Alignments for a candidate for thrC in Xanthobacter autotrophicus Py2

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Xanthobacter autotrophicus Py2

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012115499.1 XAUT_RS17780 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>NCBI__GCF_000017645.1:WP_012115499.1
          Length = 470

 Score =  572 bits (1474), Expect = e-168
 Identities = 294/463 (63%), Positives = 355/463 (76%), Gaps = 1/463 (0%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           M+YVSTRGEAPVL FSDALLAGLARDGGLYLP+ +P  + ++I AL GK Y  VA AV+ 
Sbjct: 1   MRYVSTRGEAPVLSFSDALLAGLARDGGLYLPEAWPTLSRDEIAALAGKPYAAVAKAVIG 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF G  +P    + M+ +AY  FRH AV PL Q  AN F+LELFHGPTLAFKDVAMQLLA
Sbjct: 61  PFVGDALPPRALDLMIDDAYAGFRHPAVAPLTQIGANRFLLELFHGPTLAFKDVAMQLLA 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           R+MD+VLA RG RATIVGATSGDTG AAIEAF   D  D+FIL+P+GRVS VQ+RQMT+ 
Sbjct: 121 RLMDHVLASRGSRATIVGATSGDTGSAAIEAFRRSDAVDVFILYPHGRVSEVQRRQMTTV 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
              +VHA+++EG FDDCQNLVK MFN   F D+L+L+GVNSINWARI+ QVVYYF AA +
Sbjct: 181 NSPSVHAIAVEGTFDDCQNLVKAMFNHHAFRDSLALAGVNSINWARIVAQVVYYFYAATA 240

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LGAP R VSF VPTGNFGDI AG+VAK+MGLPI  L IATN NDIL RTL++G YE++GV
Sbjct: 241 LGAPHRDVSFVVPTGNFGDILAGWVAKKMGLPIRDLTIATNVNDILVRTLDTGRYEVKGV 300

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             ++SPSMDIQISSNFERLLFEA  RD+A +R LM  L QSG F++    L+AI ++FSA
Sbjct: 301 LPSSSPSMDIQISSNFERLLFEALDRDSAVLRQLMDQLAQSGSFSVPRAALAAICADFSA 360

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVA-REKASGTAPMVVLATAHPAKFPDAV 419
           GR+   ETAATI  +    GYL DPH+A+G+ VA + + +   P VVL+TAHPAKFPDAV
Sbjct: 361 GRADEPETAATIARLYQSAGYLCDPHTAVGLAVADKVEHAARVPQVVLSTAHPAKFPDAV 420

Query: 420 KAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462
           +AA G  P LP  + DLM R+ES +VL N+L  +E ++R H+R
Sbjct: 421 EAATGHRPALPPHMADLMTRRESVSVLPNDLAAIETFIRAHAR 463


Lambda     K      H
   0.320    0.135    0.389 

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: 618
Number of extensions: 23
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: 463
Length of database: 470
Length adjustment: 33
Effective length of query: 430
Effective length of database: 437
Effective search space:   187910
Effective search space used:   187910
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_012115499.1 XAUT_RS17780 (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.3793586.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      4e-86  275.2   0.0    5.5e-86  274.7   0.0    1.1  1  NCBI__GCF_000017645.1:WP_012115499.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017645.1:WP_012115499.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.7   0.0   5.5e-86   5.5e-86      22     335 ..      79     427 ..      67     431 .. 0.92

  Alignments for each domain:
  == domain 1  score: 274.7 bits;  conditional E-value: 5.5e-86
                             TIGR00260  22 stelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaae 90 
                                            ++ fr p++a   ++ga n +++elfhgPtlaFKD+++q +a l+ ++l       t+++AtsGdtg+aa+e
  NCBI__GCF_000017645.1:WP_012115499.1  79 AYAGFRHPAVAplTQIGA-NRFLLELFHGPTLAFKDVAMQLLARLMDHVLASRGSraTIVGATSGDTGSAAIE 150
                                           677788888887788999.99***************************876543335**************** PP

                             TIGR00260  91 alagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsin 159
                                           a+++   v+v++LyP+g++s v   +++t+    ++ +a++G+FDd+q+lvk++f+++     l l  vNsin
  NCBI__GCF_000017645.1:WP_012115499.1 151 AFRRSDAVDVFILYPHGRVSEVqRRQMTTVNSPSVHAIAVEGTFDDCQNLVKAMFNHHAfrdSLALAGVNSIN 223
                                           **********************99********************************6666889********** PP

                             TIGR00260 160 parieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksg 232
                                           +ari aq++y+f ++ +lg      v ++vp gnfg+il+G+++kk++ lpi+ l ia++ + di+ r l +g
  NCBI__GCF_000017645.1:WP_012115499.1 224 WARIVAQVVYYFYAATALG-APHRDVSFVVPTGNFGDILAGWVAKKMG-LPIRDLTIATNVN-DILVRTLDTG 293
                                           *******************.556679*********************9.***********98.********** PP

                             TIGR00260 233 dlepkedkeTlstAmdignpsnverale.larrslgnledlke.........................svsde 279
                                             e k  +   s++mdi ++sn+er+l+ +  r  + l +l                           ++ + 
  NCBI__GCF_000017645.1:WP_012115499.1 294 RYEVKGVLPSSSPSMDIQISSNFERLLFeALDRDSAVLRQLMDqlaqsgsfsvpraalaaicadfsagRADEP 366
                                           88888888*******************99999999888888668999********************999999 PP

                             TIGR00260 280 eileaikklaeeegyllephtavavaalkklvekg...vs..atadpaKFeevvealtgnk 335
                                           e+  +i +l+++ gyl++phtav++a+  k   +    +   +ta+paKF+++vea tg+ 
  NCBI__GCF_000017645.1:WP_012115499.1 367 ETAATIARLYQSAGYLCDPHTAVGLAVADKVEHAArvpQVvlSTAHPAKFPDAVEAATGHR 427
                                           ***************************999887777763367****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (470 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 31.32
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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