Alignments for a candidate for thrC in Azospirillum brasilense Sp245

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.1459.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.91
//
[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