Alignments for a candidate for dapC in Thiomicrorhabdus chilensis DSM 12352

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Thiomicrorhabdus chilensis DSM 12352

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_028486637.1 B076_RS0106705 3-phosphoserine/phosphohydroxythreonine transaminase

Query= BRENDA::P23721
         (362 letters)



>NCBI__GCF_000483485.1:WP_028486637.1
          Length = 364

 Score =  381 bits (979), Expect = e-110
 Identities = 199/364 (54%), Positives = 242/364 (66%), Gaps = 4/364 (1%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           M + +NFS+GPAMLP  V+++A  E  DWN  G SVME+SHR KE++QVA + E D R++
Sbjct: 1   MTRAYNFSAGPAMLPEPVMRKAADEFLDWNQTGMSVMEMSHRSKEYMQVAHQMEADLREV 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           + +P NYKVLF HGG   QFA +PLN+     T DY + G W+  AIKEA +Y   NV  
Sbjct: 61  MEIPDNYKVLFIHGGASLQFAGIPLNLTQPGDTVDYFNTGVWSTKAIKEASRYVNVNVV- 119

Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETP---DFGADVVVAADFSS 177
           A+   +   A+    EW  S +A Y+H C NETI G+   E      F     V AD SS
Sbjct: 120 AEGDGNNPTAIPARSEWNFSPDAKYIHLCANETITGLEFQEDDLEAVFAQGKPVIADMSS 179

Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237
            I+ RPIDVS+Y +IYAGAQKNIGPAGL IVIVREDLLG+A    P++L++    DN SM
Sbjct: 180 NIMCRPIDVSKYALIYAGAQKNIGPAGLAIVIVREDLLGQARETTPTLLNWQTYADNESM 239

Query: 238 FNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSR 297
           FNTP TFAWYL+GLVF WLK  GGV E+ KINQ KA  LY  ID S+FY N +   NRS 
Sbjct: 240 FNTPATFAWYLAGLVFAWLKEIGGVKEIAKINQAKARKLYEFIDASEFYSNSIVPHNRSW 299

Query: 298 MNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEF 357
           MNV F L +S LD  FLE S +AGL +LKGH+  GGMRASIYNAMP  GV AL +FM EF
Sbjct: 300 MNVTFTLKNSELDGQFLEGSKSAGLLSLKGHKAFGGMRASIYNAMPEAGVDALIEFMREF 359

Query: 358 ERRH 361
             +H
Sbjct: 360 AAKH 363


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: 364
Number of extensions: 12
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: 364
Length adjustment: 29
Effective length of query: 333
Effective length of database: 335
Effective search space:   111555
Effective search space used:   111555
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_028486637.1 B076_RS0106705 (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.23726.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.6e-157  507.9   0.0   7.5e-157  507.7   0.0    1.0  1  lcl|NCBI__GCF_000483485.1:WP_028486637.1  B076_RS0106705 3-phosphoserine/p


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000483485.1:WP_028486637.1  B076_RS0106705 3-phosphoserine/phosphohydroxythreonine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  507.7   0.0  7.5e-157  7.5e-157       2     358 .]       5     363 ..       4     363 .. 0.98

  Alignments for each domain:
  == domain 1  score: 507.7 bits;  conditional E-value: 7.5e-157
                                 TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 
                                               +nFsaGPa+lpe v++ka++e+ld+n++g+svme+sHRske+++v+++ e dlre+++ipdny+vlf+ 
  lcl|NCBI__GCF_000483485.1:WP_028486637.1   5 YNFSAGPAMLPEPVMRKAADEFLDWNQTGMSVMEMSHRSKEYMQVAHQMEADLREVMEIPDNYKVLFIH 73 
                                               8******************************************************************** PP

                                 TIGR01364  71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139
                                               GGa+ qfa +plnl++ ++++dy +tG+ws+ka+kea+++++ v+vva+ + ++ ++ip ++e+++++d
  lcl|NCBI__GCF_000483485.1:WP_028486637.1  74 GGASLQFAGIPLNLTQPGDTVDYFNTGVWSTKAIKEASRYVN-VNVVAEGDGNNPTAIPARSEWNFSPD 141
                                               ****************************************99.************************** PP

                                 TIGR01364 140 aayvylcanetieGvefkelpevkk....aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvv 204
                                               a+y++lcaneti+G+ef+e    +     +p++aD+ss+i+ r+idvsky+liyaGaqKniGpaG+++v
  lcl|NCBI__GCF_000483485.1:WP_028486637.1 142 AKYIHLCANETITGLEFQEDDLEAVfaqgKPVIADMSSNIMCRPIDVSKYALIYAGAQKNIGPAGLAIV 210
                                               ******************654333334569*************************************** PP

                                 TIGR01364 205 ivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllY 273
                                               ivr+dll++a++++p++l++++ a+n+s++ntp+tfa+y++glv+ wlke GGvk+++k nq+Ka+ lY
  lcl|NCBI__GCF_000483485.1:WP_028486637.1 211 IVREDLLGQARETTPTLLNWQTYADNESMFNTPATFAWYLAGLVFAWLKEIGGVKEIAKINQAKARKLY 279
                                               ********************************************************************* PP

                                 TIGR01364 274 eaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalple 342
                                               e id+se fy n++ +++Rs+mnv+Ftlk++el+ +Fl+ ++++gl+slkGh++ GG+RasiYna+p +
  lcl|NCBI__GCF_000483485.1:WP_028486637.1 280 EFIDASE-FYSNSIVPHNRSWMNVTFTLKNSELDGQFLEGSKSAGLLSLKGHKAFGGMRASIYNAMPEA 347
                                               ****996.************************************************************* PP

                                 TIGR01364 343 evqaLvdfmkeFekkh 358
                                               +v aL++fm+eF++kh
  lcl|NCBI__GCF_000483485.1:WP_028486637.1 348 GVDALIEFMREFAAKH 363
                                               *************997 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: 10.19
//
[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