Alignments for a candidate for serC in Nocardioides dokdonensis FR1436

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Nocardioides dokdonensis FR1436

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_068114277.1 I601_RS03480 phosphoserine transaminase

Query= BRENDA::P9WQ73
         (376 letters)



>NCBI__GCF_001653335.1:WP_068114277.1
          Length = 372

 Score =  471 bits (1211), Expect = e-137
 Identities = 236/369 (63%), Positives = 275/369 (74%), Gaps = 1/369 (0%)

Query: 9   LEIPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSGLAEL 68
           L IP  + P DGRFGSGPSKV   +L  L    AAL GTSHRQAPV+ LVGRV  GLA L
Sbjct: 4   LSIPVDLLPLDGRFGSGPSKVPAGRLDALAGPGAALMGTSHRQAPVRALVGRVLEGLATL 63

Query: 69  FSLPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGEPIII 128
           F LP+GYEV+LGNGG+TAFWD A  GL++ RS HLTYGEF+AKFA+A    P++ EP + 
Sbjct: 64  FDLPEGYEVVLGNGGSTAFWDVATHGLVEHRSQHLTYGEFTAKFATAAGAAPWLAEPSVR 123

Query: 129 TSDPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRRPEGSDD-ALVVIDATSGAGGLPVD 187
            +  GS   P  +  VD  AWAHNETSTGV   VRRPEG+D  ALV++D TSGAGGLPVD
Sbjct: 124 EAPAGSLAHPLAESGVDTYAWAHNETSTGVMAPVRRPEGTDPGALVLVDGTSGAGGLPVD 183

Query: 188 IAETDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKN 247
           + E+D YYFAPQK FASDGGLW+AIMSPAA+ R   IAAT R VP F  LP A++N+ K 
Sbjct: 184 LRESDVYYFAPQKGFASDGGLWIAIMSPAAIERTHRIAATDRHVPAFFDLPTAIDNARKQ 243

Query: 248 QTYNTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGL 307
           QTYNTPAIATL LLAEQ+DW+ G GGL   V+RT  SSQ LY+WA+   + +PFV DP  
Sbjct: 244 QTYNTPAIATLFLLAEQLDWMNGLGGLPAMVERTTRSSQHLYAWAEAASWASPFVADPEH 303

Query: 308 RSQVVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVSALTE 367
           RS VVGT+D  + V A TV  +LRANG+VD +PYR+LGRNQLRV MFPAVE  DV+ALT 
Sbjct: 304 RSLVVGTVDLDNAVPAATVVSVLRANGVVDIDPYRRLGRNQLRVGMFPAVEAADVAALTA 363

Query: 368 CVDWVVERL 376
           CVDWVVERL
Sbjct: 364 CVDWVVERL 372


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: 529
Number of extensions: 19
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: 372
Length adjustment: 30
Effective length of query: 346
Effective length of database: 342
Effective search space:   118332
Effective search space used:   118332
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_068114277.1 I601_RS03480 (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.2157885.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-185  601.1   0.2   4.4e-185  600.9   0.2    1.0  1  NCBI__GCF_001653335.1:WP_068114277.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001653335.1:WP_068114277.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.9   0.2  4.4e-185  4.4e-185       2     361 .]      12     372 .]      11     372 .] 0.99

  Alignments for each domain:
  == domain 1  score: 600.9 bits;  conditional E-value: 4.4e-185
                             TIGR01366   2 padgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgnggatafwd 74 
                                           p dgrfg+gpskv   +l+al+  +a+l+gtshrqa+v+ lvg+v egla lf lp+gyev+lgngg+tafwd
  NCBI__GCF_001653335.1:WP_068114277.1  12 PLDGRFGSGPSKVPAGRLDALAGPGAALMGTSHRQAPVRALVGRVLEGLATLFDLPEGYEVVLGNGGSTAFWD 84 
                                           89*********************************************************************** PP

                             TIGR01366  75 aatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqaeegvdvialahnetstgvavav 147
                                           +at+gl+e++s+hl++gef++kfa aa  ap+l+ep +  a +gs  ++ ae+gvd +a+ahnetstgv+ +v
  NCBI__GCF_001653335.1:WP_068114277.1  85 VATHGLVEHRSQHLTYGEFTAKFATAAGAAPWLAEPSVREAPAGSLAHPLAESGVDTYAWAHNETSTGVMAPV 157
                                           ************************************************************************* PP

                             TIGR01366 148 rrpegsde.alvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaaleriekiaasgrfvpef 219
                                           rrpeg+d  alv++d tsgagglpvd++e+dvyyfapqk fasdgglw+a++spaa+er  +iaa++r+vp f
  NCBI__GCF_001653335.1:WP_068114277.1 158 RRPEGTDPgALVLVDGTSGAGGLPVDLRESDVYYFAPQKGFASDGGLWIAIMSPAAIERTHRIAATDRHVPAF 230
                                           *******87**************************************************************** PP

                             TIGR01366 220 lslptavdnslknqtyntpavatlllldeqvdwlngnggldfavartkdsssrlyswaeereyatpfvadaak 292
                                           ++lpta+dn++k+qtyntpa+atl+ll+eq+dw+ng ggl  +v+rt+ ss++ly+wae+   a+pfvad+ +
  NCBI__GCF_001653335.1:WP_068114277.1 231 FDLPTAIDNARKQQTYNTPAIATLFLLAEQLDWMNGLGGLPAMVERTTRSSQHLYAWAEAASWASPFVADPEH 303
                                           ************************************************************************* PP

                             TIGR01366 293 rsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidpadvealteavdfvvekl 361
                                           rs+vvgt+d+++ + aa+v  +lrang+vd +pyr+lgrnqlrv+mfpa+++adv alt +vd+vve+l
  NCBI__GCF_001653335.1:WP_068114277.1 304 RSLVVGTVDLDNAVPAATVVSVLRANGVVDIDPYRRLGRNQLRVGMFPAVEAADVAALTACVDWVVERL 372
                                           *******************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (372 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 15.26
//
[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 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