Alignments for a candidate for thrC in Novosphingobium aromaticivorans DSM 12444

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Novosphingobium aromaticivorans DSM 12444

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011444580.1 SARO_RS04600 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>NCBI__GCF_000013325.1:WP_011444580.1
          Length = 473

 Score =  444 bits (1141), Expect = e-129
 Identities = 238/464 (51%), Positives = 304/464 (65%), Gaps = 7/464 (1%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           MKYVSTRG+AP L F    LAGLA DGGLY+P+ +PQF+ ++I A+ G  Y  +A  ++ 
Sbjct: 1   MKYVSTRGQAPSLDFQGVTLAGLASDGGLYVPESWPQFSHDEIAAMAGLPYARLAQKIMQ 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           P+ G  +       +  +AYG F H AV PL Q D  ++VLELFHGPTLAFKDVA+QLL 
Sbjct: 61  PYVGDCLTPERLLELCEQAYGRFAHAAVTPLKQLDETQWVLELFHGPTLAFKDVALQLLG 120

Query: 121 RMMDYVLAQR-----GERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQR 175
            + +  LA+       E  TIVGATSGDTG AAI+A  GR   DIF+L P+GRVS VQ+R
Sbjct: 121 LLFEEFLARPREDGGDEHITIVGATSGDTGSAAIDAVAGRAKVDIFMLHPHGRVSDVQRR 180

Query: 176 QMTSSGFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYF 235
           QMT+    NVH ++I+G+FDD Q +VK MFND        ++ VNSINWAR+M QVVYYF
Sbjct: 181 QMTTVIAPNVHNIAIDGSFDDAQAMVKRMFNDSAMTGRFGIAAVNSINWARLMAQVVYYF 240

Query: 236 TAALSLGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAY 295
            AAL LGAP R V+F+VPTGNFGD+FAGYVA +MGLPIE+LI+ATN NDIL R L +G Y
Sbjct: 241 YAALQLGAPHRKVAFSVPTGNFGDVFAGYVAAKMGLPIERLIVATNVNDILHRALSAGDY 300

Query: 296 EMRGVAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIR 355
               V  T +PSMDIQ+SSNFERLLF+  GRDA+A+   M+  + +    ++     +  
Sbjct: 301 SASTVTPTAAPSMDIQVSSNFERLLFDGCGRDASALAAQMKHFEVTKAMQLTNAQRESAA 360

Query: 356 SEFSAGRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAR--EKASGTAPMVVLATAHPA 413
           + FS+ R+   + A  +       G +LDPH+AIG+  AR  E      P+V LATAHPA
Sbjct: 361 ALFSSARADAGDMANAMRWAFEATGEVLDPHTAIGLHAARAAEGIPAGVPIVTLATAHPA 420

Query: 414 KFPDAVKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYV 457
           KF DAV+ A GV P LPA + DL +R+E    L    + V  YV
Sbjct: 421 KFVDAVERATGVRPGLPARVGDLFEREERCDRLPGNYEAVAAYV 464


Lambda     K      H
   0.320    0.135    0.389 

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: 584
Number of extensions: 27
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: 463
Length of database: 473
Length adjustment: 33
Effective length of query: 430
Effective length of database: 440
Effective search space:   189200
Effective search space used:   189200
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: 51 (24.3 bits)

Align candidate WP_011444580.1 SARO_RS04600 (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.3029.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.2e-79  251.3   0.0    9.8e-79  250.9   0.0    1.1  1  lcl|NCBI__GCF_000013325.1:WP_011444580.1  SARO_RS04600 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013325.1:WP_011444580.1  SARO_RS04600 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.9   0.0   9.8e-79   9.8e-79      13     333 ..      70     431 ..      58     436 .. 0.90

  Alignments for each domain:
  == domain 1  score: 250.9 bits;  conditional E-value: 9.8e-79
                                 TIGR00260  13 kdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..... 74 
                                               ++l++l+e+ +  f+  +++  +++ +   +v+elfhgPtlaFKD++lq ++ l++++l + +e     
  lcl|NCBI__GCF_000013325.1:WP_011444580.1  70 ERLLELCEQAYGRFAHAAVTplKQLDE-TQWVLELFHGPTLAFKDVALQLLGLLFEEFLARPREdggde 137
                                               568899999999999888887677777.99*****************************999999999* PP

                                 TIGR00260  75 ..tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlv 140
                                                 t+++AtsGdtg+aa+ a ag+a v++++L P+g++s v   +++t++a n++ +ai+G FDdaq++v
  lcl|NCBI__GCF_000013325.1:WP_011444580.1 138 hiTIVGATSGDTGSAAIDAVAGRAKVDIFMLHPHGRVSDVqRRQMTTVIAPNVHNIAIDGSFDDAQAMV 206
                                               ****************************************99*************************** PP

                                 TIGR00260 141 keifedke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekke 206
                                               k +f+d+      ++ +vNsin+ar+ aq++y+f ++ qlg     kv+++vp gnfg++++G++++k+
  lcl|NCBI__GCF_000013325.1:WP_011444580.1 207 KRMFNDSAmtgRFGIAAVNSINWARLMAQVVYYFYAALQLG-APHRKVAFSVPTGNFGDVFAGYVAAKM 274
                                               *****88878899*****************99999999999.77889********************** PP

                                 TIGR00260 207 lglpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale..larrslgnledlk 273
                                               + lpie l +a++ + di++r l  gd +  +   T +++mdi  +sn+er+l+    r   + + ++k
  lcl|NCBI__GCF_000013325.1:WP_011444580.1 275 G-LPIERLIVATNVN-DILHRALSAGDYSASTVTPTAAPSMDIQVSSNFERLLFdgCGRDASALAAQMK 341
                                               9.**98888887776.**********88777777*******************9976677777777777 PP

                                 TIGR00260 274 e........................svsdeeileaikklaeeegyllephtavavaalkkl..vekg.. 314
                                               +                        ++   ++ +a++ + e  g +l+phta+++ a +    + +g  
  lcl|NCBI__GCF_000013325.1:WP_011444580.1 342 HfevtkamqltnaqresaaalfssaRADAGDMANAMRWAFEATGEVLDPHTAIGLHAARAAegIPAGvp 410
                                               7999*******************97777778999999999****************9875411445566 PP

                                 TIGR00260 315 .vs.atadpaKFeevvealtg 333
                                                v+ ata+paKF ++ve+ tg
  lcl|NCBI__GCF_000013325.1:WP_011444580.1 411 iVTlATAHPAKFVDAVERATG 431
                                               5227*************9888 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (473 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: 11.53
//
[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