Alignments for a candidate for serC in Pelobacter propionicus DSM 2379

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Pelobacter propionicus DSM 2379

Align Phosphoserine aminotransferase, chloroplastic; PSAT; Phosphohydroxythreonine aminotransferase; EC 2.6.1.52 (characterized)
to candidate WP_011734678.1 PPRO_RS03600 3-phosphoserine/phosphohydroxythreonine transaminase

Query= SwissProt::P52877
         (430 letters)



>NCBI__GCF_000015045.1:WP_011734678.1
          Length = 364

 Score =  344 bits (882), Expect = 3e-99
 Identities = 188/371 (50%), Positives = 246/371 (66%), Gaps = 15/371 (4%)

Query: 67  ERVFNFAAGPAVLPENVLQKAQSELLNWRGSGMSVMEMSHRGKEFTSIIDKAEADLRTLL 126
           +R +NF+AGP++LPE+VL KA  E+L +  SG SVMEMSHR K F +II  AEA +R  +
Sbjct: 2   KRFYNFSAGPSMLPESVLAKAADEMLCYETSGQSVMEMSHRSKPFEAIIAGAEALVRQNM 61

Query: 127 NIPSDYTVLFLQGGASTQFSAIPLNLCTPDSAVDYIVTGSWGDKAAKEAAKYAAVSSIWS 186
            IP DY VLFLQGGAS QF  +PLN  T +   D+ +TG+W  KAA+EA +    + + S
Sbjct: 62  AIPDDYHVLFLQGGASLQFHMLPLNFMTINKKADFTLTGTWAQKAAEEAKRLGTANIVGS 121

Query: 187 GKSDNYVRIPNFDGSEFVQNSQARYLHICANETIYGVEFKKYP-VPANPDGFLVADMSSN 245
            K   +  +P   G++     +A Y HIC N TI G ++   P V A P   L+ D+SS 
Sbjct: 122 SKDKKWSYLPEITGAD----PEADYFHICYNNTIEGTQYHSIPEVGAVP---LIGDISSG 174

Query: 246 FCSKPVDVTKFGLIYAGAQKNVGPSGVTIVIVRNDLIGNAQKMTPVMLDYKIHADNKSLY 305
             S P+DVT+F ++YAGAQKN+GP+GVT+VI+R D++       P ML YK H D  S+Y
Sbjct: 175 VLSAPLDVTRFAVLYAGAQKNLGPAGVTLVIIRKDMMERIPAGLPAMLSYKTHVDGGSMY 234

Query: 306 NTPPCYGIYMCGLVFEDLLNQGGLVEVEKKNKAKAQVLYDAIDESNGFYKCPVEKSVRSL 365
           NTPPCY IY+  LV E + + GG   + ++N+ KA++LYD +D S+ F+  PVEKSVRSL
Sbjct: 235 NTPPCYAIYIFKLVQEWIRDMGGAEVIYRQNQEKARLLYDFLDSSSLFFS-PVEKSVRSL 293

Query: 366 MNVPF-TLEK-----SELEGDFIKEAAKEKMVALKGHRSVGGMRASIYNAMPLAGVEKLV 419
           MNVPF T EK       L   F+KE+    +V L GHRSVGGMRASIYNAMPL GV+ LV
Sbjct: 294 MNVPFLTTEKDADKAEALNKKFVKESEAAGLVNLAGHRSVGGMRASIYNAMPLEGVQALV 353

Query: 420 AFMKEFQAKHA 430
           AFMKEF+A+ A
Sbjct: 354 AFMKEFEARCA 364


Lambda     K      H
   0.317    0.132    0.383 

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: 443
Number of extensions: 22
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 430
Length of database: 364
Length adjustment: 31
Effective length of query: 399
Effective length of database: 333
Effective search space:   132867
Effective search space used:   132867
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_011734678.1 PPRO_RS03600 (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.26590.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.8e-145  468.2   0.0   8.8e-145  468.0   0.0    1.0  1  lcl|NCBI__GCF_000015045.1:WP_011734678.1  PPRO_RS03600 3-phosphoserine/pho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015045.1:WP_011734678.1  PPRO_RS03600 3-phosphoserine/phosphohydroxythreonine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  468.0   0.0  8.8e-145  8.8e-145       2     356 ..       5     361 ..       4     363 .. 0.97

  Alignments for each domain:
  == domain 1  score: 468.0 bits;  conditional E-value: 8.8e-145
                                 TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 
                                               +nFsaGP++lpe+vl+ka++e+l ++ +g svme+sHRsk fe+++  ae  +r+ + ipd+y+vlflq
  lcl|NCBI__GCF_000015045.1:WP_011734678.1   5 YNFSAGPSMLPESVLAKAADEMLCYETSGQSVMEMSHRSKPFEAIIAGAEALVRQNMAIPDDYHVLFLQ 73 
                                               8******************************************************************** PP

                                 TIGR01364  71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139
                                               GGa+ qf ++pln+++ +k+ad+  tG+w++ka++eak+l++ +++v s+++kk+s +p+      +++
  lcl|NCBI__GCF_000015045.1:WP_011734678.1  74 GGASLQFHMLPLNFMTINKKADFTLTGTWAQKAAEEAKRLGT-ANIVGSSKDKKWSYLPEI--TGADPE 139
                                               ****************************************99.99**************55..566789 PP

                                 TIGR01364 140 aayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrk 208
                                               a+y+++c n+tieG++++++pev  +pl+ D+ss +ls ++dv++++++yaGaqKn+GpaGvt+vi+rk
  lcl|NCBI__GCF_000015045.1:WP_011734678.1 140 ADYFHICYNNTIEGTQYHSIPEVGAVPLIGDISSGVLSAPLDVTRFAVLYAGAQKNLGPAGVTLVIIRK 208
                                               99******************************************************************* PP

                                 TIGR01364 209 dllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaid 277
                                               d++er+ + lp +l+Yk++++  s+yntpp++aiy+++lv +w+++ GG + + ++nqeKa+llY+ +d
  lcl|NCBI__GCF_000015045.1:WP_011734678.1 209 DMMERIPAGLPAMLSYKTHVDGGSMYNTPPCYAIYIFKLVQEWIRDMGGAEVIYRQNQEKARLLYDFLD 277
                                               ********************************************************************* PP

                                 TIGR01364 278 esegfyknkvekkaRslmnvvFtlkke......elekeFlkeaeekglvslkGhrsvGGiRasiYnalp 340
                                               +s+ ++ ++vek+ Rslmnv+F ++++       l+k+F+ke+e++glv+l GhrsvGG+RasiYna+p
  lcl|NCBI__GCF_000015045.1:WP_011734678.1 278 SSS-LFFSPVEKSVRSLMNVPFLTTEKdadkaeALNKKFVKESEAAGLVNLAGHRSVGGMRASIYNAMP 345
                                               887.8889**************887766788888*********************************** PP

                                 TIGR01364 341 leevqaLvdfmkeFek 356
                                               le+vqaLv+fmkeFe+
  lcl|NCBI__GCF_000015045.1:WP_011734678.1 346 LEGVQALVAFMKEFEA 361
                                               **************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (364 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: 6.87
//
[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