Alignments for a candidate for dapC in Pseudarthrobacter sulfonivorans Ar51

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Pseudarthrobacter sulfonivorans Ar51

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_058929976.1 AU252_RS06200 phosphoserine transaminase

Query= BRENDA::P9WQ73
         (376 letters)



>NCBI__GCF_001484605.1:WP_058929976.1
          Length = 376

 Score =  461 bits (1185), Expect = e-134
 Identities = 222/369 (60%), Positives = 277/369 (75%), Gaps = 1/369 (0%)

Query: 9   LEIPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSGLAEL 68
           + IP  + P+DGRFG+GPSKVR EQL+ L+  +  + GTSHRQAPVKNLVG VR GL++ 
Sbjct: 6   ITIPADLLPKDGRFGAGPSKVRPEQLEALSAASKTILGTSHRQAPVKNLVGSVREGLSQF 65

Query: 69  FSLPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGEPIII 128
           F  P+GYEV+LG GG+TAFWD A+FGL++K++ HL++GEF +KFASA +K PF+    II
Sbjct: 66  FRAPEGYEVVLGVGGSTAFWDVASFGLVEKKAQHLSFGEFGSKFASATNKAPFLDASSII 125

Query: 129 TSDPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRRPEGSD-DALVVIDATSGAGGLPVD 187
            S+PG+ P    +  VDV AW  NETSTGVA  V+R  G+D  +LV++DATS AGGL VD
Sbjct: 126 KSEPGTRPVSAAEAGVDVYAWPQNETSTGVAAPVKRVAGADAGSLVLVDATSAAGGLDVD 185

Query: 188 IAETDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKN 247
           ++E D YYFAPQKNFASDGGLWL + SPAAL R   + A+GRW+PDFL L  A++NS  N
Sbjct: 186 VSEADVYYFAPQKNFASDGGLWLGLFSPAALERAARVKASGRWIPDFLDLQTAIDNSKLN 245

Query: 248 QTYNTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGL 307
           QTYNTP+++TL  L  Q+ WL  NGGLD+A  RTADS+ R+YSWA+   Y TPFV     
Sbjct: 246 QTYNTPSLSTLVTLDAQVQWLNANGGLDFASARTADSAGRIYSWAEASEYATPFVAKAED 305

Query: 308 RSQVVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVSALTE 367
           RS V+ TIDF D +DA  +AK+LRANGIVDTEPYRKLGRNQLR+A F A+EP DVSAL  
Sbjct: 306 RSNVIATIDFDDSIDAAAIAKVLRANGIVDTEPYRKLGRNQLRIATFVAIEPADVSALLA 365

Query: 368 CVDWVVERL 376
            +D+VV  L
Sbjct: 366 SIDYVVGEL 374


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: 459
Number of extensions: 8
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: 376
Length adjustment: 30
Effective length of query: 346
Effective length of database: 346
Effective search space:   119716
Effective search space used:   119716
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_058929976.1 AU252_RS06200 (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.23100.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.6e-188  611.6   3.4   2.9e-188  611.4   3.4    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058929976.1  AU252_RS06200 phosphoserine tran


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058929976.1  AU252_RS06200 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  611.4   3.4  2.9e-188  2.9e-188       2     360 ..      14     373 ..      13     374 .. 0.99

  Alignments for each domain:
  == domain 1  score: 611.4 bits;  conditional E-value: 2.9e-188
                                 TIGR01366   2 padgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgnggat 70 
                                               p+dgrfgagpskvr+eql+al+a++ ++lgtshrqa+vknlvg+vregl+++f+ p+gyev+lg gg+t
  lcl|NCBI__GCF_001484605.1:WP_058929976.1  14 PKDGRFGAGPSKVRPEQLEALSAASKTILGTSHRQAPVKNLVGSVREGLSQFFRAPEGYEVVLGVGGST 82 
                                               99******************************************************************* PP

                                 TIGR01366  71 afwdaatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqaeegvdvialahnet 139
                                               afwd+a+fgl+ekk++hlsfgef skfa+a+++apfld   i+ ++pg+ p + ae+gvdv+a+  net
  lcl|NCBI__GCF_001484605.1:WP_058929976.1  83 AFWDVASFGLVEKKAQHLSFGEFGSKFASATNKAPFLDASSIIKSEPGTRPVSAAEAGVDVYAWPQNET 151
                                               ********************************************************************* PP

                                 TIGR01366 140 stgvavavrrpegsde.alvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaalerie 207
                                               stgva +v+r++g+d  +lv++dats aggl vd++e+dvyyfapqk+fasdgglwl+++spaaler+ 
  lcl|NCBI__GCF_001484605.1:WP_058929976.1 152 STGVAAPVKRVAGADAgSLVLVDATSAAGGLDVDVSEADVYYFAPQKNFASDGGLWLGLFSPAALERAA 220
                                               ***************88**************************************************** PP

                                 TIGR01366 208 kiaasgrfvpeflslptavdnslknqtyntpavatlllldeqvdwlngnggldfavartkdsssrlysw 276
                                               +++asgr++p+fl+l+ta+dns+ nqtyntp+++tl+ ld qv+wln+nggldfa art+ds+ r+ysw
  lcl|NCBI__GCF_001484605.1:WP_058929976.1 221 RVKASGRWIPDFLDLQTAIDNSKLNQTYNTPSLSTLVTLDAQVQWLNANGGLDFASARTADSAGRIYSW 289
                                               ********************************************************************* PP

                                 TIGR01366 277 aeereyatpfvadaakrsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidpa 345
                                               ae++eyatpfva a  rs+v+ tidf+d+idaa++ak+lrangivdtepyrklgrnqlr+a f ai+pa
  lcl|NCBI__GCF_001484605.1:WP_058929976.1 290 AEASEYATPFVAKAEDRSNVIATIDFDDSIDAAAIAKVLRANGIVDTEPYRKLGRNQLRIATFVAIEPA 358
                                               ********************************************************************* PP

                                 TIGR01366 346 dvealteavdfvvek 360
                                               dv+al  ++d+vv +
  lcl|NCBI__GCF_001484605.1:WP_058929976.1 359 DVSALLASIDYVVGE 373
                                               ************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (376 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: 00:00:00.01
# Mc/sec: 10.47
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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