Alignments for a candidate for thrC in Prosthecochloris aestuarii DSM 271

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Prosthecochloris aestuarii DSM 271

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012504854.1 PAES_RS01285 threonine synthase

Query= BRENDA::P00934
         (428 letters)



>NCBI__GCF_000020625.1:WP_012504854.1
          Length = 438

 Score =  319 bits (818), Expect = 9e-92
 Identities = 179/430 (41%), Positives = 255/430 (59%), Gaps = 10/430 (2%)

Query: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60
           M  Y+    +   S  +A  +GL  + GL+ P  +P FS +EI+ + +  F   +  I  
Sbjct: 1   MIYYSTNKSSTPASLKRATLEGLAPDGGLYVPSAIPVFSPSEIELLKEAPFKDIAFAIAK 60

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
            + G EIP + L E +   F FP P+  ++++    ELFHGPTLAFKD+G RF+A+M  +
Sbjct: 61  KYTGSEIPPDRLYEIIEECFNFPTPLVPLDNNTFIEELFHGPTLAFKDYGARFLARMTGY 120

Query: 121 IAGDKP--VTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIE 178
            A +    +TIL ATSGDTG+AVA+ F G+PN +VV+LYP GK+S LQE+   T GGN+ 
Sbjct: 121 FAEEDHTLITILVATSGDTGSAVAYGFQGIPNTRVVLLYPSGKVSRLQEQQLTTAGGNVT 180

Query: 179 TVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQE-T 237
            + + GDFD CQ LVKQAF D  +K  L L SANSINISRL+ Q  YY  A  QL ++  
Sbjct: 181 ALEVKGDFDDCQRLVKQAFMDGSIKQNLTLTSANSINISRLIPQSFYYAWAALQLDRKYP 240

Query: 238 RNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATL 297
             + V SVPSGN+G+LTAG+LAK +G P+  FIAA+N ND+V R++ +G++ P  T  TL
Sbjct: 241 GKKAVFSVPSGNYGNLTAGVLAKMMGFPIDHFIAASNANDSVTRYIEEGRYEPHPTIRTL 300

Query: 298 SNAMDVSQPNNWPRVEELFRRKIWQLKE--LGYAAVDDETTQQTMRELKELGYTSEPHAA 355
           S AMDV  P+N+ R+  ++     ++     GY+  D+ET +         GY  +PH A
Sbjct: 301 STAMDVGDPSNFARLRHIYANDHTKMAADITGYSISDNETLETIRSVYDRFGYIMDPHTA 360

Query: 356 VAYRAL---RDQLNPGEY--GLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLS 410
           V  RAL   R+Q+   +    + L TAHPAKF ES+   L   + +P  L    D   ++
Sbjct: 361 VGSRALELWREQMTQADSNPAVVLSTAHPAKFLESIREALDMEISIPDRLQTVLDKQKIA 420

Query: 411 HNLPADFAAL 420
             + +D+  L
Sbjct: 421 TLIGSDYNEL 430


Lambda     K      H
   0.319    0.135    0.395 

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: 426
Number of extensions: 14
Number of successful extensions: 5
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: 428
Length of database: 438
Length adjustment: 32
Effective length of query: 396
Effective length of database: 406
Effective search space:   160776
Effective search space used:   160776
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_012504854.1 PAES_RS01285 (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.23236.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    8.1e-89  284.1   0.0    1.1e-88  283.6   0.0    1.0  1  lcl|NCBI__GCF_000020625.1:WP_012504854.1  PAES_RS01285 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020625.1:WP_012504854.1  PAES_RS01285 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.6   0.0   1.1e-88   1.1e-88      13     329 ..      67     397 ..      58     405 .. 0.90

  Alignments for each domain:
  == domain 1  score: 283.6 bits;  conditional E-value: 1.1e-88
                                 TIGR00260  13 kdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcA 79 
                                               +++  l e   e f++p++  ++   n ++ elfhgPtlaFKD g +f+a +  +++e+  +  t+l+A
  lcl|NCBI__GCF_000020625.1:WP_012504854.1  67 IPPDRLYEIIEECFNFPTPLVPLDN-NTFIEELFHGPTLAFKDYGARFLARMTGYFAEEDHTliTILVA 134
                                               5666777888899**********99.********************************999989***** PP

                                 TIGR00260  80 tsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeife... 145
                                               tsGdtg+a+a++++g +n +vv LyP+gk+s ++e+ +t+  +n++ l++kGdFDd+q+lvk++f    
  lcl|NCBI__GCF_000020625.1:WP_012504854.1 135 TSGDTGSAVAYGFQGIPNTRVVLLYPSGKVSRLQEQQLTTAGGNVTALEVKGDFDDCQRLVKQAFMdgs 203
                                               *********************************99999***************************9444 PP

                                 TIGR00260 146 dkeklklnsvNsinparieaqk.tyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpiek 213
                                                k++l l s+Nsin++r+  q  +ya+ +++   k   +k v++vpsgn g++++G + +k++g pi  
  lcl|NCBI__GCF_000020625.1:WP_012504854.1 204 IKQNLTLTSANSINISRLIPQSfYYAWAALQLDRKYPGKKAVFSVPSGNYGNLTAG-VLAKMMGFPI-D 270
                                               456*******************9*******99999999******************.6667777**5.5 PP

                                 TIGR00260 214 laiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale..larrslgnledlkesvsdee 280
                                                +iaa +a+d v+r++++g  ep+ +  TlstAmd+g psn+ r+ +  +  +++  ++  ++s+sd+e
  lcl|NCBI__GCF_000020625.1:WP_012504854.1 271 HFIAASNANDSVTRYIEEGRYEPHPTIRTLSTAMDVGDPSNFARLRHiyANDHTKMAADITGYSISDNE 339
                                               678888888**************************************6555566666677889****** PP

                                 TIGR00260 281 ileaikklaeeegyllephtavavaalkklvekg.vs........atadpaKFeevve 329
                                               +le+i+ ++ + gy+++phtav+ +al+   e+  +         +ta+paKF e++ 
  lcl|NCBI__GCF_000020625.1:WP_012504854.1 340 TLETIRSVYDRFGYIMDPHTAVGSRALELWREQMtQAdsnpavvlSTAHPAKFLESIR 397
                                               **************************9866555542233566678********98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (438 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: 8.93
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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