GapMind for Amino acid biosynthesis

 

Alignments for a candidate for thrC in Azospirillum brasilense Sp245

Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate AZOBR_RS16025 AZOBR_RS16025 threonine synthase

Query= curated2:Q58860
         (405 letters)



>FitnessBrowser__azobra:AZOBR_RS16025
          Length = 413

 Score =  227 bits (579), Expect = 4e-64
 Identities = 135/376 (35%), Positives = 199/376 (52%), Gaps = 3/376 (0%)

Query: 5   CIKCGKTYDVDEIIYTCECGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVKDE 64
           C   G+ Y+ D +    + G  L + YD E ++  ++++ L +R   +WRY E LPV+  
Sbjct: 20  CAYTGERYEADTVHNLSKAGKPLLVRYDLEGVRGALTKDALAERPQDLWRYRELLPVRRV 79

Query: 65  SKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGVEV 124
             IVSL E  TPL     L  +LG  EL VK+EG  PTGSFK RG+ + V+ A   G++ 
Sbjct: 80  QDIVSLGEAVTPLVALPKLAAKLGAAELLVKDEGRLPTGSFKARGLVMAVSMAKAFGIKH 139

Query: 125 VGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDALD 184
           +   + GN  A+LAAY+ R+G K  +  PE    +  +++    GA V +V G  DD   
Sbjct: 140 MAMPTNGNAGAALAAYATRAGIKTTIFCPEDTPEV-NVSEIELQGATVYRVNGLIDDCGK 198

Query: 185 MVKQ-LAKEKLIYLLNSINPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISAIWK 243
           +V +  AK     +     P+R+EG+KT+  E+ +QL W+VPD +  P G    +  +WK
Sbjct: 199 IVGEGKAKAGWFDVSTLKEPYRIEGKKTMGLELAEQLGWEVPDVIFYPTGGGTGLIGMWK 258

Query: 244 GFKEFEITGII-DELPKMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGNPVN 302
            F E E  G I  + P+M  +QA G  P+V A+    +    + +  TIA+ IR+   V 
Sbjct: 259 AFAELEAIGFIGSKRPRMVAVQAAGCAPMVRAYEAGEEHAPRWPDAHTIASGIRVPQAVG 318

Query: 303 APKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGIIDR 362
               L A+  SGG+A AV DE I  A    AR+EG  + P  A++ A  K+ L +G + R
Sbjct: 319 DFLILRAVRESGGFAVAVPDEAIQAALDEAAREEGFLLCPEGAATYAAYKQALGDGRVGR 378

Query: 363 DERIVCITTGHGLKDP 378
           DER V      GLK P
Sbjct: 379 DERAVLFNCATGLKYP 394


Lambda     K      H
   0.317    0.137    0.395 

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: 413
Number of extensions: 25
Number of successful extensions: 3
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: 405
Length of database: 413
Length adjustment: 31
Effective length of query: 374
Effective length of database: 382
Effective search space:   142868
Effective search space used:   142868
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate AZOBR_RS16025 AZOBR_RS16025 (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.7545.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    6.3e-54  169.3   0.0    7.8e-54  169.0   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS16025  AZOBR_RS16025 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS16025  AZOBR_RS16025 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.0   0.0   7.8e-54   7.8e-54       2     329 ..      68     384 ..      67     394 .. 0.94

  Alignments for each domain:
  == domain 1  score: 169.0 bits;  conditional E-value: 7.8e-54
                                 TIGR00260   2 vryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkal 69 
                                               +ryre+l+v   +d+v+l e +t+l++ pkla+++ga +l vk+++  Pt++FK rg   + ++++ a+
  lcl|FitnessBrowser__azobra:AZOBR_RS16025  68 WRYRELLPVRrVQDIVSLGEAVTPLVALPKLAAKLGAAELLVKDEGRLPTGSFKARG---LVMAVSMAK 133
                                               9*********99*********************************************...********* PP

                                 TIGR00260  70 elgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqd 138
                                                 g + ++  t G+ gaa+a a+a +a++k  ++ P++ +   +  +     ++a+v  ++G  Dd+ +
  lcl|FitnessBrowser__azobra:AZOBR_RS16025 134 AFGIKHMAMPTNGNAGAALA-AYATRAGIKTTIFCPED-TP--EVNVSEIELQGATVYRVNGLIDDCGK 198
                                               ********************.*****************.56..6999********************** PP

                                 TIGR00260 139 lvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekke 206
                                               +v e   +     ++      p+rie++kt+  e++eqlg+e pd +  p + +  +  ++k+f e++ 
  lcl|FitnessBrowser__azobra:AZOBR_RS16025 199 IVGEGKAKAGWFDVSTLK--EPYRIEGKKTMGLELAEQLGWEVPDVIFYPTGgGTGLIGMWKAFAELEA 265
                                               ***988777788888887..9*******************************76678889********* PP

                                 TIGR00260 207 lg.....lpieklaiaaegaadivrrflksgdlepkedk.eTlstAmdignpsnveralelarrslgnl 269
                                                g     +p ++ a++a g+a++vr++  + +  p+    +T++  +++ + +    +l+++r+s+g +
  lcl|FitnessBrowser__azobra:AZOBR_RS16025 266 IGfigskRP-RMVAVQAAGCAPMVRAYEAGEEHAPRWPDaHTIASGIRVPQAVGDFLILRAVRESGGFA 333
                                               ******999.*****************7777777665546**************99************* PP

                                 TIGR00260 270 edlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevve 329
                                                ++     de+i  a  ++a+eeg ll p +a+++aa k+ + +g   ++ ++  e++v+
  lcl|FitnessBrowser__azobra:AZOBR_RS16025 334 VAV----PDEAIQAALDEAAREEGFLLCPEGAATYAAYKQALGDG---RVGRD--ERAVL 384
                                               999....**********************************9999...88888..77776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (413 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: 00:00:00.00
# Mc/sec: 14.23
//
[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:

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