Alignments for a candidate for serC in Xenophilus azovorans DSM 13620

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Xenophilus azovorans DSM 13620

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_051953201.1 Q392_RS09580 3-phosphoserine/phosphohydroxythreonine transaminase

Query= BRENDA::P23721
         (362 letters)



>NCBI__GCF_000745855.1:WP_051953201.1
          Length = 355

 Score =  337 bits (865), Expect = 2e-97
 Identities = 184/357 (51%), Positives = 232/357 (64%), Gaps = 12/357 (3%)

Query: 14  LPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVPSNYKVLFCH 73
           +P  VL+QA  ++ DW G G SVME+SHRGKEF  + ++AE+DFR LL VP  + VLF  
Sbjct: 1   MPEAVLRQAAADMLDWQGSGMSVMEMSHRGKEFGTIRDQAEQDFRALLAVPDEFHVLFMQ 60

Query: 74  GGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVTVDGLRAVKP 133
           GGG G+ A VPLN L      D+V  G W+A + KEA++YC   V  A    D      P
Sbjct: 61  GGGLGENAIVPLN-LSRGAGVDFVVTGSWSAKSQKEAQRYCRARV--AASNADSRHTALP 117

Query: 134 M-REWQLSDNAAYMHYCPNETIDGIAIDETPDF---GADVVVAADFSSTILSRPIDVSRY 189
               WQL  +AAY+H C NETI G+   E PD    G+   +  DFSS + SR +D  R 
Sbjct: 118 APSSWQLDPDAAYVHLCSNETIHGVEFQELPDLQALGSRAPLVIDFSSHVASRRVDWRRV 177

Query: 190 GVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTFAWYLS 249
           G+ + GAQKN+GPAGLTIV+VR++LL +A   CPS  +Y ++ DN SM+NTPPT+  Y++
Sbjct: 178 GLAFGGAQKNLGPAGLTIVVVRDELLDRALEICPSAFNYRLVADNHSMYNTPPTWGIYMA 237

Query: 250 GLVFKWLKANG-----GVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304
           GL F+WL A       GV  M + N++KAELLYG ID S FY N+VA   RSRMNVPF L
Sbjct: 238 GLTFRWLLAQAEGDLRGVDAMAERNRRKAELLYGYIDASPFYFNEVAPECRSRMNVPFFL 297

Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRH 361
            D + +  FLE +  AGL  LKGH+ VGGMRASIYNAMPLEGV+AL  +M EFER H
Sbjct: 298 RDESRNADFLEGARQAGLLQLKGHKSVGGMRASIYNAMPLEGVQALVSYMREFERLH 354


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: 374
Number of extensions: 15
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: 355
Length adjustment: 29
Effective length of query: 333
Effective length of database: 326
Effective search space:   108558
Effective search space used:   108558
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 WP_051953201.1 Q392_RS09580 (3-phosphoserine/phosphohydroxythreonine transaminase)
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.12353.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-139  450.1   0.0   2.7e-139  450.0   0.0    1.0  1  lcl|NCBI__GCF_000745855.1:WP_051953201.1  Q392_RS09580 3-phosphoserine/pho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000745855.1:WP_051953201.1  Q392_RS09580 3-phosphoserine/phosphohydroxythreonine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.0   0.0  2.7e-139  2.7e-139      11     358 .]       1     354 [.       1     354 [. 0.97

  Alignments for each domain:
  == domain 1  score: 450.0 bits;  conditional E-value: 2.7e-139
                                 TIGR01364  11 lpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqfaa 79 
                                               +pe+vl++a++++ld++g+g+svme+sHR kef ++ ++ae+d+r Ll +pd+++vlf+qGG+ ++ a 
  lcl|NCBI__GCF_000745855.1:WP_051953201.1   1 MPEAVLRQAAADMLDWQGSGMSVMEMSHRGKEFGTIRDQAEQDFRALLAVPDEFHVLFMQGGGLGENAI 69 
                                               89******************************************************************* PP

                                 TIGR01364  80 vplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcan 148
                                               vplnl +    +d++vtG+ws+k+ kea+++++ ++v+as++++ ++++p  ++++l++daayv+lc+n
  lcl|NCBI__GCF_000745855.1:WP_051953201.1  70 VPLNLSRGA-GVDFVVTGSWSAKSQKEAQRYCR-ARVAASNADSRHTALPAPSSWQLDPDAAYVHLCSN 136
                                               *****9977.79********************9.999999999************************** PP

                                 TIGR01364 149 etieGvefkelpevkk....aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdller 213
                                               eti+Gvef+elp+ +     aplv D+ss++ sr++d  + gl ++GaqKn+GpaG+t+v+vr++ll+r
  lcl|NCBI__GCF_000745855.1:WP_051953201.1 137 ETIHGVEFQELPDLQAlgsrAPLVIDFSSHVASRRVDWRRVGLAFGGAQKNLGPAGLTIVVVRDELLDR 205
                                               ************998888889************************************************ PP

                                 TIGR01364 214 akkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekG.....GvkklekknqeKakllYeaid 277
                                               a +++ps ++Y+ +a+n+s+yntppt++iy++gl+++wl+++      Gv++++++n++Ka+llY +id
  lcl|NCBI__GCF_000745855.1:WP_051953201.1 206 ALEICPSAFNYRLVADNHSMYNTPPTWGIYMAGLTFRWLLAQAegdlrGVDAMAERNRRKAELLYGYID 274
                                               ***************************************9874447779******************** PP

                                 TIGR01364 278 esegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqa 346
                                               +s  fy n+v++++Rs+mnv+F l++e  ++ Fl+ a+++gl++lkGh+svGG+RasiYna+ple+vqa
  lcl|NCBI__GCF_000745855.1:WP_051953201.1 275 ASP-FYFNEVAPECRSRMNVPFFLRDESRNADFLEGARQAGLLQLKGHKSVGGMRASIYNAMPLEGVQA 342
                                               997.***************************************************************** PP

                                 TIGR01364 347 LvdfmkeFekkh 358
                                               Lv++m+eFe+ h
  lcl|NCBI__GCF_000745855.1:WP_051953201.1 343 LVSYMREFERLH 354
                                               ********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (355 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: 9.46
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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