+s+++lLtt+ay+l+gk +  yalEGs++vaG
  lcl|FitnessBrowser__Dino:3610039 256 AVPILGVAGDQQAATIGQACFEPGMLKSTYGTGCFALLNTGEAPVTSTNRLLTTIAYQLDGKPT--YALEGSIFVAG 330
                                       ************************************************************9875..*********** PP

                         TIGR01311 310 aavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraaleavafq 386
                                       a+vqwlrd lkli +a+e+++la++++ ++ v +VPaf+GL+aPyW+++ rg+++Gl+r++  e++araale+v +q
  lcl|FitnessBrowser__Dino:3610039 331 AVVQWLRDGLKLIANASETQPLAEAADPHDPVILVPAFTGLGAPYWNAECRGAVFGLSRGSGPEEFARAALESVGYQ 407
                                       ***************************************************************************** PP

                         TIGR01311 387 ardileamekdagvevk...vLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwkseeele 460
                                       +rd+leam+kd     +   +L+vDGg++++++ mq+ adi++ +v rpk++ettalG+A++ag ++g++ +   ++
  lcl|FitnessBrowser__Dino:3610039 408 TRDLLEAMHKDWSDAREgqpTLRVDGGMTASDWTMQFLADIIDAPVDRPKITETTALGVAWLAGQKAGLYPDRAGFA 484
                                       **********9884443445********************************************************* PP

                         TIGR01311 461 ksaeaeektfepemdeeerekkykkwkeaversl 494
                                       ++++ + ++fep+md+++r++ky+ wk+av+  +
  lcl|FitnessBrowser__Dino:3610039 485 ANWALD-QRFEPKMDATTRDTKYAAWKRAVAAVQ 517
                                       *****8.***********************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (496 nodes)
Target sequences:                          1  (519 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: 00:00:00.02
# Mc/sec: 9.58
//
[ok]

This GapMind analysis is from Sep 17 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