Alignments for a candidate for thrC in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Desulfovibrio vulgaris Miyazaki F

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate 8501211 DvMF_1945 threonine synthase (RefSeq)

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



>FitnessBrowser__Miya:8501211
          Length = 492

 Score =  997 bits (2578), Expect = 0.0
 Identities = 492/492 (100%), Positives = 492/492 (100%)

Query: 1   MPCPTSCPAPGHDFPTARTRMEYVCLGCGERRGIDELLYTCPSCGGVYLLEDLDFDTLAE 60
           MPCPTSCPAPGHDFPTARTRMEYVCLGCGERRGIDELLYTCPSCGGVYLLEDLDFDTLAE
Sbjct: 1   MPCPTSCPAPGHDFPTARTRMEYVCLGCGERRGIDELLYTCPSCGGVYLLEDLDFDTLAE 60

Query: 61  QRTGPEWRALFDARAATRTTALRGIFRFYELMAPVLEEEDIVYLGEGNTPIVEAAPVLRD 120
           QRTGPEWRALFDARAATRTTALRGIFRFYELMAPVLEEEDIVYLGEGNTPIVEAAPVLRD
Sbjct: 61  QRTGPEWRALFDARAATRTTALRGIFRFYELMAPVLEEEDIVYLGEGNTPIVEAAPVLRD 120

Query: 121 AVGIPFAFKNDGQNPSASFKDRGMACAFSYLKALVRKHGWDEVLTVCASTGDTSAAAALY 180
           AVGIPFAFKNDGQNPSASFKDRGMACAFSYLKALVRKHGWDEVLTVCASTGDTSAAAALY
Sbjct: 121 AVGIPFAFKNDGQNPSASFKDRGMACAFSYLKALVRKHGWDEVLTVCASTGDTSAAAALY 180

Query: 181 ASYVGGPVKSVVLLPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALL 240
           ASYVGGPVKSVVLLPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALL
Sbjct: 181 ASYVGGPVKSVVLLPHGKVTPQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYRVALL 240

Query: 241 NSKNSWRILGQESYAFEVAQWYGWDMKGQCVFVPIGNAGNVTAIMAGFLKLLRLGVIDAL 300
           NSKNSWRILGQESYAFEVAQWYGWDMKGQCVFVPIGNAGNVTAIMAGFLKLLRLGVIDAL
Sbjct: 241 NSKNSWRILGQESYAFEVAQWYGWDMKGQCVFVPIGNAGNVTAIMAGFLKLLRLGVIDAL 300

Query: 301 PRVIGVQSHHADPVWRYYSQPDPATRTYAPVTVQPSVAQAAMIGNPVSFPRVKALADRFI 360
           PRVIGVQSHHADPVWRYYSQPDPATRTYAPVTVQPSVAQAAMIGNPVSFPRVKALADRFI
Sbjct: 301 PRVIGVQSHHADPVWRYYSQPDPATRTYAPVTVQPSVAQAAMIGNPVSFPRVKALADRFI 360

Query: 361 AEGGERAFSVVQVTEQEIMDAMIRGNRHGHIACTQGGECLAGLIKARELGLVSQGEHAVL 420
           AEGGERAFSVVQVTEQEIMDAMIRGNRHGHIACTQGGECLAGLIKARELGLVSQGEHAVL
Sbjct: 361 AEGGERAFSVVQVTEQEIMDAMIRGNRHGHIACTQGGECLAGLIKARELGLVSQGEHAVL 420

Query: 421 DATAHSLKFAGFQDMYFTNSFPPEYGVTPDASLANAPALVVSPEDKARLSPEAYTLAAAK 480
           DATAHSLKFAGFQDMYFTNSFPPEYGVTPDASLANAPALVVSPEDKARLSPEAYTLAAAK
Sbjct: 421 DATAHSLKFAGFQDMYFTNSFPPEYGVTPDASLANAPALVVSPEDKARLSPEAYTLAAAK 480

Query: 481 AVVARLGLAKKA 492
           AVVARLGLAKKA
Sbjct: 481 AVVARLGLAKKA 492


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: 932
Number of extensions: 27
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: 492
Length of database: 492
Length adjustment: 34
Effective length of query: 458
Effective length of database: 458
Effective search space:   209764
Effective search space used:   209764
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 8501211 DvMF_1945 (threonine synthase (RefSeq))
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.31591.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    6.2e-57  179.2   0.0    7.9e-57  178.9   0.0    1.1  1  lcl|FitnessBrowser__Miya:8501211  DvMF_1945 threonine synthase (Re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8501211  DvMF_1945 threonine synthase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.9   0.0   7.9e-57   7.9e-57       4     325 ..      89     430 ..      85     436 .. 0.84

  Alignments for each domain:
  == domain 1  score: 178.9 bits;  conditional E-value: 7.9e-57
                         TIGR00260   4 yreilevt.ekdlvdlaegstelfrspkla.eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne.... 74 
                                       y+ + +v  e+d+v l eg+t+ +++  +    vg+     k+++ +P+ +FKDrg   +a ++++++ l ++    
  lcl|FitnessBrowser__Miya:8501211  89 YELMAPVLeEEDIVYLGEGNTPIVEAAPVLrDAVGI-PFAFKNDGQNPSASFKDRG---MACAFSYLKALVRKhgwd 161
                                       56667888899*************976655388999.999****************...*******99998888999 PP

                         TIGR00260  75 ..tvlcAtsGdtgaaaa.ealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke 148
                                         + +cA++Gdt+aaaa +a +    vk vvL+P+gk+    ++l + l ++a+vl+i G FDd+ ++v++++e+ +
  lcl|FitnessBrowser__Miya:8501211 162 evLTVCASTGDTSAAAAlYASYVGGPVKSVVLLPHGKVT--PQQLSQPLGSGATVLEIPGVFDDCMKVVEHLAENYR 236
                                       99999********9887255555566*************..9*******************************9888 PP

                         TIGR00260 149 klklnsvNsinparieaqktyafeiveqlgkespdk.vvvpvp.sgnfgailkGflekkelg....lpieklaiaae 219
                                        ++lns N     ri++q +yafe+++ +g++ + + v vp++ +gn++ai++Gfl++ +lg    lp + +++++ 
  lcl|FitnessBrowser__Miya:8501211 237 VALLNSKN---SWRILGQESYAFEVAQWYGWDMKGQcVFVPIGnAGNVTAIMAGFLKLLRLGvidaLP-RVIGVQSH 309
                                       88888888...66******************877653789****************************.******** PP

                         TIGR00260 220 gaadivrrflksg....dlepkedkeTlstAmdignpsnveralelarrslgnledlke...svsdeeileaikkla 289
                                        a ++ r + +         p + +  +++A  ignp++++r+++la r  +++ +      +v+++ei++a+ +  
  lcl|FitnessBrowser__Miya:8501211 310 HADPVWRYYSQPDpatrTYAPVTVQPSVAQAAMIGNPVSFPRVKALADRFIAEGGERAFsvvQVTEQEIMDAMIRGN 386
                                       **9999999875421114444555578899999************88777766655433344889999999887777 PP

                         TIGR00260 290 eeegyllephtavavaalkklvekg...vs......atadpaKFe 325
                                       ++ ++ + + ++  +a+l+k  e g   ++      ata+  KF+
  lcl|FitnessBrowser__Miya:8501211 387 RHGHIAC-TQGGECLAGLIKARELGlvsQGehavldATAHSLKFA 430
                                       6666666.789999******9999974422556666777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (492 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: 13.96
//
[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