Alignments for a candidate for dapC in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Acidovorax sp. GW101-3H11

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate Ac3H11_2573 Phosphoserine aminotransferase (EC 2.6.1.52)

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2573
          Length = 369

 Score =  364 bits (935), Expect = e-105
 Identities = 189/369 (51%), Positives = 244/369 (66%), Gaps = 9/369 (2%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           M + +NFS+GPA +PAEVL+QA  E+ DW+G G  VME+SHRGKEF+ + E+AE D R+L
Sbjct: 1   MTRPYNFSAGPAAIPAEVLEQAAAEMLDWHGSGMGVMEMSHRGKEFLSIYEQAEADLREL 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           L VP+NYK+LF  GGG  + A VPLN L      D+V  G W+  + KEA+KY +     
Sbjct: 61  LAVPTNYKILFMQGGGLAENAIVPLN-LSRAGAVDFVVTGSWSQKSQKEARKYASEVNIV 119

Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDF---GADVVVAADFSS 177
           A     G   +     W +S  A+Y+H C NETI+GI   + PD    G+D  +  DFSS
Sbjct: 120 ASAEDTGFTTLPDPASWTVSRGASYLHICSNETINGIEFHQLPDLKALGSDAPLVIDFSS 179

Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237
            + SRP+D SR G+ + GAQKN+GPAGLT+V+VREDLLG A  ACPS  DY  + DN SM
Sbjct: 180 HVASRPVDWSRVGLAFGGAQKNLGPAGLTLVVVREDLLGHALPACPSAFDYKTVADNQSM 239

Query: 238 FNTPPTFAWYLSGLVFKWLKAN-----GGVAEMDKINQQKAELLYGVIDNSDFYRNDVAK 292
           +NTPPT+  Y++GL F+WLK        GVA M++ N  KA LLY  ID+S  Y N VA 
Sbjct: 240 YNTPPTWGVYIAGLTFQWLKRQTEGGLTGVAAMEQRNIAKAALLYNAIDSSQLYVNKVAA 299

Query: 293 ANRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTD 352
             RSRMN+PF L D + +  FL  +   GL  LKGH+ VGGMRAS+YNAMP+EGV+AL D
Sbjct: 300 NCRSRMNIPFFLRDESRNDAFLAGAKERGLLQLKGHKSVGGMRASVYNAMPIEGVQALVD 359

Query: 353 FMVEFERRH 361
           +M EFE++H
Sbjct: 360 YMREFEQKH 368


Lambda     K      H
   0.319    0.136    0.405 

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: 399
Number of extensions: 17
Number of successful extensions: 4
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: 362
Length of database: 369
Length adjustment: 30
Effective length of query: 332
Effective length of database: 339
Effective search space:   112548
Effective search space used:   112548
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: 49 (23.5 bits)

Align candidate Ac3H11_2573 (Phosphoserine aminotransferase (EC 2.6.1.52))
to HMM TIGR01364 (serC: phosphoserine transaminase (EC 2.6.1.52))

# 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/TIGR01364.hmm
# target sequence database:        /tmp/gapView.2154.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01364  [M=358]
Accession:   TIGR01364
Description: serC_1: phosphoserine transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   3.4e-148  479.2   0.0   3.9e-148  479.1   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573  Phosphoserine aminotransferase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573  Phosphoserine aminotransferase (EC 2.6.1.52)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.1   0.0  3.9e-148  3.9e-148       2     358 .]       5     368 ..       4     368 .. 0.97

  Alignments for each domain:
  == domain 1  score: 479.1 bits;  conditional E-value: 3.9e-148
                                        TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdn 63 
                                                      +nFsaGPaa+p evle+a++e+ld++g+g++vme+sHR kef ++ e+ae dlreLl +p n
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573   5 YNFSAGPAAIPAEVLEQAAAEMLDWHGSGMGVMEMSHRGKEFLSIYEQAEADLRELLAVPTN 66 
                                                      8************************************************************* PP

                                        TIGR01364  64 yevlflqGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekky 125
                                                      y++lf+qGG+  + a vplnl +++  +d++vtG+ws+k+ kea+k+ +ev++vas+e++ +
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573  67 YKILFMQGGGLAENAIVPLNLSRAG-AVDFVVTGSWSQKSQKEARKYASEVNIVASAEDTGF 127
                                                      **********************999.99********************************** PP

                                        TIGR01364 126 skipdeeelelkedaayvylcanetieGvefkelpevkk....aplvaDlssdilsrkidvs 183
                                                      +++pd  +++++  a+y+++c+neti+G+ef++lp+ k     aplv D+ss++ sr++d s
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 128 TTLPDPASWTVSRGASYLHICSNETINGIEFHQLPDLKAlgsdAPLVIDFSSHVASRPVDWS 189
                                                      ************************************99888889****************** PP

                                        TIGR01364 184 kygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvl 245
                                                      + gl ++GaqKn+GpaG+t+v+vr+dll++a   +ps +dYk++a+n+s+yntppt+++y++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 190 RVGLAFGGAQKNLGPAGLTLVVVREDLLGHALPACPSAFDYKTVADNQSMYNTPPTWGVYIA 251
                                                      ************************************************************** PP

                                        TIGR01364 246 glvlkwlkek..G...GvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlk 302
                                                      gl+++wlk++  G   Gv+++e++n +Ka+llY+aid+s ++y nkv++++Rs+mn++F l+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 252 GLTFQWLKRQteGgltGVAAMEQRNIAKAALLYNAIDSS-QLYVNKVAANCRSRMNIPFFLR 312
                                                      *******9864453446899*****************88.5********************* PP

                                        TIGR01364 303 keelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                                      +e  ++ Fl+ a+e+gl++lkGh+svGG+Ras+Yna+p+e+vqaLvd+m+eFe+kh
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2573 313 DESRNDAFLAGAKERGLLQLKGHKSVGGMRASVYNAMPIEGVQALVDYMREFEQKH 368
                                                      ******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (369 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: 9.30
//
[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