Alignments for a candidate for thrC in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Sinorhizobium meliloti 1021

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate SMa0485 SMa0485 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>FitnessBrowser__Smeli:SMa0485
          Length = 484

 Score =  296 bits (759), Expect = 8e-85
 Identities = 176/445 (39%), Positives = 252/445 (56%), Gaps = 18/445 (4%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           +KYVST G    +GF +A+L G A DGGL++P   P    EQ++A    S+ ++A  +++
Sbjct: 2   IKYVSTTGGIEPVGFDEAVLQGFAADGGLFVPDRIPVIDQEQLQAFSTLSFQDLAFELVS 61

Query: 61  PFTGGEI-PAADFERMVREAYGTFRHDAVCPLVQTDANE--FVLELFHGPTLAFKDVAMQ 117
            +    I P  D  R++  +Y  F+   +  LV    N   +VLELFHGPT +FKD+AM 
Sbjct: 62  LYIDASIIPRQDLRRLIDNSYREFQRPDIVNLVPIRGNRDTYVLELFHGPTQSFKDMAMG 121

Query: 118 LLARMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQM 177
            L +++DY+L QR ER  IV AT+GDTG AA  A  G+   D + L+P G +S  Q+RQM
Sbjct: 122 FLMQVVDYLLGQRRERLNIVLATTGDTGPAAAWAAAGKQRIDCWPLYPRGMISREQERQM 181

Query: 178 TSSGFSNVHALSIEG---NFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYY 234
           T+    NVH + +E      DD   +V  +F+D +    L+LS VNSINW R+M Q V+Y
Sbjct: 182 TTLRADNVHPVGVENCPDGGDDLDLVVAELFSDEKLKRTLALSSVNSINWCRVMTQTVHY 241

Query: 235 F----TAALSLGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTL 290
           F     A   +G P   V F+VP+G FG++FAGY+A+ MGLP+ + + A N N+ L    
Sbjct: 242 FYSYYRAVERVGDP---VVFSVPSGAFGNLFAGYLARSMGLPVARFVCANNVNNALHTAF 298

Query: 291 ESGAYEMRGVAQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKP 350
             G      + QT S ++DI    NF RLL+ A  RD A +R  M+         +  + 
Sbjct: 299 SRGVLPRHDLVQTPSSAIDIVAPYNFWRLLYFATNRDTARIRQWMKDFAARREVVLDVET 358

Query: 351 LSAIRSEFSAGRSTVDETAATIESVLSKDG-YLLDPHSAI---GVKVAREKASGTAPMVV 406
              I+  F +   + +ET AT+ SV   +G YL+DPH+A+    V+  R+     A +V 
Sbjct: 359 TKTIQGGFISASISDEETLATVRSVYEAEGHYLIDPHTAVAVAAVEAVRDSLPAAAAIVC 418

Query: 407 LATAHPAKFPDAVKAACGVEPQLPA 431
            ATAHPAKFPD +K A  VE +LPA
Sbjct: 419 FATAHPAKFPDVIKRALDVE-ELPA 442


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: 528
Number of extensions: 28
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 463
Length of database: 484
Length adjustment: 33
Effective length of query: 430
Effective length of database: 451
Effective search space:   193930
Effective search space used:   193930
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 SMa0485 SMa0485 (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.10328.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    2.3e-69  220.1   0.0    3.2e-69  219.6   0.0    1.1  1  lcl|FitnessBrowser__Smeli:SMa0485  SMa0485 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMa0485  SMa0485 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.6   0.0   3.2e-69   3.2e-69      11     331 ..      69     435 ..      59     442 .. 0.88

  Alignments for each domain:
  == domain 1  score: 219.6 bits;  conditional E-value: 3.2e-69
                          TIGR00260  11 t.ekdlvdlaegstelfrspklaeevga...enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAt 80 
                                        +  +dl  l+  s++ f+ p + + v +   ++ yv+elfhgPt +FKD+++ f+ +++ ++l++ +e   ++ At
  lcl|FitnessBrowser__Smeli:SMa0485  69 IpRQDLRRLIDNSYREFQRPDIVNLVPIrgnRDTYVLELFHGPTQSFKDMAMGFLMQVVDYLLGQRRErlNIVLAT 144
                                        34679999***************877766699********************************9999999***** PP

                          TIGR00260  81 sGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdF...Ddaqdlvkeifedke...k 149
                                        +Gdtg+aaa a agk+ +++  LyP+g is   + +++t  a n++ ++++      Dd   +v+e+f+d++    
  lcl|FitnessBrowser__Smeli:SMa0485 145 TGDTGPAAAWAAAGKQRIDCWPLYPRGMISREqERQMTTLRADNVHPVGVENCPdggDDLDLVVAELFSDEKlkrT 220
                                        ******************************99899***************86541117888899****96555669 PP

                          TIGR00260 150 lklnsvNsinparieaqk.tyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadi 224
                                        l l+svNsin+ r+  q   y+++   +++ +  d vv++vpsg fg++++G+l+  ++ lp   +++ a+++++ 
  lcl|FitnessBrowser__Smeli:SMa0485 221 LALSSVNSINWCRVMTQTvHYFYSYYRAVE-RVGDPVVFSVPSGAFGNLFAGYLARSMG-LP-VARFVCANNVNNA 293
                                        ******************777777777777.999******************9999998.**.7788888887777 PP

                          TIGR00260 225 vrrflksgdlepkedk.eTlstAmdignpsnverale.larrslgnledlke........................ 274
                                        ++    +g ++p++d+ +T s A+di  p n+ r+l  + +r  + + +  +                        
  lcl|FitnessBrowser__Smeli:SMa0485 294 LHTAFSRG-VLPRHDLvQTPSSAIDIVAPYNFWRLLYfATNRDTARIRQWMKdfaarrevvldvettktiqggfis 368
                                        77776777.88888888******************997888888888887668999******************** PP

                          TIGR00260 275 .svsdeeileaikklaeee.gyllephtavavaalkklvekg...vs....atadpaKFeevve.al 331
                                         s+sdee+l +++ ++e e +yl++phtavavaa++   ++          ata+paKF++v+  al
  lcl|FitnessBrowser__Smeli:SMa0485 369 aSISDEETLATVRSVYEAEgHYLIDPHTAVAVAAVEAVRDSLpaaAAivcfATAHPAKFPDVIKrAL 435
                                        ****************98537*************99888766754115678***********98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (484 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.73
//
[ok]

This GapMind analysis is from Apr 09 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