Alignments for a candidate for thrC in Desulfobacter vibrioformis DSM 8776

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Desulfobacter vibrioformis DSM 8776

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_035237130.1 Q366_RS05620 threonine synthase

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



>NCBI__GCF_000745975.1:WP_035237130.1
          Length = 497

 Score =  528 bits (1360), Expect = e-154
 Identities = 259/469 (55%), Positives = 333/469 (71%), Gaps = 2/469 (0%)

Query: 12  HDFPTARTRMEYVCLGCGERRGIDELLYTCPSCGGVYLLEDLDFDTLAEQRTGPEWRALF 71
           H  P+ R  M Y CLGCG   GI++LLY CP+C  V L+ D + D L    +G  W+ +F
Sbjct: 13  HIIPSPRGEMYYKCLGCGAEYGIEKLLYVCPACNQVLLIHDRNKDQL-NAISGETWQRIF 71

Query: 72  DARAATRTTALRGIFRFYELMAPVLEEEDIVYLGEGNTPIVEAAPVLRDAVGIPFAFKND 131
           D R   +  AL+GI+R++E + P +  E I+YLGEG+TP+VEA   L++  G+ F +KND
Sbjct: 72  DYRKMLKIPALKGIYRYHEFIGPSIPLESIIYLGEGHTPVVEANAGLQEKTGVKFYYKND 131

Query: 132 GQNPSASFKDRGMACAFSYLKALVRKHGWDEVLTVCASTGDTSAAAALYASYVGGPVKSV 191
           GQNPSASFKDRGMA A S +K L+ +    EV+ +CASTGDTSA+AALYASY+G  VKS 
Sbjct: 132 GQNPSASFKDRGMASALSSIKYLIDQGFVSEVIAICASTGDTSASAALYASYLGSKVKSA 191

Query: 192 VLLPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALLNSKNSWRILGQ 251
           VLLPH KVT  QL+QPLGSGA V EIPGVFDDCMK+VEHL+ +Y V LLNSKN+WRILGQ
Sbjct: 192 VLLPHKKVTSAQLAQPLGSGARVFEIPGVFDDCMKIVEHLSSSYPVVLLNSKNAWRILGQ 251

Query: 252 ESYAFEVAQWYGWDMKGQCVFVPIGNAGNVTAIMAGFLKLLRLGVIDALPRVIGVQSHHA 311
           ESY++E+AQ + WDM  + V VPIGNAGN++AIM GFLK    G+I  LP++IGVQS HA
Sbjct: 252 ESYSYEIAQDFDWDMDKKVVMVPIGNAGNISAIMNGFLKFYNTGIIHTLPKIIGVQSEHA 311

Query: 312 DPVWRYYSQPDPATRTYAPVTVQPSVAQAAMIGNPVSFPRVKALADRFIAEGGERAFSVV 371
           DPV++YY + D + R + PV  QPSVAQAAMIGNPVS PRV  +A  + A  G R   VV
Sbjct: 312 DPVYKYYLESDESKRKFTPVQTQPSVAQAAMIGNPVSMPRVIRIAREYDAASGHRNVFVV 371

Query: 372 QVTEQEIMDAMIRGNRHGHIACTQGGECLAGLIKARELGLVSQGEHAVLDATAHSLKFAG 431
           QV EQ+IMD  +  N++GHI CTQGGECLAG+++A+ L LV   E  +LDATAH++KF+G
Sbjct: 372 QVKEQQIMDWQLTANQNGHITCTQGGECLAGMVRAKALNLVDDSETVILDATAHAIKFSG 431

Query: 432 FQDMYFTNSFPPEYGVTPDASLANAPALVVSPEDKARLSPEAYTLAAAK 480
           FQD+YF       YG++ D+   N P   +SP+D   +  +   L A++
Sbjct: 432 FQDLYFKGELAGAYGISSDSRFINLPDF-ISPDDPELIPSQEKPLGASQ 479


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: 659
Number of extensions: 20
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: 497
Length adjustment: 34
Effective length of query: 458
Effective length of database: 463
Effective search space:   212054
Effective search space used:   212054
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_035237130.1 Q366_RS05620 (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.15756.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      2e-58  184.1   0.0    2.4e-58  183.9   0.0    1.1  1  lcl|NCBI__GCF_000745975.1:WP_035237130.1  Q366_RS05620 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745975.1:WP_035237130.1  Q366_RS05620 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.9   0.0   2.4e-58   2.4e-58       3     324 ..      87     429 ..      85     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 2.4e-58
                                 TIGR00260   3 ryreilevt..ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkal 69 
                                               ry e++  +   + ++ l eg t+++++++  +e ++ + y k+++ +P+ +FKDrg   +a++l+ ++
  lcl|NCBI__GCF_000745975.1:WP_035237130.1  87 RYHEFIGPSipLESIIYLGEGHTPVVEANAGLQEKTGVKFYYKNDGQNPSASFKDRG---MASALSSIK 152
                                               555555444345678899***********999888888*******************...****99999 PP

                                 TIGR00260  70 elgne......tvlcAtsGdtgaaaa.ealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikG 131
                                                l  +      + +cA++Gdt+a+aa +a +  + vk  vL+P+ k+     +l++ l ++a+v++i G
  lcl|NCBI__GCF_000745975.1:WP_035237130.1 153 YLIDQgfvsevIAICASTGDTSASAAlYASYLGSKVKSAVLLPHKKVT--SAQLAQPLGSGARVFEIPG 219
                                               88777777998889*******99876266666788999**********..******************* PP

                                 TIGR00260 132 dFDdaqdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgk.espdkvvvpvp.sgnfgail 198
                                                FDd+ ++v+++ +  + ++lns N     ri++q +y +ei+++ ++  +++ v+vp++ +gn++ai+
  lcl|NCBI__GCF_000745975.1:WP_035237130.1 220 VFDDCMKIVEHLSSSYPVVLLNSKN---AWRILGQESYSYEIAQDFDWdMDKKVVMVPIGnAGNISAIM 285
                                               *************999988888888...89******************556667789************ PP

                                 TIGR00260 199 kGflekkelg....lpieklaiaaegaadivrrflksg....dlepkedkeTlstAmdignpsnveral 259
                                               +Gfl++ ++g    lp + +++++e a ++++ +l+s     +++p +++  +++A  ignp++++r+ 
  lcl|NCBI__GCF_000745975.1:WP_035237130.1 286 NGFLKFYNTGiihtLP-KIIGVQSEHADPVYKYYLESDeskrKFTPVQTQPSVAQAAMIGNPVSMPRVI 353
                                               ****************.***************99987511135677777788***************** PP

                                 TIGR00260 260 elarrslgnledlke..svsdeeileaikklaeeegyllephtavavaalkklvekg...vs......a 317
                                               ++ar++++   + +     + e+ + + ++ a+++g ++ + ++  +a++ +  + +    s      a
  lcl|NCBI__GCF_000745975.1:WP_035237130.1 354 RIAREYDAASGHRNVfvVQVKEQQIMDWQLTANQNGHITCTQGGECLAGMVRAKALNlvdDSetvildA 422
                                               *****9987655433334456667777788888877777788888777776655544333112345567 PP

                                 TIGR00260 318 tadpaKF 324
                                               ta+  KF
  lcl|NCBI__GCF_000745975.1:WP_035237130.1 423 TAHAIKF 429
                                               7777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (497 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: 11.89
//
[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