Alignments for a candidate for dapC in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Nocardiopsis lucentensis DSM 44048

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_026127746.1 D471_RS0114915 phosphoserine transaminase

Query= BRENDA::P9WQ73
         (376 letters)



>NCBI__GCF_000341125.1:WP_026127746.1
          Length = 374

 Score =  508 bits (1307), Expect = e-148
 Identities = 246/373 (65%), Positives = 299/373 (80%), Gaps = 1/373 (0%)

Query: 5   LTPHLEIPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSG 64
           +T  ++IP  + P DGRFGSGPSKVR EQL+ L ++ A   GTSHRQ PVK+LV RVRSG
Sbjct: 1   MTDDIQIPANLLPSDGRFGSGPSKVRPEQLEALASSGARYMGTSHRQKPVKSLVSRVRSG 60

Query: 65  LAELFSLPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGE 124
           +++LFSLP+GYEV+LGNGG TAFWD AA GL+  +S HL +GEFS+KFA   +  P++ E
Sbjct: 61  VSDLFSLPEGYEVVLGNGGTTAFWDIAAHGLLRSKSQHLAFGEFSSKFAKVAAGAPWLEE 120

Query: 125 PIIITSDPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRRPEGSDD-ALVVIDATSGAGG 183
           P ++++DPGS  E   +  VDV A  HNETSTGVA  +RR  G+DD ALV++DATSGAGG
Sbjct: 121 PTVVSTDPGSHGEAVAEAGVDVYALTHNETSTGVAAPIRRVAGADDDALVLVDATSGAGG 180

Query: 184 LPVDIAETDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVEN 243
           LPVDIAETD YYFAPQK+FA+DGGLW+A+MSP AL+R+E IAA GR++P+F SL  AV N
Sbjct: 181 LPVDIAETDVYYFAPQKSFAADGGLWIAVMSPRALARVEEIAAGGRYIPEFFSLTTAVAN 240

Query: 244 SLKNQTYNTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVT 303
           S K+QTYNTPA+ATL LLAEQ++W+   GGL+W V RTA+SS  LY WA++ P  +PFVT
Sbjct: 241 SRKDQTYNTPAVATLLLLAEQLEWMNTRGGLEWTVARTAESSSILYDWAEKSPVASPFVT 300

Query: 304 DPGLRSQVVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVS 363
           DP  RSQVVGTIDF DDVDA  +AK+LRANG+VDTEPYRKLGRNQLRVAMFPAVEP DV 
Sbjct: 301 DPAKRSQVVGTIDFSDDVDAAAIAKVLRANGVVDTEPYRKLGRNQLRVAMFPAVEPGDVH 360

Query: 364 ALTECVDWVVERL 376
            LTECVD+V+ RL
Sbjct: 361 KLTECVDFVLSRL 373


Lambda     K      H
   0.317    0.134    0.399 

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: 521
Number of extensions: 17
Number of successful extensions: 2
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: 376
Length of database: 374
Length adjustment: 30
Effective length of query: 346
Effective length of database: 344
Effective search space:   119024
Effective search space used:   119024
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: 50 (23.9 bits)

Align candidate WP_026127746.1 D471_RS0114915 (phosphoserine transaminase)
to HMM TIGR01366 (putative phosphoserine aminotransferase (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/TIGR01366.hmm
# target sequence database:        /tmp/gapView.518097.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01366  [M=361]
Accession:   TIGR01366
Description: serC_3: putative phosphoserine aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-202  657.4   0.8   3.4e-202  657.2   0.8    1.0  1  NCBI__GCF_000341125.1:WP_026127746.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000341125.1:WP_026127746.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  657.2   0.8  3.4e-202  3.4e-202       2     360 ..      13     372 ..      12     373 .. 0.99

  Alignments for each domain:
  == domain 1  score: 657.2 bits;  conditional E-value: 3.4e-202
                             TIGR01366   2 padgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgnggatafwd 74 
                                           p+dgrfg+gpskvr+eql+al++++a  +gtshrq +vk lv +vr+g+++lfslp+gyev+lgngg+tafwd
  NCBI__GCF_000341125.1:WP_026127746.1  13 PSDGRFGSGPSKVRPEQLEALASSGARYMGTSHRQKPVKSLVSRVRSGVSDLFSLPEGYEVVLGNGGTTAFWD 85 
                                           99*********************************************************************** PP

                             TIGR01366  75 aatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqaeegvdvialahnetstgvavav 147
                                           +a++gl+  ks+hl+fgefsskfak a  ap+l+ep++v++dpgs+ ea ae+gvdv+al+hnetstgva ++
  NCBI__GCF_000341125.1:WP_026127746.1  86 IAAHGLLRSKSQHLAFGEFSSKFAKVAAGAPWLEEPTVVSTDPGSHGEAVAEAGVDVYALTHNETSTGVAAPI 158
                                           ************************************************************************* PP

                             TIGR01366 148 rrpegsde.alvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaaleriekiaasgrfvpef 219
                                           rr++g+d+ alv++datsgagglpvdi+etdvyyfapqksfa+dgglw+av+sp al r+e+iaa gr++pef
  NCBI__GCF_000341125.1:WP_026127746.1 159 RRVAGADDdALVLVDATSGAGGLPVDIAETDVYYFAPQKSFAADGGLWIAVMSPRALARVEEIAAGGRYIPEF 231
                                           ******988**************************************************************** PP

                             TIGR01366 220 lslptavdnslknqtyntpavatlllldeqvdwlngnggldfavartkdsssrlyswaeereyatpfvadaak 292
                                           +sl tav ns+k+qtyntpavatllll+eq++w+n++ggl+++vart++sss ly+wae+++ a+pfv+d+ak
  NCBI__GCF_000341125.1:WP_026127746.1 232 FSLTTAVANSRKDQTYNTPAVATLLLLAEQLEWMNTRGGLEWTVARTAESSSILYDWAEKSPVASPFVTDPAK 304
                                           ************************************************************************* PP

                             TIGR01366 293 rsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidpadvealteavdfvvek 360
                                           rsqvvgtidfsdd+daa++ak+lrang+vdtepyrklgrnqlrvamfpa++p dv++lte+vdfv+ +
  NCBI__GCF_000341125.1:WP_026127746.1 305 RSQVVGTIDFSDDVDAAAIAKVLRANGVVDTEPYRKLGRNQLRVAMFPAVEPGDVHKLTECVDFVLSR 372
                                           *****************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (374 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: 00:00:00.00
# Mc/sec: 22.56
//
[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 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