Alignments for a candidate for thrC in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Cupriavidus basilensis 4G11

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate RR42_RS12535 RR42_RS12535 threonine synthase

Query= BRENDA::Q2SWH9
         (483 letters)



>FitnessBrowser__Cup4G11:RR42_RS12535
          Length = 482

 Score =  732 bits (1889), Expect = 0.0
 Identities = 367/483 (75%), Positives = 413/483 (85%), Gaps = 3/483 (0%)

Query: 1   MNYISTRGAGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTLPYADLAFEI 60
           M Y STRG  + +  TFS+ILLGGLA DGGLYLP EYPQV+ADEL  WR L YADLAFE+
Sbjct: 1   MKYQSTRGHEMPQ--TFSEILLGGLAPDGGLYLPREYPQVTADELEAWRKLSYADLAFEV 58

Query: 61  LSKFCDDIAAADLRAITRRTYTADVYRHARRGGNAADITPLTTLGTENGAPVSLLELSNG 120
           LS+FCDDI A DLRA+TR+TYTA+VY +AR G N ADITPL TLG E G  + LL LSNG
Sbjct: 59  LSRFCDDIPAEDLRALTRKTYTAEVYCNARPGDNTADITPLRTLGEEGGTQLQLLGLSNG 118

Query: 121 PTLAFKDMAMQLLGNLFEYTLAKHGETLNILGATSGDTGSAAEYAMRGKEGVRVFMLSPH 180
           PTLAFKDMAMQLLGNLFEY LA+ G+ LNILGATSGDTGSAAEYAMRGK G+RVFMLSPH
Sbjct: 119 PTLAFKDMAMQLLGNLFEYALARAGQELNILGATSGDTGSAAEYAMRGKRGIRVFMLSPH 178

Query: 181 KKMSAFQTAQMYSLQDPNIFNLAVNGVFDDCQDIVKAVSNDHAFKAQQKIGTVNSINWAR 240
           +KMSAFQTAQM+SLQDPNIFNLAV GVFDDCQDIVKAVSND  +KA+QKIGTVNSINWAR
Sbjct: 179 RKMSAFQTAQMFSLQDPNIFNLAVEGVFDDCQDIVKAVSNDLGYKARQKIGTVNSINWAR 238

Query: 241 VVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATNENDV 300
           VVAQVVYYFKG+  AT    ++VSF VPSGNFGNVCAGHIARMMGLPI+KLVVATNENDV
Sbjct: 239 VVAQVVYYFKGWLLATDGPGQKVSFCVPSGNFGNVCAGHIARMMGLPIDKLVVATNENDV 298

Query: 301 LDEFFRTGAYRVRSAQDTYHTSSPSMDISKASNFERFVFDLLGRDPARVVQLFR-DVEQK 359
           LDEFFRTG YRVR + +TYHTSSPSMDISKASNFERFVFDLLGRD  ++ ++FR DV+ K
Sbjct: 299 LDEFFRTGTYRVRKSAETYHTSSPSMDISKASNFERFVFDLLGRDGDKLAKMFREDVDTK 358

Query: 360 GGFDLAASGDFARVAEFGFVSGRSTHADRIATIRDVFERYRTMIDTHTADGLKVAREHLR 419
           GGFDL+ + +F R+  FGFVSGRSTH DR+ATIRD+ ERY   IDTHTADG+KVAREHL 
Sbjct: 359 GGFDLSGTPEFERIRAFGFVSGRSTHEDRLATIRDLSERYGITIDTHTADGIKVAREHLT 418

Query: 420 PGVPMVVLETAQPIKFGESIREALGQEPSRPAAFDGLEALPQRFEVVDANAQQVKDFIAA 479
           PGVPM+VLETA P KF ++IR ALG EP RPAAF+G+E LPQRFEV+ A+A ++K +IA 
Sbjct: 419 PGVPMLVLETALPAKFADTIRAALGHEPERPAAFEGIENLPQRFEVMPADADRIKAYIAG 478

Query: 480 HTG 482
           HTG
Sbjct: 479 HTG 481


Lambda     K      H
   0.320    0.135    0.392 

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: 769
Number of extensions: 19
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: 483
Length of database: 482
Length adjustment: 34
Effective length of query: 449
Effective length of database: 448
Effective search space:   201152
Effective search space used:   201152
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 RR42_RS12535 RR42_RS12535 (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.18679.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.4e-70  223.3   0.0      3e-70  223.0   0.0    1.1  1  lcl|FitnessBrowser__Cup4G11:RR42_RS12535  RR42_RS12535 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS12535  RR42_RS12535 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.0   0.0     3e-70     3e-70      38     335 ..     108     445 ..      90     450 .. 0.89

  Alignments for each domain:
  == domain 1  score: 223.0 bits;  conditional E-value: 3e-70
                                 TIGR00260  38 enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLy 104
                                                +l ++ l+ gPtlaFKD+++q +++l+++al +  +   +l+AtsGdtg+aa +a++gk +++v++L 
  lcl|FitnessBrowser__Cup4G11:RR42_RS12535 108 TQLQLLGLSNGPTLAFKDMAMQLLGNLFEYALARAGQelNILGATSGDTGSAAEYAMRGKRGIRVFMLS 176
                                               57889999**********************9887655589***************************** PP

                                 TIGR00260 105 Pkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeife...dkeklklnsvNsinparieaqkty 169
                                               P+ k+s     +++   + n+  la++G FDd+qd+vk++ +    k   k++ vNsin+ar+ aq++y
  lcl|FitnessBrowser__Cup4G11:RR42_RS12535 177 PHRKMSAFqTAQMFSLQDPNIFNLAVEGVFDDCQDIVKAVSNdlgYKARQKIGTVNSINWARVVAQVVY 245
                                               ********99*******************************966556699*****************99 PP

                                 TIGR00260 170 afeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksg.dlepk 237
                                               +f           +kv + vpsgnfg++ +G   ++++glpi+kl +a++++ d++++f ++g +   +
  lcl|FitnessBrowser__Cup4G11:RR42_RS12535 246 YFKGWLLATDGPGQKVSFCVPSGNFGNVCAG-HIARMMGLPIDKLVVATNEN-DVLDEFFRTGtY-RVR 311
                                               99887777778999*****************.6667777************9.**********54.444 PP

                                 TIGR00260 238 edk...eTlstAmdignpsnverale.larrslgnledlke............................ 274
                                               ++    +T s++mdi++ sn+er ++ l  r + +l ++                              
  lcl|FitnessBrowser__Cup4G11:RR42_RS12535 312 KSAetyHTSSPSMDISKASNFERFVFdLLGRDGDKLAKMFRedvdtkggfdlsgtpeferirafgfvsg 380
                                               444256888**************99887777776666664469999*********************** PP

                                 TIGR00260 275 svsdeeileaikklaeeegyllephtavavaalkklvekg....vsatadpaKFeevvealtgnk 335
                                               + + e+ l +i+ l e+ g+++++hta ++++ ++ +  g    v  ta paKF++++ a +g++
  lcl|FitnessBrowser__Cup4G11:RR42_RS12535 381 RSTHEDRLATIRDLSERYGITIDTHTADGIKVAREHLTPGvpmlVLETALPAKFADTIRAALGHE 445
                                               9***************************************765444************9988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (482 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.63
//
[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