GapMind for Amino acid biosynthesis

 

Aligments for a candidate for serC in Pseudomonas stutzeri RCH2

Align phosphoserine aminotransferase; EC 2.6.1.52 (characterized)
to candidate GFF1940 Psest_1983 phosphoserine aminotransferase

Query= CharProtDB::CH_002572
         (362 letters)



>lcl|FitnessBrowser__psRCH2:GFF1940 Psest_1983 phosphoserine
           aminotransferase
          Length = 361

 Score =  416 bits (1068), Expect = e-121
 Identities = 208/358 (58%), Positives = 260/358 (72%), Gaps = 2/358 (0%)

Query: 5   FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64
           FNF +GPA LP  VL++AQ EL DW+G G SVME+SHR  E+  +AE+AE+D RDLL +P
Sbjct: 6   FNFCAGPAALPEAVLQRAQAELLDWHGKGLSVMEMSHRSDEYTAIAEKAEQDLRDLLAIP 65

Query: 65  SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124
           SNYKVLF  GG   QFA +PLN+L +   ADY+D G W+  AI+EA+++   NV  +   
Sbjct: 66  SNYKVLFLQGGASQQFAEIPLNLLPEDGVADYIDTGIWSRKAIEEARRFGNVNVAASAKP 125

Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184
           +D   A+    +WQLS+ AAY+HY  NETI G+  D  P+ G D  +  D SS ILSR I
Sbjct: 126 LDYF-AIPGQNDWQLSERAAYLHYASNETIGGLQFDWVPEVG-DTPLVVDMSSDILSRTI 183

Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244
           DVS++G+IYAGAQKNIGP+GL +VIVREDLLG+A  ACP++LDY I  DNGSM+NTP TF
Sbjct: 184 DVSKFGLIYAGAQKNIGPSGLVVVIVREDLLGRARSACPTMLDYKIAADNGSMYNTPATF 243

Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304
           +WYLSGLVF+WLK  GGV  M++ N+ K ++LYG ID SDFY N +A   RS MNVPF+L
Sbjct: 244 SWYLSGLVFEWLKEQGGVEAMEQRNRAKKDMLYGAIDASDFYTNPIAVNARSWMNVPFRL 303

Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
           AD  LDK FL  + A GL  LKGHR VGGMRASIYNA+ L+ V+AL  +M EFE+ HG
Sbjct: 304 ADERLDKSFLAGADARGLLNLKGHRSVGGMRASIYNAVGLDAVEALVAYMAEFEKEHG 361


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: 421
Number of extensions: 13
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: 362
Length of database: 361
Length adjustment: 29
Effective length of query: 333
Effective length of database: 332
Effective search space:   110556
Effective search space used:   110556
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 GFF1940 Psest_1983 (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.5484.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.7e-168  544.3   0.0   6.4e-168  544.1   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1940  Psest_1983 phosphoserine aminotr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1940  Psest_1983 phosphoserine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  544.1   0.0  6.4e-168  6.4e-168       2     358 .]       6     360 ..       5     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 544.1 bits;  conditional E-value: 6.4e-168
                           TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattq 76 
                                         +nF+aGPaalpe+vl++aq+elld++g+glsvme+sHRs+e+++++e+ae+dlr+Ll ip+ny+vlflqGGa++q
  lcl|FitnessBrowser__psRCH2:GFF1940   6 FNFCAGPAALPEAVLQRAQAELLDWHGKGLSVMEMSHRSDEYTAIAEKAEQDLRDLLAIPSNYKVLFLQGGASQQ 80 
                                         8************************************************************************** PP

                           TIGR01364  77 faavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcaneti 151
                                         fa++plnll e+ vadyi tG ws+ka++ea+++++ v+v+as++  +y +ip +++++l+e+aay+++++neti
  lcl|FitnessBrowser__psRCH2:GFF1940  81 FAEIPLNLLPEDGVADYIDTGIWSRKAIEEARRFGN-VNVAASAKPLDYFAIPGQNDWQLSERAAYLHYASNETI 154
                                         **********************************99.************************************** PP

                           TIGR01364 152 eGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYki 226
                                          G++f+++pev ++plv+D+ssdilsr+idvsk+gliyaGaqKniGp+G++vvivr+dll+ra++ +p++ldYki
  lcl|FitnessBrowser__psRCH2:GFF1940 155 GGLQFDWVPEVGDTPLVVDMSSDILSRTIDVSKFGLIYAGAQKNIGPSGLVVVIVREDLLGRARSACPTMLDYKI 229
                                         *************************************************************************** PP

                           TIGR01364 227 laendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtl 301
                                         +a+n s+yntp+tf++y++glv++wlke+GGv+++e++n++K+++lY aid+s+ fy+n+++ +aRs+mnv+F+l
  lcl|FitnessBrowser__psRCH2:GFF1940 230 AADNGSMYNTPATFSWYLSGLVFEWLKEQGGVEAMEQRNRAKKDMLYGAIDASD-FYTNPIAVNARSWMNVPFRL 303
                                         ***************************************************996.******************** PP

                           TIGR01364 302 kkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                         ++e+l+k+Fl+ a ++gl++lkGhrsvGG+RasiYna+ l++v+aLv++m eFek+h
  lcl|FitnessBrowser__psRCH2:GFF1940 304 ADERLDKSFLAGADARGLLNLKGHRSVGGMRASIYNAVGLDAVEALVAYMAEFEKEH 360
                                         ******************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (361 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: 9.68
//
[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 preprint 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