Alignments for a candidate for thrC in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Derxia gummosa DSM 723

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_028311180.1 H566_RS0109010 threonine synthase

Query= BRENDA::Q2SWH9
         (483 letters)



>NCBI__GCF_000482785.1:WP_028311180.1
          Length = 482

 Score =  675 bits (1741), Expect = 0.0
 Identities = 346/482 (71%), Positives = 385/482 (79%)

Query: 1   MNYISTRGAGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTLPYADLAFEI 60
           M Y STRGA      +F DILL GLA DGGLYLP  YPQVSAD+LARWR L YADLAFEI
Sbjct: 1   MKYFSTRGAAHDAPKSFLDILLAGLADDGGLYLPLTYPQVSADDLARWRGLSYADLAFEI 60

Query: 61  LSKFCDDIAAADLRAITRRTYTADVYRHARRGGNAADITPLTTLGTENGAPVSLLELSNG 120
           LS+F DDI A DLRAITR+ YTA+VYR+ R G NAADITPL  LG E G  +SLL LSNG
Sbjct: 61  LSRFADDIPADDLRAITRKVYTAEVYRNVRDGENAADITPLRVLGEEGGTRLSLLALSNG 120

Query: 121 PTLAFKDMAMQLLGNLFEYTLAKHGETLNILGATSGDTGSAAEYAMRGKEGVRVFMLSPH 180
           PTLAFKDMAMQLLG LFEY LA+ G  LNILGATSGDTGSAAEYAMRG++GV+VFMLSP 
Sbjct: 121 PTLAFKDMAMQLLGALFEYALARTGMHLNILGATSGDTGSAAEYAMRGRKGVKVFMLSPK 180

Query: 181 KKMSAFQTAQMYSLQDPNIFNLAVNGVFDDCQDIVKAVSNDHAFKAQQKIGTVNSINWAR 240
            KMSAFQTAQM+SLQDPNIFNLAV GVFDD QDIVKAVSND AFKA+  IGTVNSINWAR
Sbjct: 181 GKMSAFQTAQMFSLQDPNIFNLAVEGVFDDAQDIVKAVSNDIAFKAKWAIGTVNSINWAR 240

Query: 241 VVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATNENDV 300
           VVAQVVYYFKGYF AT SNDERVSFTVPSGNFGN+CAGHIAR MGLPI KLV ATNENDV
Sbjct: 241 VVAQVVYYFKGYFEATSSNDERVSFTVPSGNFGNICAGHIARQMGLPIAKLVCATNENDV 300

Query: 301 LDEFFRTGAYRVRSAQDTYHTSSPSMDISKASNFERFVFDLLGRDPARVVQLFRDVEQKG 360
           LDEFFRTG+YR R + +TYHT+SPSMDISKASNFERFVFDL  RD A     +  ++ +G
Sbjct: 301 LDEFFRTGSYRPRKSVETYHTTSPSMDISKASNFERFVFDLFDRDVAAFRATWLKIDSEG 360

Query: 361 GFDLAASGDFARVAEFGFVSGRSTHADRIATIRDVFERYRTMIDTHTADGLKVAREHLRP 420
            F L A        +FGF SGRS+HADR+ATIRD+  RY  ++DTHTADG+K ARE L P
Sbjct: 361 SFTLDADKRALVATKFGFASGRSSHADRLATIRDIDARYGVVVDTHTADGIKAAREQLEP 420

Query: 421 GVPMVVLETAQPIKFGESIREALGQEPSRPAAFDGLEALPQRFEVVDANAQQVKDFIAAH 480
           G+PMVVLETA P KF E+I EALG+   RPA F+ LE+LPQR +V+  + + VK +I  H
Sbjct: 421 GIPMVVLETALPAKFTETIEEALGRPAPRPAGFENLESLPQRSDVIANDVEAVKAYIVKH 480

Query: 481 TG 482
            G
Sbjct: 481 AG 482


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: 752
Number of extensions: 25
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: 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 WP_028311180.1 H566_RS0109010 (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.9234.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.3e-75  239.8   0.0    3.1e-75  239.4   0.0    1.1  1  lcl|NCBI__GCF_000482785.1:WP_028311180.1  H566_RS0109010 threonine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028311180.1  H566_RS0109010 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  239.4   0.0   3.1e-75   3.1e-75      38     331 ..     110     442 ..      79     449 .. 0.90

  Alignments for each domain:
  == domain 1  score: 239.4 bits;  conditional E-value: 3.1e-75
                                 TIGR00260  38 enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLy 104
                                                +l ++ l+ gPtlaFKD+++q ++ l+++al ++     +l+AtsGdtg+aa +a++g+++vkv++L 
  lcl|NCBI__GCF_000482785.1:WP_028311180.1 110 TRLSLLALSNGPTLAFKDMAMQLLGALFEYALARTGMhlNILGATSGDTGSAAEYAMRGRKGVKVFMLS 178
                                               69999*************************9998776689***************************** PP

                                 TIGR00260 105 Pkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeife...dkeklklnsvNsinparieaqkty 169
                                               Pkgk+s     +++   + n+  la++G FDdaqd+vk++ +    k k+ ++ vNsin+ar+ aq++y
  lcl|NCBI__GCF_000482785.1:WP_028311180.1 179 PKGKMSAFqTAQMFSLQDPNIFNLAVEGVFDDAQDIVKAVSNdiaFKAKWAIGTVNSINWARVVAQVVY 247
                                               ********99*******************************9444455*******************77 PP

                                 TIGR00260 170 af.eiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepk 237
                                               +f + +e++   + ++v + vpsgnfg+i +G  + +++ lpi+kl  a++++ d++++f ++g   p+
  lcl|NCBI__GCF_000482785.1:WP_028311180.1 248 YFkGYFEATS-SNDERVSFTVPSGNFGNICAGHIARQMG-LPIAKLVCATNEN-DVLDEFFRTGSYRPR 313
                                               7725677777.8899*****************8888887.************9.**********99999 PP

                                 TIGR00260 238 edk...eTlstAmdignpsnverale.larrslgnledlke...........................s 275
                                               +++   +T s++mdi++ sn+er ++ l+ r  + + +                              +
  lcl|NCBI__GCF_000482785.1:WP_028311180.1 314 KSVetyHTTSPSMDISKASNFERFVFdLFDRDVAAFRATWLkidsegsftldadkralvatkfgfasgR 382
                                               998556678**************9988999999988876446799999********************* PP

                                 TIGR00260 276 vsdeeileaikklaeeegyllephtavavaalkklvekg....vsatadpaKFeevveal 331
                                                s ++ l +i+ + ++ g+++++hta +++a ++++e g    v  ta paKF e++e  
  lcl|NCBI__GCF_000482785.1:WP_028311180.1 383 SSHADRLATIRDIDARYGVVVDTHTADGIKAAREQLEPGipmvVLETALPAKFTETIEEA 442
                                               ***************************************9864449*********99844 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: 9.43
//
[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