Alignments for a candidate for dapC in Desulfacinum hydrothermale DSM 13146

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Desulfacinum hydrothermale DSM 13146

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_084057322.1 B9A12_RS07725 3-phosphoserine/phosphohydroxythreonine transaminase

Query= SwissProt::Q59196
         (362 letters)



>NCBI__GCF_900176285.1:WP_084057322.1
          Length = 361

 Score =  393 bits (1010), Expect = e-114
 Identities = 204/364 (56%), Positives = 262/364 (71%), Gaps = 5/364 (1%)

Query: 1   MSKRAYNFNAGPAALPLEVLERAQAEFVDYQHTGMSIMEMSHRGAVYEAVHNEAQARLLA 60
           MS R YNFN GPAALPL VLE+AQ E ++Y+ +GMSI+E+SHR A ++ V N+A AR   
Sbjct: 1   MSHRIYNFNPGPAALPLPVLEQAQGELLNYRGSGMSILEVSHRSAWFDEVLNDAVARTKR 60

Query: 61  LLGNPTGYKVLFIQGGASTQFAMIPMNFLKEGQTANYVMTGSWASKALKEAKLIG-DTHV 119
           LLG    ++VLF+QGGAS QF + PMN     +  +YV TG+W++KA+KEA++ G +  V
Sbjct: 61  LLGLDERFRVLFMQGGASLQFCLAPMNLSAGDKPLDYVDTGTWSTKAIKEARIQGKNVRV 120

Query: 120 AASSEASNYMTLPKLQEIQLQDNAAYLHLTSNETIEGAQFKAFPDTGSVPLIGDMSSDIL 179
            ASSE  NY  +P   +I + + AA+LH+TSN TI G QF+ FP    VPLI DMSSDI 
Sbjct: 121 IASSEDRNYTYIPT--DIPVDEEAAFLHITSNNTIRGTQFREFPKAEKVPLISDMSSDIF 178

Query: 180 SRPFDLNQFGLVYAGAQKNLGPSGVTVVIVREDLVAESPKHLPTMLRYDTYVKNNSLYNT 239
           SR FD + FGL+YAGAQKN GP+GVT+VIVRED++   P  LPTML+Y TY + NSLYNT
Sbjct: 179 SRRFDPSPFGLIYAGAQKNAGPAGVTLVIVREDMLERVPAELPTMLKYTTYAEKNSLYNT 238

Query: 240 PPSFGIYMVNEVLKWIEER-GGLEGVQQANRKKASLIYDAIDQSGGFYRGCVDVDSRSDM 298
           PP+F IY+   VLKW+EE  GGLE +++ NR+KA L+Y  +D +  FYRG  +  SRS M
Sbjct: 239 PPAFAIYITGLVLKWLEEEIGGLERMEEINRRKAELLYGYLD-AQDFYRGTAEPASRSWM 297

Query: 299 NITFRLASEELEKEFVKASEQEGFVGLKGHRSVGGLRASIYNAVPYESCEALVQFMEHFK 358
           N+TFRL SEELEK F++ +++ G  GLKGHRSVGG RASIYNA+P E  EALV +M+ F 
Sbjct: 298 NVTFRLPSEELEKAFIEEAQRNGLGGLKGHRSVGGCRASIYNAMPLEGVEALVNWMKDFA 357

Query: 359 RSRG 362
              G
Sbjct: 358 AKNG 361


Lambda     K      H
   0.316    0.132    0.378 

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: 411
Number of extensions: 13
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: 362
Length of database: 361
Length adjustment: 29
Effective length of query: 333
Effective length of database: 332
Effective search space:   110556
Effective search space used:   110556
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_084057322.1 B9A12_RS07725 (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.2828792.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-148  478.5   0.0   6.5e-148  478.3   0.0    1.0  1  NCBI__GCF_900176285.1:WP_084057322.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900176285.1:WP_084057322.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.3   0.0  6.5e-148  6.5e-148       1     357 [.       5     359 ..       5     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 478.3 bits;  conditional E-value: 6.5e-148
                             TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGa 73 
                                           i+nF++GPaalp  vle+aq ell+++g+g+s++e+sHRs  f++v+++a    ++Ll + + ++vlf+qGGa
  NCBI__GCF_900176285.1:WP_084057322.1   5 IYNFNPGPAALPLPVLEQAQGELLNYRGSGMSILEVSHRSAWFDEVLNDAVARTKRLLGLDERFRVLFMQGGA 77 
                                           69*********************************************************************** PP

                             TIGR01364  74 ttqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylc 146
                                           + qf   p+nl + +k  dy+ tG+ws+ka+kea++ +k+v+v+as+e+++y+ ip   ++ ++e+aa+++++
  NCBI__GCF_900176285.1:WP_084057322.1  78 SLQFCLAPMNLSAGDKPLDYVDTGTWSTKAIKEARIQGKNVRVIASSEDRNYTYIP--TDIPVDEEAAFLHIT 148
                                           ********************************************************..88999********** PP

                             TIGR01364 147 anetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelp 219
                                           +n+ti+G++f+e p+ +k+pl++D+ssdi+sr++d s +gliyaGaqKn+GpaGvt+vivr+d+ler  +elp
  NCBI__GCF_900176285.1:WP_084057322.1 149 SNNTIRGTQFREFPKAEKVPLISDMSSDIFSRRFDPSPFGLIYAGAQKNAGPAGVTLVIVREDMLERVPAELP 221
                                           ************************************************************************* PP

                             TIGR01364 220 svldYkilaendslyntpptfaiyvlglvlkwlkek.GGvkklekknqeKakllYeaidesegfyknkvekka 291
                                           ++l+Y++ ae++slyntpp faiy++glvlkwl e+ GG++++e+ n++Ka+llY ++d+++ fy++++e+++
  NCBI__GCF_900176285.1:WP_084057322.1 222 TMLKYTTYAEKNSLYNTPPAFAIYITGLVLKWLEEEiGGLERMEEINRRKAELLYGYLDAQD-FYRGTAEPAS 293
                                           *********************************8654**********************885.********** PP

                             TIGR01364 292 RslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekk 357
                                           Rs+mnv+F+l++eelek F++ea+++gl +lkGhrsvGG+RasiYna+ple+v+aLv++mk+F++k
  NCBI__GCF_900176285.1:WP_084057322.1 294 RSWMNVTFRLPSEELEKAFIEEAQRNGLGGLKGHRSVGGCRASIYNAMPLEGVEALVNWMKDFAAK 359
                                           ***************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (361 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: 00:00:00.00
# Mc/sec: 29.41
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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