Alignments for a candidate for dapC in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Derxia gummosa DSM 723

Align Phosphoserine aminotransferase, chloroplastic; PSAT; Phosphohydroxythreonine aminotransferase; EC 2.6.1.52 (characterized)
to candidate WP_028311002.1 H566_RS0107805 3-phosphoserine/phosphohydroxythreonine transaminase

Query= SwissProt::P52877
         (430 letters)



>NCBI__GCF_000482785.1:WP_028311002.1
          Length = 366

 Score =  382 bits (980), Expect = e-110
 Identities = 202/367 (55%), Positives = 259/367 (70%), Gaps = 9/367 (2%)

Query: 68  RVFNFAAGPAVLPENVLQKAQSELLNWRGSGMSVMEMSHRGKEFTSIIDKAEADLRTLLN 127
           R FNFAAGPA LP  VLQ+AQ+E+L W+G+G SVME+SHRGK+F +   +AE DLR LL 
Sbjct: 3   RAFNFAAGPATLPLEVLQQAQAEMLEWQGTGCSVMEVSHRGKQFEACNAEAEQDLRDLLA 62

Query: 128 IPSDYTVLFLQGGASTQFSAIPLNLCTPDSAVDYIVTGSWGDKAAKEAAKY-----AAVS 182
           IPS+Y VLFLQGGAS Q++    NLC  +   DYI+TG W ++A  EA K       +V+
Sbjct: 63  IPSNYKVLFLQGGASMQWAQFLFNLCGSNPNGDYILTGEWTNRAVAEARKLLPLWGGSVN 122

Query: 183 SIWSGKSDNYVRIPNFDGSEFVQNSQARYLHICANETIYGVEFKKYPVPANPDGFLVADM 242
            + S +  NY  IP  D   + +   A +LHIC+NETI G+E+   P     D  LVADM
Sbjct: 123 IVASSEDRNYSYIP--DEGSWKRRKDANFLHICSNETIQGLEYNFIPEQLG-DVTLVADM 179

Query: 243 SSNFCSKPVDVTKFGLIYAGAQKNVGPSGVTIVIVRNDLIGNAQKMTPVMLDYKIHADNK 302
           SS+  S+PVDV+++GLIYAGAQKN+GP+G+TIVIVR+DLIG A+  TP M DYK+ ADN 
Sbjct: 180 SSHIVSRPVDVSRYGLIYAGAQKNIGPAGITIVIVRDDLIGKARPDTPRMFDYKLMADNH 239

Query: 303 SLYNTPPCYGIYMCGLVFEDLLNQGGLVEVEKKNKAKAQVLYDAIDESNGFYKCPVEKSV 362
           SL NTPP +GIY+ GLVF+ L  QGG+  +E+KN AKA++LY  +D S  FY  PVEK  
Sbjct: 240 SLLNTPPTFGIYLAGLVFKWLKRQGGVEAIERKNIAKAELLYGYLD-SQDFYYAPVEKGS 298

Query: 363 RSLMNVPFTLEKSELEGDFIKEAAKEKMVALKGHRSVGGMRASIYNAMPLAGVEKLVAFM 422
           RS MNVPF L+   L   F+ E     +VALKGH++VGGMRASIYNAMP+ GV+ LVAFM
Sbjct: 299 RSRMNVPFRLKDESLNAKFLAETEAAGLVALKGHKAVGGMRASIYNAMPMEGVQALVAFM 358

Query: 423 KEFQAKH 429
           ++F A++
Sbjct: 359 RDFAARN 365


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: 434
Number of extensions: 17
Number of successful extensions: 4
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: 430
Length of database: 366
Length adjustment: 31
Effective length of query: 399
Effective length of database: 335
Effective search space:   133665
Effective search space used:   133665
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_028311002.1 H566_RS0107805 (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.10047.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-159  515.5   0.0   3.6e-159  515.3   0.0    1.0  1  lcl|NCBI__GCF_000482785.1:WP_028311002.1  H566_RS0107805 3-phosphoserine/p


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_028311002.1  H566_RS0107805 3-phosphoserine/phosphohydroxythreonine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  515.3   0.0  3.6e-159  3.6e-159       2     357 ..       5     364 ..       4     365 .. 0.98

  Alignments for each domain:
  == domain 1  score: 515.3 bits;  conditional E-value: 3.6e-159
                                 TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 
                                               +nF+aGPa+lp evl++aq+e+l+++g+g+svme+sHR k+fe+   eae+dlr+Ll ip+ny+vlflq
  lcl|NCBI__GCF_000482785.1:WP_028311002.1   5 FNFAAGPATLPLEVLQQAQAEMLEWQGTGCSVMEVSHRGKQFEACNAEAEQDLRDLLAIPSNYKVLFLQ 73 
                                               8******************************************************************** PP

                                 TIGR01364  71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltk....evkvvaseeekkyskipdeeele 135
                                               GGa+ q+a+  +nl+ ++ + dyi tG+w+++a++ea+kl      +v++vas+e+++ys ipde +++
  lcl|NCBI__GCF_000482785.1:WP_028311002.1  74 GGASMQWAQFLFNLCGSNPNGDYILTGEWTNRAVAEARKLLPlwggSVNIVASSEDRNYSYIPDEGSWK 142
                                               ***************************************98888899********************** PP

                                 TIGR01364 136 lkedaayvylcanetieGvefkelpevkk.aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtv 203
                                                ++da+++++c+neti+G+e++ +pe+   ++lvaD+ss+i+sr++dvs+ygliyaGaqKniGpaG+t+
  lcl|NCBI__GCF_000482785.1:WP_028311002.1 143 RRKDANFLHICSNETIQGLEYNFIPEQLGdVTLVADMSSHIVSRPVDVSRYGLIYAGAQKNIGPAGITI 211
                                               *************************87655*************************************** PP

                                 TIGR01364 204 vivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakll 272
                                               vivr+dl+++a+ ++p ++dYk +a+n+sl+ntpptf+iy++glv+kwlk++GGv+++e+kn +Ka+ll
  lcl|NCBI__GCF_000482785.1:WP_028311002.1 212 VIVRDDLIGKARPDTPRMFDYKLMADNHSLLNTPPTFGIYLAGLVFKWLKRQGGVEAIERKNIAKAELL 280
                                               ********************************************************************* PP

                                 TIGR01364 273 YeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpl 341
                                               Y ++d++ +fy ++vek +Rs+mnv+F+lk+e l+++Fl+e+e++glv+lkGh++vGG+RasiYna+p+
  lcl|NCBI__GCF_000482785.1:WP_028311002.1 281 YGYLDSQ-DFYYAPVEKGSRSRMNVPFRLKDESLNAKFLAETEAAGLVALKGHKAVGGMRASIYNAMPM 348
                                               *****55.6************************************************************ PP

                                 TIGR01364 342 eevqaLvdfmkeFekk 357
                                               e+vqaLv+fm++F+++
  lcl|NCBI__GCF_000482785.1:WP_028311002.1 349 EGVQALVAFMRDFAAR 364
                                               *************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (366 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 12.21
//
[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