GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrC in Phyllobacterium endophyticum PEPV15

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_106716046.1 CU100_RS06650 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>NCBI__GCF_003010935.1:WP_106716046.1
          Length = 468

 Score =  723 bits (1866), Expect = 0.0
 Identities = 359/463 (77%), Positives = 405/463 (87%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           MKYVSTRGEAPVLGFSDALL+GLARDGGLYLP+++PQF+  +IR++RGKSY EVA+ VLT
Sbjct: 1   MKYVSTRGEAPVLGFSDALLSGLARDGGLYLPEQFPQFSPAEIRSMRGKSYAEVAIEVLT 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF  G++  ADFE MV EAYGTFRH+AVCPLVQT  NEFVLELFHGPTLAFKDVAMQLLA
Sbjct: 61  PFVTGDLDQADFEEMVHEAYGTFRHEAVCPLVQTGHNEFVLELFHGPTLAFKDVAMQLLA 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           R+MD +L++R ERATIVGATSGDTGGAAIEAF  RD TDIFILFP+ RVS VQQRQMT+S
Sbjct: 121 RLMDRILSERNERATIVGATSGDTGGAAIEAFANRDRTDIFILFPHNRVSQVQQRQMTTS 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
             +NVHAL+I+GNFDDCQ+LVKGMFNDL F D+LSLSGVNSINWARIMPQ+VYYFTAA+S
Sbjct: 181 AAANVHALAIDGNFDDCQSLVKGMFNDLVFRDSLSLSGVNSINWARIMPQIVYYFTAAVS 240

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LG+P+R +SFTVPTGNFGDIFAGYVAKRMGLPI++L+IATNDNDILSRT+E+G YE RGV
Sbjct: 241 LGSPERPISFTVPTGNFGDIFAGYVAKRMGLPIDRLVIATNDNDILSRTIETGIYETRGV 300

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             TTSPSMDIQ+SSNFERLLFEAHGRDAAAVR LM GL QSG FTI++  L+AIR+EF A
Sbjct: 301 LHTTSPSMDIQVSSNFERLLFEAHGRDAAAVRRLMSGLNQSGSFTIADTVLAAIRAEFDA 360

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVK 420
           G ST  ET   I +VL + GYLLDPHSAIG+K+AREKA    P VVLATAHPAKFPDAV+
Sbjct: 361 GSSTTAETDQAIANVLKQSGYLLDPHSAIGLKIAREKAGKETPSVVLATAHPAKFPDAVE 420

Query: 421 AACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSRA 463
           AA G+ P LP WL DLMQRKE +TVL N+LK VEEYVR HSRA
Sbjct: 421 AASGIRPALPLWLGDLMQRKEQYTVLPNDLKSVEEYVRRHSRA 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: 713
Number of extensions: 23
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: 468
Length adjustment: 33
Effective length of query: 430
Effective length of database: 435
Effective search space:   187050
Effective search space used:   187050
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_106716046.1 CU100_RS06650 (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.1267418.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      1e-85  273.9   0.0    1.3e-85  273.5   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106716046.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106716046.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.5   0.0   1.3e-85   1.3e-85      12     334 ..      69     425 ..      59     430 .. 0.91

  Alignments for each domain:
  == domain 1  score: 273.5 bits;  conditional E-value: 1.3e-85
                             TIGR00260  12 ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAts 81 
                                           ++d +++ +  + +fr +++   v+  +n +v+elfhgPtlaFKD+++q +a l+ ++l + ne  t+++Ats
  NCBI__GCF_003010935.1:WP_106716046.1  69 QADFEEMVHEAYGTFRHEAVCPLVQTgHNEFVLELFHGPTLAFKDVAMQLLARLMDRILSERNEraTIVGATS 141
                                           4566666677788999999999998899*********************************99999******* PP

                             TIGR00260  82 GdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...kl 150
                                           Gdtg aa+ea+a +   ++++L P+ ++s v + +++t  a n++ lai+G+FDd+q lvk +f+d      l
  NCBI__GCF_003010935.1:WP_106716046.1 142 GDTGGAAIEAFANRDRTDIFILFPHNRVSQVqQRQMTTSAAANVHALAIDGNFDDCQSLVKGMFNDLVfrdSL 214
                                           ****************************************************************9655677** PP

                             TIGR00260 151 klnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaad 223
                                            l+ vNsin+ari  q++y+f ++  lg   +  + + vp gnfg+i++G+++k+++ lpi+ l ia++++ d
  NCBI__GCF_003010935.1:WP_106716046.1 215 SLSGVNSINWARIMPQIVYYFTAAVSLG-SPERPISFTVPTGNFGDIFAGYVAKRMG-LPIDRLVIATNDN-D 284
                                           ****************************.55567******************99999.************9.* PP

                             TIGR00260 224 ivrrflksgdlepkedk.eTlstAmdignpsnverale.larrslgnledlke.................... 274
                                           i+ r +++g +++ + + +T s++mdi  +sn+er+l+ +  r  + +  l +                    
  NCBI__GCF_003010935.1:WP_106716046.1 285 ILSRTIETG-IYETRGVlHTTSPSMDIQVSSNFERLLFeAHGRDAAAVRRLMSglnqsgsftiadtvlaaira 356
                                           *********.66666656******************987777777778888669999**************** PP

                             TIGR00260 275 .....svsdeeileaikklaeeegyllephtavavaalkklvekg....vsatadpaKFeevvealtgn 334
                                                s + +e+ +ai +++++ gyll+ph+a++++  ++ + k+    v ata+paKF+++vea +g 
  NCBI__GCF_003010935.1:WP_106716046.1 357 efdagSSTTAETDQAIANVLKQSGYLLDPHSAIGLKIAREKAGKEtpsvVLATAHPAKFPDAVEAASGI 425
                                           *****99****************************9887777766575444*************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (468 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: 28.44
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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