Alignments for a candidate for thrC in Thiomicrospira pelophila DSM 1534

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Thiomicrospira pelophila DSM 1534

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_029934615.1 N746_RS0105395 threonine synthase

Query= curated2:O24924
         (486 letters)



>NCBI__GCF_000711195.1:WP_029934615.1
          Length = 490

 Score =  385 bits (990), Expect = e-111
 Identities = 217/489 (44%), Positives = 302/489 (61%), Gaps = 13/489 (2%)

Query: 1   MPFVPTRSLK---EKKIDFIEAILNPNAPKGGLYTLERFETLQWQDC---LNLSYNDLVE 54
           M F+ TR       K++ F +AIL+P +  GGLY+ +    L        LN +Y  L +
Sbjct: 1   MNFIETRGNDGQFPKEVTFSQAILSPMSSFGGLYSPKSLPQLGLDFLKAHLNSNYKTLAK 60

Query: 55  CVFERLGLEIPKNLLASALKRYENFDNPKNPAPIFALNERLFVQELYHGPSLAFKDMALQ 114
            +     ++I + ++  AL  Y+ FD+P NP P+  + + LFV ELYHGP+ AFKDMALQ
Sbjct: 61  AILAEFEVDIDQAVIDQALALYDQFDDPTNPVPVVKVRDDLFVSELYHGPTRAFKDMALQ 120

Query: 115 PLASLFSNLAVGKNEKYLMLVSTSGDTGPATLESLAGMPNVFVVCLYPKDGTSLVQKLQM 174
           P  ++ S +A  +NEK+L+L +TSGDTGPA L++    PNV VVC+YP  GTS VQ+LQM
Sbjct: 121 PFGTVLSAVAQKRNEKFLILAATSGDTGPAALDTFRNKPNVQVVCMYPDGGTSDVQRLQM 180

Query: 175 VTQSASNLKVFGISGDFDDAQNALKNLLKDDDFNEALKACQLKLSVANSVNFGRIAFQIV 234
           VT++  NLKV GI GDFDDAQ ALK+LL    F + LK   +++S ANSVNFGRI FQ +
Sbjct: 181 VTETGENLKVIGIKGDFDDAQTALKSLLVSTSFRDTLKQQGVQVSAANSVNFGRIIFQTI 240

Query: 235 YHIWGFLELYKKGAINSKEKITLAIPSGNFGNALGAFYAKKMGLNIDKIKVVTNSNDVLR 294
           YH+  +LEL +   I   +++ L +PSGNFGNALG +YA KMGL + KI + +N N+VL 
Sbjct: 241 YHVHSYLELVRLQEIGLGDQVYLDVPSGNFGNALGGYYAYKMGLPVAKILIASNQNNVLT 300

Query: 295 EFIETGRYDLTHRSLKQTYSPAMDILKSSNVERALFSLFGFERTLELMQALEEEKFYALK 354
           +FIE G+YDL    +  T SPAMDILKSSN+ER LF LFG ERT ELM AL+++KFY L 
Sbjct: 301 QFIEEGKYDLRDSGVIATTSPAMDILKSSNIERILFDLFGAERTKELMLALDKDKFYQLT 360

Query: 355 PKELALLQEHFSCASCSDEACLKTIQEVYAEHQYLIDPHTATALNASLKTHE---KTLVS 411
             EL ++Q  F+   C+++     I++ Y E  YL+DPHTAT L       +   KT+  
Sbjct: 361 SDELGMVQTIFAADFCTNQEGQDYIKQAY-EDGYLMDPHTATCLKVYDTKRDQKLKTIAY 419

Query: 412 ATASYEKF-PRITLLALNEQKKNDNDKAALETLKNSYNTPDSQRLDDLFERGIKHQEVLK 470
           +TA + KF P I       +  +D D  AL+ + +    P   ++  LF+      +V+ 
Sbjct: 420 STAEWTKFSPVIAKTLFGGELTSDID--ALKRIADKGQIPIPAQISRLFDLPATQAKVID 477

Query: 471 LNEIKSSIL 479
              I++ IL
Sbjct: 478 KQNIETEIL 486


Lambda     K      H
   0.318    0.134    0.381 

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: 559
Number of extensions: 24
Number of successful extensions: 4
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: 486
Length of database: 490
Length adjustment: 34
Effective length of query: 452
Effective length of database: 456
Effective search space:   206112
Effective search space used:   206112
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_029934615.1 N746_RS0105395 (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.10665.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.7e-84  268.7   0.0      5e-84  268.3   0.0    1.1  1  lcl|NCBI__GCF_000711195.1:WP_029934615.1  N746_RS0105395 threonine synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000711195.1:WP_029934615.1  N746_RS0105395 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.3   0.0     5e-84     5e-84      10     336 ..      68     440 ..      59     443 .. 0.90

  Alignments for each domain:
  == domain 1  score: 268.3 bits;  conditional E-value: 5e-84
                                 TIGR00260  10 vt.ekdlvdlaegstelfrspklaeevga..enlyvkelfhgPtlaFKDrglqfvavlltkalelgne. 74 
                                               v  ++ ++d a   +  f+ p+++ +v +   +l+v el+hgPt aFKD++lq+ + +l++++++ ne 
  lcl|NCBI__GCF_000711195.1:WP_029934615.1  68 VDiDQAVIDQALALYDQFDDPTNPVPVVKvrDDLFVSELYHGPTRAFKDMALQPFGTVLSAVAQKRNEk 136
                                               44567778888899999****99988888889************************************9 PP

                                 TIGR00260  75 .tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvk 141
                                                ++l AtsGdtg+aa+  ++ k+nv+vv++yP+g++s v   ++vt   en+kv++ikGdFDdaq+++k
  lcl|NCBI__GCF_000711195.1:WP_029934615.1 137 fLILAATSGDTGPAALDTFRNKPNVQVVCMYPDGGTSDVqRLQMVTETGENLKVIGIKGDFDDAQTALK 205
                                               9**************************************99**************************** PP

                                 TIGR00260 142 eife.dke........klklnsvNsinparieaqk.tyafeiveqlgk...espdkvvvpvpsgnfgai 197
                                               +++              ++++++Ns+n++ri +q  +++++ +e +        d+v + vpsgnfg++
  lcl|NCBI__GCF_000711195.1:WP_029934615.1 206 SLLVsT-SfrdtlkqqGVQVSAANSVNFGRIIFQTiYHVHSYLELVRLqeiGLGDQVYLDVPSGNFGNA 273
                                               *99852.33556666699****************99****99998887334568*************** PP

                                 TIGR00260 198 lkGflekkelglpieklaiaaegaadivrrflksg.dlepkedk.eTlstAmdignpsnverale...l 261
                                               l G++++k++ lp++k+ ia++++ +++++f+++g +++  + + +T s+Amdi+++sn+er+l+   +
  lcl|NCBI__GCF_000711195.1:WP_029934615.1 274 LGGYYAYKMG-LPVAKILIASNQN-NVLTQFIEEGkYDLRDSGViATTSPAMDILKSSNIERILFdlfG 340
                                               **********.************9.**********7666666669*******************99999 PP

                                 TIGR00260 262 arrslgnledlke.....................svsdeeileaikklaeeegyllephtavavaalkk 309
                                               a+r+++ + +l++                      ++++e  + ik+++e  gyl++phta+ +++   
  lcl|NCBI__GCF_000711195.1:WP_029934615.1 341 AERTKELMLALDKdkfyqltsdelgmvqtifaadFCTNQEGQDYIKQAYE-DGYLMDPHTATCLKVYDT 408
                                               9**********99********************999****9999998885.7***********999877 PP

                                 TIGR00260 310 lvekg....vsatadpaKFeevve.altgnkl 336
                                                 ++      ++ta+  KF+ v++  l g +l
  lcl|NCBI__GCF_000711195.1:WP_029934615.1 409 KRDQKlktiAYSTAEWTKFSPVIAkTLFGGEL 440
                                               66666655777*********999978877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (490 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: 10.98
//
[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