GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrC in Marivita geojedonensis DPG-138

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_085636009.1 MGEO_RS06980 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>NCBI__GCF_002115805.1:WP_085636009.1
          Length = 462

 Score =  517 bits (1331), Expect = e-151
 Identities = 262/458 (57%), Positives = 327/458 (71%), Gaps = 1/458 (0%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           M+Y+STRG+AP LGF D +L+GLARDGGLY+P+  P  +A  IRA+ G SY E+A  V+ 
Sbjct: 1   MQYISTRGKAPALGFEDTMLSGLARDGGLYVPETIPTLSAGDIRAMHGLSYEEIAFRVMR 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF G       F  ++ +AY  F HDA  PLVQ     F+LELFHGPTLAFKD AMQL+ 
Sbjct: 61  PFVGDAFTDEVFADLIAKAYAGFGHDARAPLVQLGNGHFLLELFHGPTLAFKDFAMQLIG 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           +M    L++ G+R TIVGATSGDTG AAIEAF G D  D+FIL+P+GRVS VQ+RQMT+ 
Sbjct: 121 QMFQEALSRSGKRVTIVGATSGDTGSAAIEAFRGLDAVDVFILYPHGRVSEVQRRQMTTP 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
             SNVHAL+++G FDDCQ  +K MFN  EF DA+ L+GVNSINW R++ QVVYYF++A+S
Sbjct: 181 VESNVHALALDGTFDDCQARLKDMFNHFEFRDAVKLAGVNSINWGRVLAQVVYYFSSAVS 240

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LGAPDR VSFTVPTGNFGDIFAGY+AKRMGLPI++L++ATN NDIL R L +G Y    V
Sbjct: 241 LGAPDRTVSFTVPTGNFGDIFAGYIAKRMGLPIDRLVVATNQNDILHRCLTTGGYVTDSV 300

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             + SPSMDIQ+SSNFER LF+A+ RD  AV  LM  LK +GGF +S+  +  +R  + +
Sbjct: 301 TPSISPSMDIQVSSNFERALFDAYNRDGNAVSQLMDELK-AGGFHVSQGAMEVLRDHYDS 359

Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVK 420
           GR + DET + I       G LL PHSAIGVKVA ++     PM+ LATAHPAKFPDAV+
Sbjct: 360 GRVSEDETLSMITHAHRHMGELLCPHSAIGVKVAEDQRDPATPMITLATAHPAKFPDAVE 419

Query: 421 AACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVR 458
            A GV P LP  + DL  R E  T + N+L  +E  ++
Sbjct: 420 QASGVRPPLPERMADLFDRAERVTRVANDLDQLEALIK 457


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: 603
Number of extensions: 22
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: 462
Length adjustment: 33
Effective length of query: 430
Effective length of database: 429
Effective search space:   184470
Effective search space used:   184470
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_085636009.1 MGEO_RS06980 (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.1059370.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.5e-84  269.3   0.0    3.2e-84  268.9   0.0    1.1  1  NCBI__GCF_002115805.1:WP_085636009.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085636009.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.9   0.0   3.2e-84   3.2e-84      15     334 ..      72     424 ..      60     430 .. 0.90

  Alignments for each domain:
  == domain 1  score: 268.9 bits;  conditional E-value: 3.2e-84
                             TIGR00260  15 lvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdt 84 
                                            +dl+++ ++ f  ++ a  v++ +  +++elfhgPtlaFKD+++q +++++++al +  +  t+++AtsGdt
  NCBI__GCF_002115805.1:WP_085636009.1  72 FADLIAKAYAGFGHDARAPLVQLgNGHFLLELFHGPTLAFKDFAMQLIGQMFQEALSRSGKrvTIVGATSGDT 144
                                           5788899999998888887777666889**************************998766556********** PP

                             TIGR00260  85 gaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klkln 153
                                           g+aa+ea++g   v+v++LyP+g++s v   +++t + +n++ la +G+FDd+q+ +k++f++ e   ++kl 
  NCBI__GCF_002115805.1:WP_085636009.1 145 GSAAIEAFRGLDAVDVFILYPHGRVSEVqRRQMTTPVESNVHALALDGTFDDCQARLKDMFNHFEfrdAVKLA 217
                                           ****************************99*******************************9655677***** PP

                             TIGR00260 154 svNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivr 226
                                            vNsin++r++aq++y+f+ +  lg      v + vp gnfg+i++G+ +k+++ lpi+ l +a++++ di++
  NCBI__GCF_002115805.1:WP_085636009.1 218 GVNSINWGRVLAQVVYYFSSAVSLG-APDRTVSFTVPTGNFGDIFAGYIAKRMG-LPIDRLVVATNQN-DILH 287
                                           *************************.4444699**************9999999.************8.**** PP

                             TIGR00260 227 rflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke........................ 274
                                           r l +g  ++ +    +s++mdi  +sn+eral+ + +r ++ + +l                          
  NCBI__GCF_002115805.1:WP_085636009.1 288 RCLTTGGYVTDSVTPSISPSMDIQVSSNFERALFdAYNRDGNAVSQLMDelkaggfhvsqgamevlrdhydsg 360
                                           ******7777777789*****************95555555555555446777******************** PP

                             TIGR00260 275 svsdeeileaikklaeeegyllephtavavaalkklvekg....vsatadpaKFeevvealtgn 334
                                           +vs++e+l+ i  + ++ g ll ph+a++v++ +++ +      + ata+paKF+++ve  +g 
  NCBI__GCF_002115805.1:WP_085636009.1 361 RVSEDETLSMITHAHRHMGELLCPHSAIGVKVAEDQRDPAtpmiTLATAHPAKFPDAVEQASGV 424
                                           **************************************99775444************988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (462 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: 28.26
//
[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