Alignments for a candidate for thrC in Rhizobium leguminosarum 3841

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Rhizobium leguminosarum 3841

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011650794.1 RL_RS05510 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>NCBI__GCF_000009265.1:WP_011650794.1
          Length = 474

 Score =  648 bits (1672), Expect = 0.0
 Identities = 315/460 (68%), Positives = 377/460 (81%)

Query: 3   YVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLTPF 62
           Y+STRGEAP LGF DALL GLARDGGLY+P+++P F+ ++IRALRGK+Y E+A  +L+PF
Sbjct: 6   YISTRGEAPSLGFCDALLTGLARDGGLYVPRKWPSFSKKEIRALRGKTYQEIAFTILSPF 65

Query: 63  TGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLARM 122
           T GEIP   F  M+ EAYGTFRH A+ PLVQT  N FV+ELFHG TLAFKDVAMQLLAR+
Sbjct: 66  TNGEIPDDTFRAMIDEAYGTFRHPAIAPLVQTGPNSFVMELFHGTTLAFKDVAMQLLARL 125

Query: 123 MDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSSGF 182
           MDY L +RGERATIVGATSGDTGGAAI+AF GR+ TDIFILFP+G+VSPVQQRQMT+S  
Sbjct: 126 MDYALEKRGERATIVGATSGDTGGAAIDAFAGRERTDIFILFPHGKVSPVQQRQMTTSSS 185

Query: 183 SNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALSLG 242
           +NVHAL++EGNFDDCQNLVK MFND+ F D + LSGVNSINWARIM Q+VYYFTAA++LG
Sbjct: 186 ANVHALAVEGNFDDCQNLVKAMFNDVTFRDKVRLSGVNSINWARIMAQIVYYFTAAVALG 245

Query: 243 APDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGVAQ 302
            PDR +SFTVPTGNFGDIFAGY AKRMGLPI++L+IATN+NDIL+RTL++G Y+M+ V  
Sbjct: 246 GPDRKISFTVPTGNFGDIFAGYCAKRMGLPIDRLVIATNENDILARTLKTGRYDMKAVKA 305

Query: 303 TTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSAGR 362
           T+SPSMDIQISSNFERLLFEA+ RDA+ VR  M+ LKQS GF I  + L AIR +F AGR
Sbjct: 306 TSSPSMDIQISSNFERLLFEAYDRDASKVRAAMESLKQSNGFEIGSQALKAIRRDFRAGR 365

Query: 363 STVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVKAA 422
           ++  + A TI    ++ GYLLDPHSAIGV VA +K     PMV L+TAHPAKFP AVK+A
Sbjct: 366 ASEKQVAETIRKTHAETGYLLDPHSAIGVFVAAKKEKPNTPMVTLSTAHPAKFPAAVKSA 425

Query: 423 CGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462
           CG++P LP WL DLM R+E F ++  ELK VE ++  H+R
Sbjct: 426 CGIDPALPTWLADLMHREERFQIIKPELKAVETFIGKHAR 465


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: 641
Number of extensions: 17
Number of successful extensions: 1
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: 474
Length adjustment: 33
Effective length of query: 430
Effective length of database: 441
Effective search space:   189630
Effective search space used:   189630
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_011650794.1 RL_RS05510 (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.11324.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.7e-90  289.6   0.0    2.3e-90  289.1   0.0    1.1  1  lcl|NCBI__GCF_000009265.1:WP_011650794.1  RL_RS05510 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_011650794.1  RL_RS05510 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.1   0.0   2.3e-90   2.3e-90      15     331 ..      75     425 ..      67     432 .. 0.91

  Alignments for each domain:
  == domain 1  score: 289.1 bits;  conditional E-value: 2.3e-90
                                 TIGR00260  15 lvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAt 80 
                                                 +++   + +fr p++a  v+   n +v elfhg tlaFKD+++q +a l+ +ale+  e  t+++At
  lcl|NCBI__GCF_000009265.1:WP_011650794.1  75 FRAMIDEAYGTFRHPAIAPLVQTgPNSFVMELFHGTTLAFKDVAMQLLARLMDYALEKRGEraTIVGAT 143
                                               5567788999********9999999*******************************9877677****** PP

                                 TIGR00260  81 sGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke 148
                                               sGdtg aa+ a+ag++  ++++L P+gk+spv + +++t +  n++ la++G+FDd+q+lvk++f+d  
  lcl|NCBI__GCF_000009265.1:WP_011650794.1 144 SGDTGGAAIDAFAGRERTDIFILFPHGKVSPVqQRQMTTSSSANVHALAVEGNFDDCQNLVKAMFNDVT 212
                                               *****************************************************************9665 PP

                                 TIGR00260 149 ...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpiekl 214
                                                  k+ l+ vNsin+ari aq++y+f ++ +lg+    k+ + vp gnfg+i++G+++k+++ lpi+ l
  lcl|NCBI__GCF_000009265.1:WP_011650794.1 213 frdKVRLSGVNSINWARIMAQIVYYFTAAVALGG-PDRKISFTVPTGNFGDIFAGYCAKRMG-LPIDRL 279
                                               677******************************5.4568**********************9.****** PP

                                 TIGR00260 215 aiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.....larrslgnledlke.... 274
                                                ia++++ di+ r lk+g  + k+ k+T s++mdi ++sn+er+l+      a +  + +e+lk+    
  lcl|NCBI__GCF_000009265.1:WP_011650794.1 280 VIATNEN-DILARTLKTGRYDMKAVKATSSPSMDIQISSNFERLLFeaydrDASKVRAAMESLKQsngf 347
                                               ******9.**********99999999******************996322223333444555555**** PP

                                 TIGR00260 275 .................svsdeeileaikklaeeegyllephtavavaalkklvekg...vs.atadpa 322
                                                                ++s++++ e+i+k  +e gyll+ph+a++v +  k  + +   v+ +ta+pa
  lcl|NCBI__GCF_000009265.1:WP_011650794.1 348 eigsqalkairrdfragRASEKQVAETIRKTHAETGYLLDPHSAIGVFVAAKKEKPNtpmVTlSTAHPA 416
                                               ***********************************************9988888877676337****** PP

                                 TIGR00260 323 KFeevveal 331
                                               KF+ +v   
  lcl|NCBI__GCF_000009265.1:WP_011650794.1 417 KFPAAVKSA 425
                                               *****9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (474 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: 14.74
//
[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