GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapC in Dechlorosoma suillum PS

Align phosphoserine aminotransferase; EC 2.6.1.52 (characterized)
to candidate Dsui_1939 Dsui_1939 phosphoserine aminotransferase

Query= CharProtDB::CH_002572
         (362 letters)



>lcl|FitnessBrowser__PS:Dsui_1939 Dsui_1939 phosphoserine
           aminotransferase
          Length = 376

 Score =  393 bits (1010), Expect = e-114
 Identities = 207/372 (55%), Positives = 258/372 (69%), Gaps = 15/372 (4%)

Query: 3   QIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLN 62
           +++NFS+GPA LPAEVL+Q Q E+ DW G G  VME+SHRGKEF  +A+ AE D R+L+ 
Sbjct: 2   RLWNFSAGPAALPAEVLEQVQDEMLDWQGAGCGVMEMSHRGKEFTSIAQRAEADLRELMG 61

Query: 63  VPSNYKVLFCHGGGRGQFAAVPLNILG---DKTTADYVDAGYWAASAIKEAKKYC----- 114
           +P+NYKVLF  GG   QFA VPLN+L    DK  ADY+  G W+  A KE  + C     
Sbjct: 62  IPANYKVLFLQGGATQQFAQVPLNLLAGVKDKQPADYIVTGSWSKKAFKETLRVCGETAA 121

Query: 115 --TPNVFDAKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDF----GAD 168
               +  D     DG   +    E Q++ +AAY+H C NETI G+ + +   F     A 
Sbjct: 122 RCIASTEDKAAVADGFTRLPAAAELQVNADAAYLHLCTNETIHGVELLDEAAFLAGVPAG 181

Query: 169 VVVAADFSSTILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDY 228
           V V AD SS ILSRP+DVSRYG+IYAGAQKNIGP+GLT+VIVREDLLGKA  + P++LDY
Sbjct: 182 VPVVADMSSHILSRPMDVSRYGLIYAGAQKNIGPSGLTLVIVREDLLGKAPASLPTVLDY 241

Query: 229 SILNDNGSMFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSD-FYR 287
           +++ +N SM NTPPTFA Y++GLVF+WLK  GG+ EM +IN +KA LLY  ID SD FYR
Sbjct: 242 AVMAENDSMLNTPPTFAIYVAGLVFQWLKRIGGINEMARINAEKARLLYAAIDGSDGFYR 301

Query: 288 NDVAKANRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGV 347
           N V  A RS+MNVPF L D+ALD  FL  +  AGL ALKGH+ VGGMRASIYNAMPL+GV
Sbjct: 302 NPVDPACRSQMNVPFTLRDAALDAEFLAGAKEAGLLALKGHKSVGGMRASIYNAMPLDGV 361

Query: 348 KALTDFMVEFER 359
           +AL  +M  F +
Sbjct: 362 RALVAYMDAFAK 373


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: 410
Number of extensions: 17
Number of successful extensions: 5
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: 376
Length adjustment: 30
Effective length of query: 332
Effective length of database: 346
Effective search space:   114872
Effective search space used:   114872
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 Dsui_1939 Dsui_1939 (phosphoserine aminotransferase)
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.663.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.2e-157  510.3   0.0   1.3e-157  510.2   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_1939  Dsui_1939 phosphoserine aminotra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1939  Dsui_1939 phosphoserine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  510.2   0.0  1.3e-157  1.3e-157       2     356 ..       4     373 ..       3     375 .. 0.94

  Alignments for each domain:
  == domain 1  score: 510.2 bits;  conditional E-value: 1.3e-157
                         TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqfa 78 
                                        nFsaGPaalp evle++q+e+ld++g g++vme+sHR kef++++++ae dlreL+ ip ny+vlflqGGat+qfa
  lcl|FitnessBrowser__PS:Dsui_1939   4 WNFSAGPAALPAEVLEQVQDEMLDWQGAGCGVMEMSHRGKEFTSIAQRAEADLRELMGIPANYKVLFLQGGATQQFA 80 
                                       69*************************************************************************** PP

                         TIGR01364  79 avplnllk...ekkvadyivtGawskkalkeakkltk..evkvvaseee.....kkyskipdeeelelkedaayvyl 145
                                       +vplnll+   +k+ adyivtG+wskka+ke  +++    ++ +as+e+     + ++++p   el+++ daay++l
  lcl|FitnessBrowser__PS:Dsui_1939  81 QVPLNLLAgvkDKQPADYIVTGSWSKKAFKETLRVCGetAARCIASTEDkaavaDGFTRLPAAAELQVNADAAYLHL 157
                                       ******997656779*******************999663444444433111115799******************* PP

                         TIGR01364 146 canetieGvefkelpevkk.....aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakke 217
                                       c+neti+Gve  ++  +       +p+vaD+ss+ilsr++dvs+ygliyaGaqKniGp+G+t+vivr+dll++a ++
  lcl|FitnessBrowser__PS:Dsui_1939 158 CTNETIHGVELLDEAAFLAgvpagVPVVADMSSHILSRPMDVSRYGLIYAGAQKNIGPSGLTLVIVREDLLGKAPAS 234
                                       ***********98887776678889**************************************************** PP

                         TIGR01364 218 lpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRsl 294
                                       lp+vldY+++aends++ntpptfaiyv+glv++wlk+ GG++++++ n eKa+llY aid s+gfy+n+v++++Rs+
  lcl|FitnessBrowser__PS:Dsui_1939 235 LPTVLDYAVMAENDSMLNTPPTFAIYVAGLVFQWLKRIGGINEMARINAEKARLLYAAIDGSDGFYRNPVDPACRSQ 311
                                       ***************************************************************************** PP

                         TIGR01364 295 mnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFek 356
                                       mnv+Ftl+++ l++eFl+ a+e+gl++lkGh+svGG+RasiYna+pl++v+aLv++m  F+k
  lcl|FitnessBrowser__PS:Dsui_1939 312 MNVPFTLRDAALDAEFLAGAKEAGLLALKGHKSVGGMRASIYNAMPLDGVRALVAYMDAFAK 373
                                       ************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (376 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: 00:00:00.01
# Mc/sec: 10.51
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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