Alignments for a candidate for thrC in Chlorobium limicola DSM 245

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Chlorobium limicola DSM 245

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012467222.1 CLIM_RS11720 threonine synthase

Query= BRENDA::P00934
         (428 letters)



>NCBI__GCF_000020465.1:WP_012467222.1
          Length = 437

 Score =  315 bits (806), Expect = 2e-90
 Identities = 175/409 (42%), Positives = 249/409 (60%), Gaps = 8/409 (1%)

Query: 1   MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILS 60
           M  ++    +  VS  +A  +GL  + GL+ P ++P FS  E+  +    F   +  I  
Sbjct: 1   MIYFSTNKSSTPVSIKKATLEGLAPDGGLYVPSEIPVFSAPEMQLLEDGSFNNIAFAIAR 60

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
            FI  EIP + L + + + + F  P+  +E      ELF GPTLAFKD+G RF+A++  +
Sbjct: 61  KFICGEIPPDQLSDIIDSCYPFETPLVELEKGTFIEELFSGPTLAFKDYGARFLARLTGY 120

Query: 121 IAGD--KPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIE 178
            A +  K +T+L ATSGDTG+AVA+ F G+ N +VV+LYP GK+S LQE+   T GGN++
Sbjct: 121 FASEERKLITVLVATSGDTGSAVAYGFQGIQNTRVVLLYPSGKVSRLQEQQLTTAGGNVQ 180

Query: 179 TVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQL-PQET 237
            + + GDFD CQ LVKQAF D ELK  L L SANSINISRL+ Q  YY  A   L  Q  
Sbjct: 181 ALEVQGDFDDCQRLVKQAFTDPELKERLTLTSANSINISRLIPQSFYYAWATLHLKAQYG 240

Query: 238 RNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATL 297
             Q V SVPSGN+G+LTAG+LA+ +G P+  FIAA+N ND+V R+L +G++ P  T  TL
Sbjct: 241 LEQPVFSVPSGNYGNLTAGVLARMMGFPIGHFIAASNANDSVTRYLDEGRYDPHPTIPTL 300

Query: 298 SNAMDVSQPNNWPRVEELFRRKIWQL-KELGYAAVDDETTQQTMREL-KELGYTSEPHAA 355
           S AMDV  P+N+ R+   +      + K++   A+ D+ T  T+R++ +  GY  +PH A
Sbjct: 301 STAMDVGNPSNFARLRHFYGNDHHAMGKDITGIAISDDATVATIRDIFRRYGYVIDPHTA 360

Query: 356 VAYRAL---RDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELA 401
           V +RAL   R        G+ L TAHPAKF E +E  L + +++P+ L+
Sbjct: 361 VGFRALEEYRQTSGSRSPGIVLSTAHPAKFLEVIEDALEKEIEIPERLS 409


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: 411
Number of extensions: 11
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: 437
Length adjustment: 32
Effective length of query: 396
Effective length of database: 405
Effective search space:   160380
Effective search space used:   160380
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_012467222.1 CLIM_RS11720 (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.25078.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    2.6e-83  265.9   0.0    3.1e-83  265.7   0.0    1.0  1  lcl|NCBI__GCF_000020465.1:WP_012467222.1  CLIM_RS11720 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020465.1:WP_012467222.1  CLIM_RS11720 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.7   0.0   3.1e-83   3.1e-83      24     331 ..      78     398 ..      59     406 .. 0.89

  Alignments for each domain:
  == domain 1  score: 265.7 bits;  conditional E-value: 3.1e-83
                                 TIGR00260  24 elfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaae 90 
                                               + + ++++  e+++   ++ elf+gPtlaFKD g +f+a l  +++ + ++  tvl+AtsGdtg+a+a+
  lcl|NCBI__GCF_000020465.1:WP_012467222.1  78 SCYPFETPLVELEK-GTFIEELFSGPTLAFKDYGARFLARLTGYFASEERKliTVLVATSGDTGSAVAY 145
                                               55666666667776.89****************************98888877**************** PP

                                 TIGR00260  91 alagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeife...dkeklklnsvN 156
                                               +++g +n +vv LyP+gk+s ++e+ +t+  +n++ l+++GdFDd+q+lvk++f     ke l l s+N
  lcl|NCBI__GCF_000020465.1:WP_012467222.1 146 GFQGIQNTRVVLLYPSGKVSRLQEQQLTTAGGNVQALEVQGDFDDCQRLVKQAFTdpeLKERLTLTSAN 214
                                               **********************99999***************************9665666******** PP

                                 TIGR00260 157 sinparieaqk.tyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadi 224
                                               sin++r+  q  +ya+  +    +   ++ v++vpsgn g++++G + ++++g p    +iaa +a+d 
  lcl|NCBI__GCF_000020465.1:WP_012467222.1 215 SINISRLIPQSfYYAWATLHLKAQYGLEQPVFSVPSGNYGNLTAG-VLARMMGFP-IGHFIAASNANDS 281
                                               ***********9*******99999999******************.7777777**.67889999999** PP

                                 TIGR00260 225 vrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke.svsdeeileaikklaee 291
                                               v+r+l +g  +p+ +  TlstAmd+gnpsn+ r+ +   +   + ++d+   ++sd++++ +i+ + ++
  lcl|NCBI__GCF_000020465.1:WP_012467222.1 282 VTRYLDEGRYDPHPTIPTLSTAMDVGNPSNFARLRHfYGNDHHAMGKDITGiAISDDATVATIRDIFRR 350
                                               **********************************9954455555556653249**************** PP

                                 TIGR00260 292 egyllephtavavaalkklvekg..vs.....atadpaKFeevve.al 331
                                                gy+++phtav+ +al++  + +   s     +ta+paKF ev+e al
  lcl|NCBI__GCF_000020465.1:WP_012467222.1 351 YGYVIDPHTAVGFRALEEYRQTSgsRSpgivlSTAHPAKFLEVIEdAL 398
                                               *****************998887662256778***********99555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (437 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: 10.85
//
[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