Alignments for a candidate for serC in Hydrogenovibrio marinus DSM 11271

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Hydrogenovibrio marinus DSM 11271

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_029908941.1 P166_RS0103880 3-phosphoserine/phosphohydroxythreonine transaminase

Query= BRENDA::P23721
         (362 letters)



>NCBI__GCF_000711315.1:WP_029908941.1
          Length = 354

 Score =  392 bits (1006), Expect = e-113
 Identities = 196/357 (54%), Positives = 248/357 (69%), Gaps = 7/357 (1%)

Query: 5   FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64
           FNFS+GPAMLP EV+++AQ E  DW   G SVMEVSHR KEF+ +A + E D R+++++P
Sbjct: 4   FNFSAGPAMLPEEVMRKAQAEFLDWKNTGMSVMEVSHRSKEFMALAHKMEADLREVMHIP 63

Query: 65  SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124
            NYKVLF HGG   QF A+P+N+  +  T DY++ G W+  AIKEA +Y   N      T
Sbjct: 64  DNYKVLFVHGGASLQFTAIPMNLTQEGDTVDYINTGVWSEKAIKEASRYVNVNEVATSET 123

Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184
                A+    E   S +A Y+H C NETI G+     P    D ++ ADFSSTILSRPI
Sbjct: 124 -----AIPNFDEMTFSKDAKYIHICQNETITGVEYQSLPK--TDKIIVADFSSTILSRPI 176

Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244
           +VS YGVIYAGAQKNIGPAGL IVIVREDL+G A    P+++++   NDN SMFNTP T+
Sbjct: 177 NVSDYGVIYAGAQKNIGPAGLAIVIVREDLIGNARSDTPTLMNWQTYNDNESMFNTPSTY 236

Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304
           AWYL+ LVF+W+K  GGV +M +INQ+KA  LY ++D SDFY N++  + RS MNV F+L
Sbjct: 237 AWYLASLVFEWIKDQGGVEKMAEINQRKANKLYELVDASDFYYNEIEPSVRSWMNVTFKL 296

Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRH 361
            +  LD LFLEES  AGL +LKGH+V GGMRASIYNAMP  G+ AL  FM +FE +H
Sbjct: 297 KNPELDTLFLEESKKAGLLSLKGHKVYGGMRASIYNAMPEAGIDALVSFMKDFEEKH 353


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: 389
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: 354
Length adjustment: 29
Effective length of query: 333
Effective length of database: 325
Effective search space:   108225
Effective search space used:   108225
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_029908941.1 P166_RS0103880 (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.29856.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.1e-158  511.6   0.6   5.7e-158  511.4   0.6    1.0  1  lcl|NCBI__GCF_000711315.1:WP_029908941.1  P166_RS0103880 3-phosphoserine/p


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000711315.1:WP_029908941.1  P166_RS0103880 3-phosphoserine/phosphohydroxythreonine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.4   0.6  5.7e-158  5.7e-158       2     358 .]       4     353 ..       3     353 .. 0.98

  Alignments for each domain:
  == domain 1  score: 511.4 bits;  conditional E-value: 5.7e-158
                                 TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 
                                               +nFsaGPa+lpeev++kaq+e+ld++++g+svme+sHRskef++++++ e dlre+++ipdny+vlf+ 
  lcl|NCBI__GCF_000711315.1:WP_029908941.1   4 FNFSAGPAMLPEEVMRKAQAEFLDWKNTGMSVMEVSHRSKEFMALAHKMEADLREVMHIPDNYKVLFVH 72 
                                               8******************************************************************** PP

                                 TIGR01364  71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139
                                               GGa+ qf+a+p+nl++e++++dyi+tG+ws+ka+kea+++++ v+ va++e    ++ip+ +e+++++d
  lcl|NCBI__GCF_000711315.1:WP_029908941.1  73 GGASLQFTAIPMNLTQEGDTVDYINTGVWSEKAIKEASRYVN-VNEVATSE----TAIPNFDEMTFSKD 136
                                               ****************************************98.88888775....78************ PP

                                 TIGR01364 140 aayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrk 208
                                               a+y+++c+neti+Gve+++lp ++++++vaD+ss ilsr+i+vs+yg+iyaGaqKniGpaG+++vivr+
  lcl|NCBI__GCF_000711315.1:WP_029908941.1 137 AKYIHICQNETITGVEYQSLP-KTDKIIVADFSSTILSRPINVSDYGVIYAGAQKNIGPAGLAIVIVRE 204
                                               *********************.67889****************************************** PP

                                 TIGR01364 209 dllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaid 277
                                               dl+++a++++p+++++++  +n+s++ntp+t+a+y+++lv++w+k++GGv+k+++ nq+Ka+ lYe++d
  lcl|NCBI__GCF_000711315.1:WP_029908941.1 205 DLIGNARSDTPTLMNWQTYNDNESMFNTPSTYAWYLASLVFEWIKDQGGVEKMAEINQRKANKLYELVD 273
                                               ********************************************************************* PP

                                 TIGR01364 278 esegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqa 346
                                               +s+ fy n++e++ Rs+mnv+F+lk+ el++ Fl+e++++gl+slkGh++ GG+RasiYna+p +++ a
  lcl|NCBI__GCF_000711315.1:WP_029908941.1 274 ASD-FYYNEIEPSVRSWMNVTFKLKNPELDTLFLEESKKAGLLSLKGHKVYGGMRASIYNAMPEAGIDA 341
                                               996.***************************************************************** PP

                                 TIGR01364 347 LvdfmkeFekkh 358
                                               Lv+fmk+Fe+kh
  lcl|NCBI__GCF_000711315.1:WP_029908941.1 342 LVSFMKDFEEKH 353
                                               **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (354 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: 9.51
//
[ok]

This GapMind analysis is from Apr 10 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