Alignments for a candidate for glpK in Marinobacter adhaerens HP15

GapMind for catabolism of small carbon sources

Alignments for a candidate for glpK in Marinobacter adhaerens HP15

Align Glycerol kinase (EC 2.7.1.30) (characterized)
to candidate GFF769 HP15_748 glycerol kinase

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



>FitnessBrowser__Marino:GFF769
          Length = 493

 Score =  593 bits (1529), Expect = e-174
 Identities = 287/492 (58%), Positives = 363/492 (73%), Gaps = 3/492 (0%)

Query: 1   MGGYILAIDQGTTSTRAIVFDGNQKIAGVGQKEFKQHFPKSGWVEHDPEEIWQTVVSTVK 60
           M  Y+LAIDQGTTS+RAIVFD         Q+EF Q+FPK GWVEHD  EIW + ++  +
Sbjct: 1   MTRYLLAIDQGTTSSRAIVFDQTGNSVATDQQEFHQYFPKDGWVEHDAREIWDSTLAVCR 60

Query: 61  EAIEKSGITANDIAAIGITNQRETVVVWDRETGKPIHNAIVWQDRRTAAFCDKLKKKGLE 120
            A++K+GI A+++A IGITNQRET V+WDR TG+PI++AIVWQDRRTA++C KLK  G E
Sbjct: 61  GALDKAGIDASELAGIGITNQRETTVIWDRATGEPIYHAIVWQDRRTASWCTKLKSDGHE 120

Query: 121 KTFVKKTGLLLDPYFSGTKLNWLLSNVKGAQVRAAKGELCFGTIDTFLIWRLTGGECFCT 180
            T V++TGLL+DPYFS TK+ W+L NV+GA+ RA  G L FGT+D++L+W LT G+  CT
Sbjct: 121 DTVVERTGLLIDPYFSATKIAWILDNVEGARARAESGALAFGTVDSWLLWNLTNGKSHCT 180

Query: 181 DATNASRTLLYNIAENAWDDELTEVLRVPKEMLPEVKDCAADFGVTDPSLFGAAIPILGV 240
           DATNASRT L+NI +  WDD+L  + RVP+ +LPEV D AAD+G  +    GA + I G+
Sbjct: 181 DATNASRTALFNIHKQDWDDDLLALFRVPRALLPEVLDSAADYGTAEAQWLGAPVMIAGI 240

Query: 241 AGDQQAATIGQACFKPGMLKSTYGTGCFALLNTGKDMVRSKNRLLTTIAYRLDGETTYAL 300
           AGDQ AA +GQACF PGM KSTYGTGCF +LNTG   VRS+NRLLTT+AYRL+G+  YA+
Sbjct: 241 AGDQHAALVGQACFYPGMAKSTYGTGCFLMLNTGDKAVRSENRLLTTMAYRLNGKPCYAV 300

Query: 301 EGSIFVAGAAVQWLRDGLKVIKAAPDTGSLAESADPSQEVYLVPAFTGLGAPHWDPDARG 360
           EGSIFVAGAA+QWLRDGLK+I  A ++ + AE+      VYLVPAFTGLGAPHWDP ARG
Sbjct: 301 EGSIFVAGAAMQWLRDGLKLIAHANESSAHAEAVGVDNPVYLVPAFTGLGAPHWDPHARG 360

Query: 361 AIFGMTRNTGPAEFARAALEAVCYQTRDLLEAMHKDWRRNGNDTVLRVDGGMVASDWTMQ 420
           AI G+TR+TG  E   A L++VCYQT+DL+ A+  D  R  +   LRVDGGMV +DW MQ
Sbjct: 361 AIMGLTRDTGIGEIVTAGLQSVCYQTKDLVRAIQNDGARLES---LRVDGGMVVNDWVMQ 417

Query: 421 RLSDLLDAPVDRPVILETTALGVAWLAGSRAGVWPNQEAFAKSWARDRRFEPHMDEATRK 480
            L+D+L+  VDRP + ETTALG A+LAG + GV+ N E  +  W  +R+F P M  A R+
Sbjct: 418 FLADILNVTVDRPRVTETTALGAAYLAGLQTGVFDNLEQISALWECERQFHPEMRPALRE 477

Query: 481 VKLKGWRSAVKR 492
               GW  AV+R
Sbjct: 478 SLYAGWLDAVER 489


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: 843
Number of extensions: 41
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: 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 GFF769 HP15_748 (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.11558.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.5e-217  708.0   0.2   2.8e-217  707.8   0.2    1.0  1  lcl|FitnessBrowser__Marino:GFF769  HP15_748 glycerol kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF769  HP15_748 glycerol kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  707.8   0.2  2.8e-217  2.8e-217       2     494 ..       4     491 ..       3     493 .] 0.99

  Alignments for each domain:
  == domain 1  score: 707.8 bits;  conditional E-value: 2.8e-217
                          TIGR01311   2 liaaiDqGttssraivfdkegeevakaqkelsqifpkegwvEhdpleilesvvkvlaealekleikaeeiaaiGit 77 
                                        +++aiDqGttssraivfd++g+ va++q+e++q+fpk+gwvEhd+ ei++s+++v++ al+k++i+a+e+a iGit
  lcl|FitnessBrowser__Marino:GFF769   4 YLLAIDQGTTSSRAIVFDQTGNSVATDQQEFHQYFPKDGWVEHDAREIWDSTLAVCRGALDKAGIDASELAGIGIT 79 
                                        99************************************************************************** PP

                          TIGR01311  78 nqREttvvWdketgkplvnaivWqdtrtakiveelkeetkeeelrektGLplstYfsatKlrWlldnveevrkaae 153
                                        nqREttv+Wd++tg+p+++aivWqd+rta+ +++lk++++e+++ e+tGL++++YfsatK++W+ldnve++r++ae
  lcl|FitnessBrowser__Marino:GFF769  80 NQRETTVIWDRATGEPIYHAIVWQDRRTASWCTKLKSDGHEDTVVERTGLLIDPYFSATKIAWILDNVEGARARAE 155
                                        **************************************************************************** PP

                          TIGR01311 154 egellfGtvdtwliykLtggkvhvtdvtNASRtlllnletlkwdeellelfkipkellPeirsssevygeieekel 229
                                        +g l fGtvd+wl+++Lt+gk h+td+tNASRt l+n+++++wd++ll+lf++p++llPe+ +s++ yg+ e++ +
  lcl|FitnessBrowser__Marino:GFF769 156 SGALAFGTVDSWLLWNLTNGKSHCTDATNASRTALFNIHKQDWDDDLLALFRVPRALLPEVLDSAADYGTAEAQ-W 230
                                        **********************************************************************9999.* PP

                          TIGR01311 230 lkeevpitgvlGdqqaalvgqlclkkgeaKntYgtGcFlllntGekkviskhglLttvayklggkkptkyalEGsv 305
                                        l++ v i+g++Gdq+aalvgq+c+ +g+aK+tYgtGcFl+lntG+k+v s+++lLtt+ay+l+gk    ya+EGs+
  lcl|FitnessBrowser__Marino:GFF769 231 LGAPVMIAGIAGDQHAALVGQACFYPGMAKSTYGTGCFLMLNTGDKAVRSENRLLTTMAYRLNGKPC--YAVEGSI 304
                                        ***************************************************************9875..******* PP

                          TIGR01311 306 avaGaavqwlrdnlklikkaeeveklaksvedsegvyfVPafsGLfaPyWdsdArgtivGltrkttkehiaraale 381
                                        +vaGaa+qwlrd lkli +a+e+ + a++v  ++ vy+VPaf+GL+aP+Wd++Arg+i+Gltr+t   +i++a l+
  lcl|FitnessBrowser__Marino:GFF769 305 FVAGAAMQWLRDGLKLIAHANESSAHAEAVGVDNPVYLVPAFTGLGAPHWDPHARGAIMGLTRDTGIGEIVTAGLQ 380
                                        **************************************************************************** PP

                          TIGR01311 382 avafqardileamekdagvevkvLkvDGglsknnllmqiqadilgvkverpkvaettalGaAlaaglavgvwksee 457
                                        +v++q++d+++a+++d  +++++L+vDGg++ n+++mq+ adil+v+v rp+v+ettalGaA++agl++gv++++e
  lcl|FitnessBrowser__Marino:GFF769 381 SVCYQTKDLVRAIQNDG-ARLESLRVDGGMVVNDWVMQFLADILNVTVDRPRVTETTALGAAYLAGLQTGVFDNLE 455
                                        **************996.89******************************************************** PP

                          TIGR01311 458 eleksaeaeektfepemdeeerekkykkwkeaversl 494
                                        ++++ +e e ++f+pem  + re+ y+ w +aver +
  lcl|FitnessBrowser__Marino:GFF769 456 QISALWECE-RQFHPEMRPALRESLYAGWLDAVERVC 491
                                        ********7.************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.64
//
[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