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 (EC 4.2.3.1) (characterized)
to candidate AZOBR_RS10545 AZOBR_RS10545 threonine synthase

Query= BRENDA::Q8YFS0
         (463 letters)



>FitnessBrowser__azobra:AZOBR_RS10545
          Length = 470

 Score =  523 bits (1347), Expect = e-153
 Identities = 265/465 (56%), Positives = 337/465 (72%), Gaps = 2/465 (0%)

Query: 1   MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60
           +KYVSTRG+APVLGF + LLAGLARDGGLY+P  +PQF+A++IRA+RG  Y E+A+ V+ 
Sbjct: 1   LKYVSTRGQAPVLGFEEVLLAGLARDGGLYVPDSWPQFSADEIRAMRGLPYSEIAVRVML 60

Query: 61  PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120
           PF GG I   DF  +V++AY +F H AV PLVQ D   +V+ELFHGPTLAFKDVA+QLL 
Sbjct: 61  PFLGGAIAEDDFRAIVKDAYASFDHAAVVPLVQLDQRTWVMELFHGPTLAFKDVALQLLG 120

Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180
           R+ D+VLA+RG+R TIVGATSGDTG AAIEA   R N DIFIL P GR S VQ+RQMTS 
Sbjct: 121 RLFDHVLAKRGKRVTIVGATSGDTGSAAIEACRDRQNVDIFILHPKGRTSEVQRRQMTSV 180

Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240
              NVH +++ G FDDCQ+LVK +FND+ F D + LS VNSINWARIM Q+VYYF AA++
Sbjct: 181 LSDNVHNIALHGTFDDCQDLVKALFNDMAFRDKMGLSAVNSINWARIMAQIVYYFAAAVA 240

Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300
           LGAPDR V+FTVPTGNFG+++A Y A+ MGLP+E+L++ +N NDIL+R   SG      V
Sbjct: 241 LGAPDRKVAFTVPTGNFGNVYAAYGARAMGLPVERLVVGSNANDILARFFASGTMSAAPV 300

Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360
             T SPSMDIQISSNFERLLF+  GRD AAV+  M G +  G F +++  L+   + F+A
Sbjct: 301 VPTLSPSMDIQISSNFERLLFDLLGRDGAAVQAAMDGFRAEGKFAVTDAQLAEAHAIFAA 360

Query: 361 GRSTVDETAATIESVLSK-DGYLLDPHSAIGV-KVAREKASGTAPMVVLATAHPAKFPDA 418
           GR+    T   I+ V  K  GY +DPH+A+G+   A      + P+VV+ATAHPAKFPDA
Sbjct: 361 GRADDARTMDVIKEVWEKTGGYQVDPHTAVGIHSAATAPVDPSVPVVVMATAHPAKFPDA 420

Query: 419 VKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSRA 463
           V+ A G  P LP  L DL +R+E  + L N++  V+E+V   +RA
Sbjct: 421 VETATGRRPVLPPRLADLYEREERLSELPNDVAAVQEFVVARARA 465


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: 605
Number of extensions: 23
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: 463
Length of database: 470
Length adjustment: 33
Effective length of query: 430
Effective length of database: 437
Effective search space:   187910
Effective search space used:   187910
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 AZOBR_RS10545 AZOBR_RS10545 (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.28690.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.3e-84  268.2   0.0    7.1e-84  267.8   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS10545  AZOBR_RS10545 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS10545  AZOBR_RS10545 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.8   0.0   7.1e-84   7.1e-84      12     334 ..      69     427 ..      57     431 .. 0.91

  Alignments for each domain:
  == domain 1  score: 267.8 bits;  conditional E-value: 7.1e-84
                                 TIGR00260  12 ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvl 77 
                                               e d  ++ +  ++ f+  ++   v++ ++ +v elfhgPtlaFKD++lq ++ l+ ++l +  +  t++
  lcl|FitnessBrowser__azobra:AZOBR_RS10545  69 EDDFRAIVKDAYASFDHAAVVPLVQLdQRTWVMELFHGPTLAFKDVALQLLGRLFDHVLAKRGKrvTIV 137
                                               6677788888999999999999999999*****************************876544446*** PP

                                 TIGR00260  78 cAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeife 145
                                               +AtsGdtg+aa+ea + ++nv++++L Pkg++s v   +++ +l  n++ +a +G+FDd+qdlvk++f+
  lcl|FitnessBrowser__azobra:AZOBR_RS10545 138 GATSGDTGSAAIEACRDRQNVDIFILHPKGRTSEVqRRQMTSVLSDNVHNIALHGTFDDCQDLVKALFN 206
                                               ***********************************99*******************************9 PP

                                 TIGR00260 146 dke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpi 211
                                               d     k++l++vNsin+ari aq++y+f ++ +lg     kv++ vp gnfg++++++ +  ++ lp+
  lcl|FitnessBrowser__azobra:AZOBR_RS10545 207 DMAfrdKMGLSAVNSINWARIMAQIVYYFAAAVALG-APDRKVAFTVPTGNFGNVYAAYGARAMG-LPV 273
                                               665688******************************.55568****************9998888.**9 PP

                                 TIGR00260 212 eklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke..... 274
                                               e l + ++ + di+ rf  sg ++    + Tls++mdi ++sn+er+l+ l  r ++ +++        
  lcl|FitnessBrowser__azobra:AZOBR_RS10545 274 ERLVVGSNAN-DILARFFASGTMSAAPVVPTLSPSMDIQISSNFERLLFdLLGRDGAAVQAAMDgfrae 341
                                               9888888887.**********99999999*******************99999999999998679**** PP

                                 TIGR00260 275 ....................svsdeeileaikklaee.egyllephtavava.alkklvekg....vsa 317
                                                                   ++ d+ +++ ik++ e+  gy ++phtav++  a    v+ +    v a
  lcl|FitnessBrowser__azobra:AZOBR_RS10545 342 gkfavtdaqlaeahaifaagRADDARTMDVIKEVWEKtGGYQVDPHTAVGIHsAATAPVDPSvpvvVMA 410
                                               ***********************************98679***********72455667877876445* PP

                                 TIGR00260 318 tadpaKFeevvealtgn 334
                                               ta+paKF+++ve  tg 
  lcl|FitnessBrowser__azobra:AZOBR_RS10545 411 TAHPAKFPDAVETATGR 427
                                               ************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (470 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 14.43
//
[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