Alignments for a candidate for hcs in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for hcs in Dechlorosoma suillum PS

Align Homocitrate synthase; EC 2.3.3.14 (characterized)
to candidate Dsui_0578 Dsui_0578 homocitrate synthase NifV

Query= SwissProt::P05342
         (385 letters)



>FitnessBrowser__PS:Dsui_0578
          Length = 384

 Score =  436 bits (1120), Expect = e-127
 Identities = 220/368 (59%), Positives = 280/368 (76%), Gaps = 1/368 (0%)

Query: 1   MASVIIDDTTLRDGEQSAGVAFNADEKIAIARALAELGVPELEIGIPSMGEEEREVMHAI 60
           M ++ I+DTTLRDGEQ+AGVAF A EK+AIA+ALA  GVPE+E+GIP+MGE+E+EV+ AI
Sbjct: 1   MTTITINDTTLRDGEQTAGVAFTAAEKLAIAQALAAAGVPEMEVGIPAMGEQEQEVIRAI 60

Query: 61  AGLGLSSRLLAWCRLCDVDLAAARSTGVTMVDLSLPVSDLMLHHKLNRDRDWALREVARL 120
           AGLGLSSRL+ W R+C  DL   R     +V+LS+PVSD  + HKLN+D  W L  + R 
Sbjct: 61  AGLGLSSRLMVWGRMCAADLEVTRRCNAHIVNLSIPVSDQQIRHKLNKDHRWVLDSIRRF 120

Query: 121 VGEARMAGLEVCLGCEDASRADLEFVVQVGEVAQAAGARRLRFADTVGVMEPFGMLDRFR 180
           V EAR AGLEVC+G ED+SRADL+F+ +V E AQAAGARR RFADT+GV++PF    R  
Sbjct: 121 VPEARAAGLEVCVGGEDSSRADLDFLHRVMEAAQAAGARRFRFADTLGVLDPFITHQRIA 180

Query: 181 FLSRRLDMELEVHAHDDFGLATANTLAAVMGGATHINTTVNGLGERAGNAALEECVLALK 240
            L  R D+E+E+HAHDD GLATANTLAAV  GATHINTTVNGLGERAGNA LEE V+AL+
Sbjct: 181 ALRARSDLEIEIHAHDDLGLATANTLAAVTAGATHINTTVNGLGERAGNAPLEESVIALR 240

Query: 241 NLHGIDTGIDTRGIPAISALVERASGRQVAWQKSVVGAGVFTHEAGIHVDGLLKHRRNYE 300
           +L+ ID+G+D   +PAIS LV +ASGR VA  KS+VGA VFTHEAGIHVDGL K+  NY+
Sbjct: 241 HLYDIDSGVDPLQLPAISDLVAKASGRPVAVNKSIVGANVFTHEAGIHVDGLAKNPANYQ 300

Query: 301 GLNPDELGRSHSLVLGKHSGAHMVRNTYRDLGIELADWQSQALLGRIRAFSTRTKRRSPQ 360
             +P E+G+ H +VLGKHSG+  V + Y+DLGI++ +  ++ +L R+R+++   K R P 
Sbjct: 301 AFDPAEVGKGHRIVLGKHSGSTAVIHAYKDLGIDIDEGMARRILSRVRSYAMAFK-RPPG 359

Query: 361 PAELQDFY 368
             EL  +Y
Sbjct: 360 FRELMSYY 367


Lambda     K      H
   0.320    0.135    0.396 

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: 489
Number of extensions: 16
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: 385
Length of database: 384
Length adjustment: 30
Effective length of query: 355
Effective length of database: 354
Effective search space:   125670
Effective search space used:   125670
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: 50 (23.9 bits)

Align candidate Dsui_0578 Dsui_0578 (homocitrate synthase NifV)
to HMM TIGR02660 (nifV: homocitrate synthase (EC 2.3.3.14))

# 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.aa/TIGR02660.hmm
# target sequence database:        /tmp/gapView.4641.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02660  [M=365]
Accession:   TIGR02660
Description: nifV_homocitr: homocitrate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.4e-165  535.7   2.5   3.9e-165  535.5   2.5    1.0  1  lcl|FitnessBrowser__PS:Dsui_0578  Dsui_0578 homocitrate synthase N


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0578  Dsui_0578 homocitrate synthase NifV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  535.5   2.5  3.9e-165  3.9e-165       2     363 ..       4     365 ..       3     367 .. 0.99

  Alignments for each domain:
  == domain 1  score: 535.5 bits;  conditional E-value: 3.9e-165
                         TIGR02660   2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaWcRlraedi 78 
                                       ++inDttLRDGEq+agvaF+a+EKlaiA+aL++aGv+e+EvGipamge+E+++iraia lgl++rl++W R++a+d+
  lcl|FitnessBrowser__PS:Dsui_0578   4 ITINDTTLRDGEQTAGVAFTAAEKLAIAQALAAAGVPEMEVGIPAMGEQEQEVIRAIAGLGLSSRLMVWGRMCAADL 80 
                                       89*************************************************************************** PP

                         TIGR02660  79 eaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRadeeflvelaevakeag 155
                                       e ++++  + v+ls+pvsd+q+++kl+kd++wvl++++++v  a+ +gl+v+vg+eD+sRad +fl++++e a++ag
  lcl|FitnessBrowser__PS:Dsui_0578  81 EVTRRCNAHIVNLSIPVSDQQIRHKLNKDHRWVLDSIRRFVPEARAAGLEVCVGGEDSSRADLDFLHRVMEAAQAAG 157
                                       ***************************************************************************** PP

                         TIGR02660 156 akRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavkaGassvsvtvlGlGERAGnAalee 232
                                       a+R+RfaDt+gvldPf t+++++alra+++le+E+HaH+DlGlAtAntlaav+aGa+++++tv+GlGERAGnA+lee
  lcl|FitnessBrowser__PS:Dsui_0578 158 ARRFRFADTLGVLDPFITHQRIAALRARSDLEIEIHAHDDLGLATANTLAAVTAGATHINTTVNGLGERAGNAPLEE 234
                                       ***************************************************************************** PP

                         TIGR02660 233 valalkellgldtgidlselkelsqlvakasgraleaqkavvGesvFaHEsGiHvdgllkdeatYesldPeevGrer 309
                                        ++al++l+++d g+d  +l+++s+lvakasgr+++++k++vG++vF+HE+GiHvdgl k++a+Y+++dP+evG+ +
  lcl|FitnessBrowser__PS:Dsui_0578 235 SVIALRHLYDIDSGVDPLQLPAISDLVAKASGRPVAVNKSIVGANVFTHEAGIHVDGLAKNPANYQAFDPAEVGKGH 311
                                       ***************************************************************************** PP

                         TIGR02660 310 elviGKHsgraaviealkelgleleeeeaeelleavravaerlKrsleeeelaa 363
                                       ++v+GKHsg++avi+a+k+lg++++e  a+++l++vr++a ++Kr++  +el++
  lcl|FitnessBrowser__PS:Dsui_0578 312 RIVLGKHSGSTAVIHAYKDLGIDIDEGMARRILSRVRSYAMAFKRPPGFRELMS 365
                                       ************************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (365 nodes)
Target sequences:                          1  (384 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: 00:00:00.01
# Mc/sec: 7.57
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis