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.28732.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: 13.92
//
[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:

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:

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:

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:

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