Alignments for a candidate for serC in Thermomonospora curvata DSM 43183

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Thermomonospora curvata DSM 43183

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_012851206.1 TCUR_RS04095 phosphoserine transaminase

Query= BRENDA::P9WQ73
         (376 letters)



>NCBI__GCF_000024385.1:WP_012851206.1
          Length = 370

 Score =  503 bits (1294), Expect = e-147
 Identities = 244/366 (66%), Positives = 293/366 (80%), Gaps = 1/366 (0%)

Query: 11  IPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSGLAELFS 70
           IP  +KP DGRFG GPSKVR EQL+ L  + AA  GTSHRQAPVK+LV RVR GLAELFS
Sbjct: 6   IPADLKPADGRFGCGPSKVRPEQLRALAESGAAYLGTSHRQAPVKSLVRRVREGLAELFS 65

Query: 71  LPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGEPIIITS 130
           LP+GY V+L NGG TAFWDAAAFGLI ++S HLT+GEFS+KFA      P++ EP +I++
Sbjct: 66  LPEGYRVLLSNGGTTAFWDAAAFGLIRRKSQHLTFGEFSSKFAKVAKAAPWLEEPSLISA 125

Query: 131 DPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRRPEGSDDALVVIDATSGAGGLPVDIAE 190
           +PGS P P+ +  VDV A  HNETSTGVA+ ++R  G +D+LV++DATSGAGGLPVDI +
Sbjct: 126 EPGSHPLPRAEDGVDVYALTHNETSTGVAMPIQRV-GGEDSLVLVDATSGAGGLPVDITQ 184

Query: 191 TDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKNQTY 250
            D YYFAPQK FASDGGLW+A++SPAAL RIE IA++ R++P+F +L   ++NS K+QTY
Sbjct: 185 ADVYYFAPQKCFASDGGLWVALVSPAALERIEQIASSDRYIPEFFNLKTVIDNSAKDQTY 244

Query: 251 NTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGLRSQ 310
           NTPA+ATL L AEQI+W+   GGL W   RTADS+QRLY+WA++  Y TPFV DP  RSQ
Sbjct: 245 NTPAVATLLLFAEQIEWMNAQGGLAWTTARTADSAQRLYTWAEKSSYATPFVADPAQRSQ 304

Query: 311 VVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVSALTECVD 370
           VVGTIDFVD VDA  VAK LRANGIVDTEPYRKLGRNQLR+ MFPAV+P DV ALT C+D
Sbjct: 305 VVGTIDFVDSVDAAAVAKTLRANGIVDTEPYRKLGRNQLRIGMFPAVDPADVEALTACID 364

Query: 371 WVVERL 376
           +VVERL
Sbjct: 365 YVVERL 370


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: 489
Number of extensions: 12
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: 370
Length adjustment: 30
Effective length of query: 346
Effective length of database: 340
Effective search space:   117640
Effective search space used:   117640
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_012851206.1 TCUR_RS04095 (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.28136.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.2e-206  671.0   0.1   2.5e-206  670.9   0.1    1.0  1  lcl|NCBI__GCF_000024385.1:WP_012851206.1  TCUR_RS04095 phosphoserine trans


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024385.1:WP_012851206.1  TCUR_RS04095 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  670.9   0.1  2.5e-206  2.5e-206       1     361 []      11     370 .]      11     370 .] 0.99

  Alignments for each domain:
  == domain 1  score: 670.9 bits;  conditional E-value: 2.5e-206
                                 TIGR01366   1 kpadgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgngga 69 
                                               kpadgrfg+gpskvr+eql al++++a+ lgtshrqa+vk lv +vreglaelfslp+gy v+l+ngg+
  lcl|NCBI__GCF_000024385.1:WP_012851206.1  11 KPADGRFGCGPSKVRPEQLRALAESGAAYLGTSHRQAPVKSLVRRVREGLAELFSLPEGYRVLLSNGGT 79 
                                               7******************************************************************** PP

                                 TIGR01366  70 tafwdaatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqaeegvdvialahne 138
                                               tafwdaa+fgli +ks+hl+fgefsskfak ak ap+l+ep +++a+pgs+p ++ae+gvdv+al+hne
  lcl|NCBI__GCF_000024385.1:WP_012851206.1  80 TAFWDAAAFGLIRRKSQHLTFGEFSSKFAKVAKAAPWLEEPSLISAEPGSHPLPRAEDGVDVYALTHNE 148
                                               ********************************************************************* PP

                                 TIGR01366 139 tstgvavavrrpegsdealvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaalerie 207
                                               tstgva++++r+   +++lv++datsgagglpvdi+++dvyyfapqk+fasdgglw+a++spaalerie
  lcl|NCBI__GCF_000024385.1:WP_012851206.1 149 TSTGVAMPIQRVG-GEDSLVLVDATSGAGGLPVDITQADVYYFAPQKCFASDGGLWVALVSPAALERIE 216
                                               ***********95.5889*************************************************** PP

                                 TIGR01366 208 kiaasgrfvpeflslptavdnslknqtyntpavatlllldeqvdwlngnggldfavartkdsssrlysw 276
                                               +ia+s+r++pef++l+t +dns k+qtyntpavatlll++eq++w+n++ggl +++art+ds++rly+w
  lcl|NCBI__GCF_000024385.1:WP_012851206.1 217 QIASSDRYIPEFFNLKTVIDNSAKDQTYNTPAVATLLLFAEQIEWMNAQGGLAWTTARTADSAQRLYTW 285
                                               ********************************************************************* PP

                                 TIGR01366 277 aeereyatpfvadaakrsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidpa 345
                                               ae++ yatpfvad+a+rsqvvgtidf+d++daa+vak lrangivdtepyrklgrnqlr++mfpa+dpa
  lcl|NCBI__GCF_000024385.1:WP_012851206.1 286 AEKSSYATPFVADPAQRSQVVGTIDFVDSVDAAAVAKTLRANGIVDTEPYRKLGRNQLRIGMFPAVDPA 354
                                               ********************************************************************* PP

                                 TIGR01366 346 dvealteavdfvvekl 361
                                               dvealt ++d+vve+l
  lcl|NCBI__GCF_000024385.1:WP_012851206.1 355 DVEALTACIDYVVERL 370
                                               **************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (370 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.46
//
[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