Alignments for a candidate for thrC in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Chlorobaculum parvum NCIB 8327

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012503136.1 CPAR_RS09710 threonine synthase

Query= BRENDA::P00934
         (428 letters)



>NCBI__GCF_000020505.1:WP_012503136.1
          Length = 438

 Score =  323 bits (829), Expect = 5e-93
 Identities = 177/416 (42%), Positives = 255/416 (61%), Gaps = 9/416 (2%)

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

Query: 61  AFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTH 120
            F+GDEIP + L   +   F F  P+  +++D    ELFHGPTLAFKD+G RF+A+M   
Sbjct: 61  KFVGDEIPLDRLSALIDDCFTFETPLHELDADTFVEELFHGPTLAFKDYGARFLARMTGF 120

Query: 121 IAGDKP--VTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIE 178
            A ++   +T+L ATSGDTG+AVA+ F+G+PN +VV+LYP GK+S LQE+   T G N+ 
Sbjct: 121 YAAEESRMITVLVATSGDTGSAVAYGFHGIPNTRVVLLYPSGKVSHLQEQQLTTAGDNVH 180

Query: 179 TVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETR 238
            + + GDFD CQ LVKQAF D+ L+  L L SANSINISRL+ Q  YY  A  QL Q   
Sbjct: 181 ALEVKGDFDDCQRLVKQAFVDQSLRQKLTLTSANSINISRLIPQSFYYAWAALQLRQHQS 240

Query: 239 NQL-VVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATL 297
           N L   SVPSGN+G+LTAG++AK +G P+  FIAA+N ND+V R+L +G++ P+ T  TL
Sbjct: 241 NALPTFSVPSGNYGNLTAGVMAKMMGFPIGGFIAASNANDSVTRYLDEGRFEPRPTIKTL 300

Query: 298 SNAMDVSQPNNWPRVEELFRRKIWQL-KELGYAAVDDETTQQTMRELKE-LGYTSEPHAA 355
           + AMDV  P+N+ R+   +     ++  ++   AV D  T +T+R + +  GY  +PH A
Sbjct: 301 TTAMDVGNPSNFARLLHFYEGDFRKMGVDIAGIAVSDAETVETIRAVHDRYGYIMDPHTA 360

Query: 356 VAYRAL---RD-QLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLP 407
           V YRAL   RD +   G+  + L TAHP KF E++    G+ + +P+ + +  + P
Sbjct: 361 VGYRALEHFRDTRSGAGKPAVVLSTAHPVKFDEAIRTATGKEVPIPESMHDIMNKP 416


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: 457
Number of extensions: 20
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_012503136.1 CPAR_RS09710 (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.20394.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-87  279.3   0.0    2.8e-87  279.0   0.0    1.1  1  lcl|NCBI__GCF_000020505.1:WP_012503136.1  CPAR_RS09710 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012503136.1  CPAR_RS09710 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.0   0.0   2.8e-87   2.8e-87      13     336 ..      67     403 ..      57     407 .. 0.91

  Alignments for each domain:
  == domain 1  score: 279.0 bits;  conditional E-value: 2.8e-87
                                 TIGR00260  13 kdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavl..ltkalelgnetvlcA 79 
                                               ++l  l +     f+++++ +e+ a + +v elfhgPtlaFKD g +f+a +  + +a e  + tvl+A
  lcl|NCBI__GCF_000020505.1:WP_012503136.1  67 IPLDRLSALIDDCFTFETPLHELDA-DTFVEELFHGPTLAFKDYGARFLARMtgFYAAEESRMITVLVA 134
                                               666777777888999**********.***********************976448899999999***** PP

                                 TIGR00260  80 tsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifedke 148
                                               tsGdtg+a+a+++ g +n +vv LyP+gk+s ++e+ +t+   n++ l++kGdFDd+q+lvk++f d+ 
  lcl|NCBI__GCF_000020505.1:WP_012503136.1 135 TSGDTGSAVAYGFHGIPNTRVVLLYPSGKVSHLQEQQLTTAGDNVHALEVKGDFDDCQRLVKQAFVDQS 203
                                               *********************************99999***************************9655 PP

                                 TIGR00260 149 ...klklnsvNsinparieaqk.tyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpiek 213
                                                  kl l s+Nsin++r+  q  +ya+ +++  +++s+   +++vpsgn g++++G + +k++g p   
  lcl|NCBI__GCF_000020505.1:WP_012503136.1 204 lrqKLTLTSANSINISRLIPQSfYYAWAALQLRQHQSNALPTFSVPSGNYGNLTAG-VMAKMMGFP-IG 270
                                               566*******************9*******99998999999***************.6777777**.67 PP

                                 TIGR00260 214 laiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale....larrslgnledlkesvsd 278
                                                +iaa +a+d v+r+l +g +ep+ + +Tl tAmd+gnpsn+ r+l+     +r+ + ++  +  +vsd
  lcl|NCBI__GCF_000020505.1:WP_012503136.1 271 GFIAASNANDSVTRYLDEGRFEPRPTIKTLTTAMDVGNPSNFARLLHfyegDFRKMGVDIAGI--AVSD 337
                                               889999999*************************************97766678888888888..**** PP

                                 TIGR00260 279 eeileaikklaeeegyllephtavavaalkklvekg..vs......atadpaKFeevvealtgnkl 336
                                               +e++e+i+ +  + gy+++phtav+++al+   +     +      +ta+p KF e++   tg++ 
  lcl|NCBI__GCF_000020505.1:WP_012503136.1 338 AETVETIRAVHDRYGYIMDPHTAVGYRALEHFRDTRsgAGkpavvlSTAHPVKFDEAIRTATGKEV 403
                                               ******************************9988765522556678*************9999876 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.90
//
[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