Alignments for a candidate for dapC in Desulfotalea psychrophila LSv54

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Desulfotalea psychrophila LSv54

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_011189174.1 DP_RS09895 3-phosphoserine/phosphohydroxythreonine transaminase

Query= SwissProt::Q9RME2
         (361 letters)



>NCBI__GCF_000025945.1:WP_011189174.1
          Length = 361

 Score =  366 bits (940), Expect = e-106
 Identities = 181/360 (50%), Positives = 254/360 (70%), Gaps = 2/360 (0%)

Query: 1   MVKQVFNFNAGPSALPKPALERAQKELLNFNDTQMSVMELSHRSQSYEEVHEQAQNLLRE 60
           M  +V+NF+AGP+ LP   LE+A K+++NF +T   ++E+SHRS  + EV E+ ++L+RE
Sbjct: 1   MADRVYNFSAGPATLPFEVLEQAGKDIVNFKETGSGLIEISHRSPEFIEVIEKTESLVRE 60

Query: 61  LLQIPNDYQILFLQGGASLQFTMLPMNLLTKGTIGNYVLTGSWSEKALKEAKLLGETHIA 120
           LL++P++Y++LFLQGGAS QF M+PMNLL  G    Y+ TG+W++KA+KEA+L G+  +A
Sbjct: 61  LLEVPDNYKVLFLQGGASSQFFMVPMNLLGAGKKATYLNTGTWAKKAIKEAQLFGDIDVA 120

Query: 121 ASTKANSYQSIPDFSEFQLNENDAYLHITSNNTIYGTQYQNFPEINHAPLIADMSSDILS 180
            S++ + +  +P    +Q+ E   YL+  SNNTIYGTQ++  P+ +   L+ADMSSDI S
Sbjct: 121 YSSEESIFNHVPANDAYQVAEESEYLYFASNNTIYGTQFETMPQ-SKKMLVADMSSDIFS 179

Query: 181 RPLKVNQFGMIYAGAQKNLGPSGVTVVIVKKDLLNTKVEQVPTMLQYATHIKSDSLYNTP 240
           R + V++FG+I+AGAQKNLGP+GVT+VI++ DLL       PTML Y TH    S++NTP
Sbjct: 180 RKVDVSKFGLIFAGAQKNLGPAGVTLVIIRDDLLEKTPAHTPTMLSYKTHADKGSMFNTP 239

Query: 241 PTFSIYMLRNVLDWIKDLGGAEAIAKQNEEKAKIIYDTIDESNGFYVGHAEKGSRSLMNV 300
           P F+IY++  VL W+K+LGG E I + N EKA ++Y  ID S+ +Y  HA+ GSRSLMNV
Sbjct: 240 PCFAIYVMGEVLAWLKNLGGVEKIEEINREKAALLYSQIDASD-YYRVHAQDGSRSLMNV 298

Query: 301 TFNLRNEELNQQFLAKAKEQGFVGLNGHRSVGGCRASIYNAVPIDACIALRELMIQFKEN 360
           TFNL   EL  +F+A+A      GL GHRS+GGCRASIYNA P +  + L E M  F  N
Sbjct: 299 TFNLPTAELEAKFIAEASALQMKGLKGHRSIGGCRASIYNAFPREGVVKLVEFMQVFAAN 358


Lambda     K      H
   0.316    0.132    0.372 

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: 376
Number of extensions: 11
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: 361
Length of database: 361
Length adjustment: 29
Effective length of query: 332
Effective length of database: 332
Effective search space:   110224
Effective search space used:   110224
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_011189174.1 DP_RS09895 (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.1523452.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-156  506.7   0.1   1.8e-156  506.5   0.1    1.0  1  NCBI__GCF_000025945.1:WP_011189174.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025945.1:WP_011189174.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  506.5   0.1  1.8e-156  1.8e-156       1     357 [.       5     358 ..       5     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 506.5 bits;  conditional E-value: 1.8e-156
                             TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGa 73 
                                           ++nFsaGPa+lp evle+a k++++f+++g +++eisHRs ef +v+e++es +reLl++pdny+vlflqGGa
  NCBI__GCF_000025945.1:WP_011189174.1   5 VYNFSAGPATLPFEVLEQAGKDIVNFKETGSGLIEISHRSPEFIEVIEKTESLVRELLEVPDNYKVLFLQGGA 77 
                                           59*********************************************************************** PP

                             TIGR01364  74 ttqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylc 146
                                           ++qf +vp+nll ++k+a+y++tG+w+kka+kea+ +++ ++v+ s+ee+ ++++p ++ ++++e+++y+y++
  NCBI__GCF_000025945.1:WP_011189174.1  78 SSQFFMVPMNLLGAGKKATYLNTGTWAKKAIKEAQLFGD-IDVAYSSEESIFNHVPANDAYQVAEESEYLYFA 149
                                           *************************************99.********************************* PP

                             TIGR01364 147 anetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelp 219
                                           +n+ti+G++f+++p ++k++lvaD+ssdi+srk+dvsk+gli+aGaqKn+GpaGvt+vi+r+dlle++ +++p
  NCBI__GCF_000025945.1:WP_011189174.1 150 SNNTIYGTQFETMP-QSKKMLVADMSSDIFSRKVDVSKFGLIFAGAQKNLGPAGVTLVIIRDDLLEKTPAHTP 221
                                           **************.67789***************************************************** PP

                             TIGR01364 220 svldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaR 292
                                           ++l+Yk++a++ s++ntpp+faiyv+g vl wlk+ GGv+k+e+ n+eKa+llY  id+s+ +y+++++  +R
  NCBI__GCF_000025945.1:WP_011189174.1 222 TMLSYKTHADKGSMFNTPPCFAIYVMGEVLAWLKNLGGVEKIEEINREKAALLYSQIDASD-YYRVHAQDGSR 293
                                           **********************************************************996.*********** PP

                             TIGR01364 293 slmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekk 357
                                           slmnv+F+l+ +ele++F++ea++ ++ +lkGhrs+GG+RasiYna+p e+v +Lv+fm+ F+++
  NCBI__GCF_000025945.1:WP_011189174.1 294 SLMNVTFNLPTAELEAKFIAEASALQMKGLKGHRSIGGCRASIYNAFPREGVVKLVEFMQVFAAN 358
                                           **************************************************************876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.86
//
[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