Alignments for a candidate for thrC in Desulfarculus baarsii DSM 2075

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Desulfarculus baarsii DSM 2075

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_013258180.1 DEBA_RS06790 threonine synthase

Query= reanno::Miya:8501211
         (492 letters)



>NCBI__GCF_000143965.1:WP_013258180.1
          Length = 500

 Score =  601 bits (1549), Expect = e-176
 Identities = 306/486 (62%), Positives = 366/486 (75%), Gaps = 10/486 (2%)

Query: 15  PTARTRMEYVCLGCGERRGIDELLYTCPSCGGVYLLEDLDFDTLAEQRTGPEWRALFDAR 74
           PT   +M Y CLGCG   GI++LLYTCP+CG V L+ED  FD L +   GP WR +FD R
Sbjct: 16  PTPGGQMAYRCLGCGGHHGIEKLLYTCPNCGQVLLIEDRAFDRL-KALDGPGWRRIFDLR 74

Query: 75  AATRTTALRGIFRFYELMAPVLEEEDIVYLGEGNTPIVEAAPVLRDAVGIPFAFKNDGQN 134
                 AL+G+FR+ EL+APV+  + ++YLGEG+TPIVEA+P+L+  +G+ FAFKNDGQN
Sbjct: 75  RMLNIPALKGVFRYAELLAPVIPLDSVLYLGEGHTPIVEASPLLKQTLGLDFAFKNDGQN 134

Query: 135 PSASFKDRGMACAFSYLKALVRKHGWDEVLTVCASTGDTSAAAALYASYVGGPVKSVVLL 194
           PSASFKDRGMA A SY+  L++  G  ++L++CASTGDTSAAAALY +Y+   VKS VLL
Sbjct: 135 PSASFKDRGMAVALSYINYLIKHRGAGQILSICASTGDTSAAAALYGAYLAPAVKSAVLL 194

Query: 195 PHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALLNSKNSWRILGQESY 254
           P GKVTPQQLSQPLG+GA VLEIPGVFDDCMKVVEHLA+NY+VALLNSKN+WRILGQESY
Sbjct: 195 PRGKVTPQQLSQPLGAGAAVLEIPGVFDDCMKVVEHLADNYQVALLNSKNAWRILGQESY 254

Query: 255 AFEVAQWYGWDMKGQCVFVPIGNAGNVTAIMAGFLKLLRLGVIDALPRVIGVQSHHADPV 314
           A+E+AQ   WDM G+ V  PIGNAGN++AIM+GF+KLL LGVI +LP++IGVQSHHADPV
Sbjct: 255 AYELAQDLDWDMTGRLVLAPIGNAGNISAIMSGFMKLLDLGVITSLPKIIGVQSHHADPV 314

Query: 315 WRYYSQPDPATRTYAPVTVQPSVAQAAMIGNPVSFPRVKALADRFIAEGGERAFSVVQVT 374
           ++YY Q  P  R + PVTVQ S AQAAMIGNPVS PRV  LA R+    G   F VVQV+
Sbjct: 315 FQYYQQSSPEKRVWRPVTVQASTAQAAMIGNPVSMPRVIELARRYDDLFGGGGFYVVQVS 374

Query: 375 EQEIMDAMIRGNRHGHIACTQGGECLAGLIKARELGLVSQGEHAVLDATAHSLKFAGFQD 434
           EQ+IMD MI  NRHGHI CTQGGE LAGL +AR  GLV   E A+ DATAH LKFAGFQ 
Sbjct: 375 EQQIMDHMILANRHGHIVCTQGGESLAGLAQARAAGLVGASERAICDATAHQLKFAGFQQ 434

Query: 435 MYFTNSFPPEYGVTPDASLANAPALVVS-PEDK-----ARLSPEA---YTLAAAKAVVAR 485
           MYF NSFP E+GV+P   L N P LV + PE++       L P+A   +  A + AV AR
Sbjct: 435 MYFENSFPAEFGVSPRPELVNMPQLVAALPEEQLPAPGRPLEPQAFRRFVEATSDAVAAR 494

Query: 486 LGLAKK 491
           LGL KK
Sbjct: 495 LGLEKK 500


Lambda     K      H
   0.320    0.136    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: 722
Number of extensions: 25
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: 492
Length of database: 500
Length adjustment: 34
Effective length of query: 458
Effective length of database: 466
Effective search space:   213428
Effective search space used:   213428
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_013258180.1 DEBA_RS06790 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))

# 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/TIGR00260.hmm
# target sequence database:        /tmp/gapView.3564.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00260  [M=340]
Accession:   TIGR00260
Description: thrC: threonine 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    9.7e-57  178.6   0.0    1.2e-56  178.3   0.0    1.0  1  lcl|NCBI__GCF_000143965.1:WP_013258180.1  DEBA_RS06790 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000143965.1:WP_013258180.1  DEBA_RS06790 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.3   0.0   1.2e-56   1.2e-56       3     325 ..      87     430 ..      85     440 .. 0.85

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 1.2e-56
                                 TIGR00260   3 ryreil.evt.ekdlvdlaegstelfrspkla.eevgaenlyvkelfhgPtlaFKDrglqfvavlltka 68 
                                               ry+e+l +v+    ++ l eg t+ +++  l  + +g+ +   k+++ +P+ +FKDrg   +av+l+++
  lcl|NCBI__GCF_000143965.1:WP_013258180.1  87 RYAELLaPVIpLDSVLYLGEGHTPIVEASPLLkQTLGL-DFAFKNDGQNPSASFKDRG---MAVALSYI 151
                                               566555245555568899********976665277888.*******************...******99 PP

                                 TIGR00260  69 lelgne......tvlcAtsGdtgaaaa.ealagkanvkvvvLyPkgkispvkeklvtalaenakvlaik 130
                                               + l ++      + +cA++Gdt+aaaa ++ +  + vk  vL+P+gk+    ++l + l  +a vl+i 
  lcl|NCBI__GCF_000143965.1:WP_013258180.1 152 NYLIKHrgagqiLSICASTGDTSAAAAlYGAYLAPAVKSAVLLPRGKVT--PQQLSQPLGAGAAVLEIP 218
                                               877666677777899*******9887637777889**************..9***************** PP

                                 TIGR00260 131 GdFDdaqdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvv.pvp.sgnfgai 197
                                               G FDd+ ++v++++++ + ++lns N     ri++q +ya+e++++l+++   ++v+ p++ +gn++ai
  lcl|NCBI__GCF_000143965.1:WP_013258180.1 219 GVFDDCMKVVEHLADNYQVALLNSKN---AWRILGQESYAYELAQDLDWDMTGRLVLaPIGnAGNISAI 284
                                               **************998888888888...89******************9888876538********** PP

                                 TIGR00260 198 lkGflekkelg....lpieklaiaaegaadivrrflksg....dlepkedkeTlstAmdignpsnvera 258
                                               + Gf+++  lg    lp + +++++  a ++ + +++s      + p + ++  ++A  ignp++++r+
  lcl|NCBI__GCF_000143965.1:WP_013258180.1 285 MSGFMKLLDLGvitsLP-KIIGVQSHHADPVFQYYQQSSpekrVWRPVTVQASTAQAAMIGNPVSMPRV 352
                                               *****************.**************999876431126888888899999999********** PP

                                 TIGR00260 259 lelarrslgnledlke..svsdeeileaikklaeeegyllephtavavaalkklvekg.vs........ 316
                                                elarr++  +   +     ++e+ + + + la+++g ++ + ++ ++a+l +  ++g v+        
  lcl|NCBI__GCF_000143965.1:WP_013258180.1 353 IELARRYDDLFGGGGFyvVQVSEQQIMDHMILANRHGHIVCTQGGESLAGLAQARAAGlVGaseraicd 421
                                               *******9887765543334556667778899999999999*****************83344667778 PP

                                 TIGR00260 317 atadpaKFe 325
                                               ata++ KF+
  lcl|NCBI__GCF_000143965.1:WP_013258180.1 422 ATAHQLKFA 430
                                               899988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (500 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.98
//
[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