Alignments for a candidate for serC in Thioalkalivibrio thiocyanodenitrificans ARhD 1

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Thioalkalivibrio thiocyanodenitrificans ARhD 1

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_018231476.1 THITHI_RS0102405 3-phosphoserine/phosphohydroxythreonine transaminase

Query= BRENDA::P23721
         (362 letters)



>NCBI__GCF_000378965.1:WP_018231476.1
          Length = 360

 Score =  421 bits (1083), Expect = e-122
 Identities = 213/362 (58%), Positives = 259/362 (71%), Gaps = 2/362 (0%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           M ++FNFS+GPAMLP  VL+QA+ E+ DWNG G SVME+SHRGK F+ +AE AE+D R L
Sbjct: 1   MTRVFNFSAGPAMLPEPVLEQARDEMLDWNGTGMSVMEMSHRGKAFMSIAEAAERDLRVL 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           + +P +YKVLF  GG   QFA VP+N+L  +T  DYV+ G W+  AI EA+++   NV  
Sbjct: 61  MGIPDDYKVLFLQGGASAQFAMVPMNLLRGRTRVDYVNTGAWSGKAIAEARRFADVNVV- 119

Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180
           A     G  A+     WQ +D+AAY+HY PNETI G+     PD G DV + AD SSTIL
Sbjct: 120 ATGEDSGFNAIPAFESWQRTDDAAYLHYTPNETIGGVEFHWIPDTG-DVPLVADMSSTIL 178

Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240
           SRP+DVSRYGVIYAGAQKNIGPAGLTI IVREDL+G+   + P++ DY    ++GSM+NT
Sbjct: 179 SRPVDVSRYGVIYAGAQKNIGPAGLTIAIVREDLIGEVVPSTPTMFDYKTHAESGSMYNT 238

Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV 300
           PPT+ WYL+GLVFKWL   GG+  M  IN++KAE LY  ID SDFY N V  A RS MNV
Sbjct: 239 PPTYGWYLAGLVFKWLLGMGGLEAMAGINRRKAEKLYAAIDGSDFYTNPVNPACRSWMNV 298

Query: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360
           PF LA+  LD  FL+E+ A GL  LKGHR VGGMRASIYNAMP  GV AL DFM +FE+R
Sbjct: 299 PFTLANPDLDGEFLKEAAALGLTTLKGHRSVGGMRASIYNAMPEAGVSALVDFMADFEQR 358

Query: 361 HG 362
            G
Sbjct: 359 KG 360


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: 419
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: 360
Length adjustment: 29
Effective length of query: 333
Effective length of database: 331
Effective search space:   110223
Effective search space used:   110223
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_018231476.1 THITHI_RS0102405 (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.2878867.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-163  527.9   0.0   6.2e-163  527.7   0.0    1.0  1  NCBI__GCF_000378965.1:WP_018231476.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000378965.1:WP_018231476.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.7   0.0  6.2e-163  6.2e-163       1     357 [.       4     358 ..       4     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 527.7 bits;  conditional E-value: 6.2e-163
                             TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGa 73 
                                           ++nFsaGPa+lpe vle+a++e+ld+ng+g+svme+sHR k+f++++e ae+dlr L+ ipd+y+vlflqGGa
  NCBI__GCF_000378965.1:WP_018231476.1   4 VFNFSAGPAMLPEPVLEQARDEMLDWNGTGMSVMEMSHRGKAFMSIAEAAERDLRVLMGIPDDYKVLFLQGGA 76 
                                           58*********************************************************************** PP

                             TIGR01364  74 ttqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylc 146
                                           + qfa+vp+nll+ ++ +dy++tGaws ka++ea+++ + v+vva+ e++ +++ip  e+++ ++daay++++
  NCBI__GCF_000378965.1:WP_018231476.1  77 SAQFAMVPMNLLRGRTRVDYVNTGAWSGKAIAEARRFAD-VNVVATGEDSGFNAIPAFESWQRTDDAAYLHYT 148
                                           *************************************99.********************************* PP

                             TIGR01364 147 anetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelp 219
                                            neti Gvef+++p++ ++plvaD+ss ilsr++dvs+yg+iyaGaqKniGpaG+t+ ivr+dl+++   ++p
  NCBI__GCF_000378965.1:WP_018231476.1 149 PNETIGGVEFHWIPDTGDVPLVADMSSTILSRPVDVSRYGVIYAGAQKNIGPAGLTIAIVREDLIGEVVPSTP 221
                                           ************************************************************************* PP

                             TIGR01364 220 svldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaR 292
                                           +++dYk++ae+ s+yntppt+++y++glv+kwl+  GG+++++  n++Ka+ lY aid s+ fy+n+v++++R
  NCBI__GCF_000378965.1:WP_018231476.1 222 TMFDYKTHAESGSMYNTPPTYGWYLAGLVFKWLLGMGGLEAMAGINRRKAEKLYAAIDGSD-FYTNPVNPACR 293
                                           **********************************************************996.*********** PP

                             TIGR01364 293 slmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekk 357
                                           s+mnv+Ftl++ +l+ eFlkea++ gl++lkGhrsvGG+RasiYna+p ++v aLvdfm +Fe++
  NCBI__GCF_000378965.1:WP_018231476.1 294 SWMNVPFTLANPDLDGEFLKEAAALGLTTLKGHRSVGGMRASIYNAMPEAGVSALVDFMADFEQR 358
                                           **************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (360 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: 00:00:00.02
# Mc/sec: 4.93
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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