GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Dechlorosoma suillum PS

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

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__PS:Dsui_1939
          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.4251.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.26
//
[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