Alignments for a candidate for metB in Steroidobacter denitrificans DSM 18526

GapMind for Amino acid biosynthesis

Alignments for a candidate for metB in Steroidobacter denitrificans DSM 18526

Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_066920229.1 ACG33_RS08115 O-succinylhomoserine (thiol)-lyase

Query= SwissProt::P00935
         (386 letters)



>NCBI__GCF_001579945.1:WP_066920229.1
          Length = 404

 Score =  421 bits (1082), Expect = e-122
 Identities = 216/378 (57%), Positives = 268/378 (70%), Gaps = 1/378 (0%)

Query: 6   ATIAVRSGLNDDEQYGCVVPPIHLSSTYNFTGFNEPRAHDYSRRGNPTRDVVQRALAELE 65
           AT AVR+GL  D+Q+G VVPP+HLSST+ F  F E R +DYSR GNPTRD +  ALA+LE
Sbjct: 14  ATCAVRAGLETDDQHGAVVPPLHLSSTFAFKAFGERRQYDYSRSGNPTRDALATALADLE 73

Query: 66  GGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQG 125
           GGAGA +T++GM+A  L   + L   DLL+APHDCYGG+YRL  SLA RG  RV+FVDQ 
Sbjct: 74  GGAGATVTSSGMAAAQLACQL-LHADDLLIAPHDCYGGTYRLLSSLAARGALRVVFVDQT 132

Query: 126 DEQALRAALAEKPKLVLVESPSNPLLRVVDIAKICHLAREVGAVSVVDNTFLSPALQNPL 185
           D+ A  AALA  PKLV VE+PSNPLLR+VDI          GA+ +VDNTFLSP  Q P 
Sbjct: 133 DDAAFSAALAGGPKLVWVETPSNPLLRIVDIRAAARQVHAAGALLLVDNTFLSPVWQQPF 192

Query: 186 ALGADLVLHSCTKYLNGHSDVVAGVVIAKDPDVVTELAWWANNIGVTGGAFDSYLLLRGL 245
           ALGADLVLHS TKYLNGHSDVV G +++   ++   + WWAN IGVTG  FDS+L LRG+
Sbjct: 193 ALGADLVLHSTTKYLNGHSDVVGGALVSATAELHERVQWWANCIGVTGAPFDSFLTLRGV 252

Query: 246 RTLVPRMELAQRNAQAIVKYLQTQPLVKKLYHPSLPENQGHEIAARQQKGFGAMLSFELD 305
           R+L  RM     NA  + + L     V+++Y P LP +  H++A  QQ GFGAM+SFEL 
Sbjct: 253 RSLHARMRAHGENALQVAQLLNGHSAVRQIYFPGLPTHPQHDLARTQQSGFGAMMSFELH 312

Query: 306 GDEQTLRRFLGGLSLFTLAESLGGVESLISHAATMTHAGMAPEARAAAGISETLLRISTG 365
           G   ++R FL GL  F+LAESLGGVESL++H A+MTHA M  +AR AAGIS++LLR+S G
Sbjct: 313 GGLASVRAFLDGLQCFSLAESLGGVESLVAHPASMTHAAMDAQARQAAGISDSLLRLSIG 372

Query: 366 IEDGEDLIADLENGFRAA 383
           IE  +DL+ DL+ G   A
Sbjct: 373 IETAQDLLNDLQAGLDRA 390


Lambda     K      H
   0.319    0.136    0.394 

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: 436
Number of extensions: 17
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: 386
Length of database: 404
Length adjustment: 31
Effective length of query: 355
Effective length of database: 373
Effective search space:   132415
Effective search space used:   132415
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_066920229.1 ACG33_RS08115 (O-succinylhomoserine (thiol)-lyase)
to HMM TIGR02080 (metB: O-succinylhomoserine (thiol)-lyase (EC 2.5.1.48))

# 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/TIGR02080.hmm
# target sequence database:        /tmp/gapView.14907.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02080  [M=382]
Accession:   TIGR02080
Description: O_succ_thio_ly: O-succinylhomoserine (thiol)-lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-182  592.2   0.0   2.2e-182  591.9   0.0    1.0  1  lcl|NCBI__GCF_001579945.1:WP_066920229.1  ACG33_RS08115 O-succinylhomoseri


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001579945.1:WP_066920229.1  ACG33_RS08115 O-succinylhomoserine (thiol)-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  591.9   0.0  2.2e-182  2.2e-182       5     380 ..      14     388 ..      11     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 591.9 bits;  conditional E-value: 2.2e-182
                                 TIGR02080   5 atiavrsGlesdkqygavvpPiylsttyefagfnepraydysrsgnPtrdllekalaelekGadavvts 73 
                                               at avr Gle+d+q+gavvpP++ls+t++f++f e r+ydysrsgnPtrd l+ ala+le+Ga+a vts
  lcl|NCBI__GCF_001579945.1:WP_066920229.1  14 ATCAVRAGLETDDQHGAVVPPLHLSSTFAFKAFGERRQYDYSRSGNPTRDALATALADLEGGAGATVTS 82 
                                               79******************************************************************* PP

                                 TIGR02080  74 sGmsaiellviallkpddllvaPhdcyGGtyrllkalakkgklkvqlvdqsdeealekalaekpklvli 142
                                               sGm+a +l +  ll++ddll+aPhdcyGGtyrll++la +g l+v +vdq+d +a+++ala  pklv++
  lcl|NCBI__GCF_001579945.1:WP_066920229.1  83 SGMAAAQLAC-QLLHADDLLIAPHDCYGGTYRLLSSLAARGALRVVFVDQTDDAAFSAALAGGPKLVWV 150
                                               **********.9********************************************************* PP

                                 TIGR02080 143 etPsnPllrvvdiaklcklakaagavvvvdntflsPilqkPlalGadlvlhsatkylnGhsdviaGavi 211
                                               etPsnPllr+vdi++ ++  +aaga+  vdntflsP+ q+P+alGadlvlhs+tkylnGhsdv++Ga++
  lcl|NCBI__GCF_001579945.1:WP_066920229.1 151 ETPSNPLLRIVDIRAAARQVHAAGALLLVDNTFLSPVWQQPFALGADLVLHSTTKYLNGHSDVVGGALV 219
                                               ********************************************************************* PP

                                 TIGR02080 212 akdkqlaeelawwanalGvtgaafdsylllrGlrtlaarvreqernakkiveylqkqplvkkvyypglp 280
                                               ++  +l+e ++wwan++Gvtga+fds+l+lrG+r+l ar+r + +na +++++l+ +++v+++y+pglp
  lcl|NCBI__GCF_001579945.1:WP_066920229.1 220 SATAELHERVQWWANCIGVTGAPFDSFLTLRGVRSLHARMRAHGENALQVAQLLNGHSAVRQIYFPGLP 288
                                               ********************************************************************* PP

                                 TIGR02080 281 dhagheiaakqqkGfGallsfelkGgeeevkkflkklklftlaeslGGvesliahpatmthaamekear 349
                                                h++h++a+ qq+GfGa++sfel+Gg ++v++fl+ l++f+laeslGGvesl+ahpa+mthaam+ +ar
  lcl|NCBI__GCF_001579945.1:WP_066920229.1 289 THPQHDLARTQQSGFGAMMSFELHGGLASVRAFLDGLQCFSLAESLGGVESLVAHPASMTHAAMDAQAR 357
                                               ********************************************************************* PP

                                 TIGR02080 350 eeaGikdellrlsvGledaddliadleqala 380
                                               ++aGi+d+llrls+G+e a+dl++dl+++l 
  lcl|NCBI__GCF_001579945.1:WP_066920229.1 358 QAAGISDSLLRLSIGIETAQDLLNDLQAGLD 388
                                               ****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (382 nodes)
Target sequences:                          1  (404 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: 10.00
//
[ok]

This GapMind analysis is from Apr 10 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