Alignments for a candidate for serC in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Saccharomonospora cyanea NA-134

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_005459498.1 SACCYDRAFT_RS21840 phosphoserine transaminase

Query= BRENDA::P9WQ73
         (376 letters)



>NCBI__GCF_000244975.1:WP_005459498.1
          Length = 377

 Score =  544 bits (1401), Expect = e-159
 Identities = 261/368 (70%), Positives = 299/368 (81%)

Query: 9   LEIPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSGLAEL 68
           L +P  +KP DGRFG GPSKVR EQL  L    A + GTSHRQ PVK+LVGRVR+GL EL
Sbjct: 7   LTLPADLKPSDGRFGCGPSKVRPEQLANLAKEGANVLGTSHRQKPVKSLVGRVRAGLTEL 66

Query: 69  FSLPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGEPIII 128
           F LPDGYEV+LGNGG TAFWDAAAFGL+ +R+ H TYGEFS KFA    K PF+GE II+
Sbjct: 67  FGLPDGYEVVLGNGGTTAFWDAAAFGLVRERAQHFTYGEFSTKFAKVTDKAPFLGESIIV 126

Query: 129 TSDPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRRPEGSDDALVVIDATSGAGGLPVDI 188
             +PGSAPE       D++AWAHNETSTGVAV VRRPEGSD ALV IDATSGAGGLPV+ 
Sbjct: 127 KGEPGSAPEIAYQQGADLVAWAHNETSTGVAVPVRRPEGSDGALVAIDATSGAGGLPVNA 186

Query: 189 AETDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKNQ 248
           A+ D YYFAPQK+FASDGGLW+A+MSPAA+ R+  I AT RWVPDFLSLP A++NS K+Q
Sbjct: 187 ADFDVYYFAPQKSFASDGGLWIALMSPAAIERVGEIGATDRWVPDFLSLPTALDNSRKDQ 246

Query: 249 TYNTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGLR 308
           TYNTPA+ATL LLA+QI+W++G GGL+W   RT +SS RLY WA++  YTTPFV+DPGLR
Sbjct: 247 TYNTPAVATLFLLADQIEWMLGAGGLEWTTARTRESSNRLYEWAEKTSYTTPFVSDPGLR 306

Query: 309 SQVVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVSALTEC 368
           SQVVGTIDF D VDA  VA+ LRANGIVD EPYRKLGRNQLRV MFPA+EPDDV+ALT C
Sbjct: 307 SQVVGTIDFDDSVDASLVARTLRANGIVDVEPYRKLGRNQLRVGMFPAIEPDDVTALTRC 366

Query: 369 VDWVVERL 376
           V+WVVE L
Sbjct: 367 VEWVVENL 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: 533
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: 377
Length adjustment: 30
Effective length of query: 346
Effective length of database: 347
Effective search space:   120062
Effective search space used:   120062
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_005459498.1 SACCYDRAFT_RS21840 (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.29039.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     8e-198  642.8   0.1   9.1e-198  642.7   0.1    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005459498.1  SACCYDRAFT_RS21840 phosphoserine


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005459498.1  SACCYDRAFT_RS21840 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  642.7   0.1  9.1e-198  9.1e-198       1     360 [.      14     373 ..      14     374 .. 1.00

  Alignments for each domain:
  == domain 1  score: 642.7 bits;  conditional E-value: 9.1e-198
                                 TIGR01366   1 kpadgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgngga 69 
                                               kp+dgrfg+gpskvr+eql  l++ +a +lgtshrq +vk lvg+vr gl+elf lpdgyev+lgngg+
  lcl|NCBI__GCF_000244975.1:WP_005459498.1  14 KPSDGRFGCGPSKVRPEQLANLAKEGANVLGTSHRQKPVKSLVGRVRAGLTELFGLPDGYEVVLGNGGT 82 
                                               79******************************************************************* PP

                                 TIGR01366  70 tafwdaatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqaeegvdvialahne 138
                                               tafwdaa+fgl+ ++++h+++gefs+kfak +++apfl+e +iv  +pgsape   ++g+d++a+ahne
  lcl|NCBI__GCF_000244975.1:WP_005459498.1  83 TAFWDAAAFGLVRERAQHFTYGEFSTKFAKVTDKAPFLGESIIVKGEPGSAPEIAYQQGADLVAWAHNE 151
                                               ********************************************************************* PP

                                 TIGR01366 139 tstgvavavrrpegsdealvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaalerie 207
                                               tstgvav+vrrpegsd+alv+idatsgagglpv+ ++ dvyyfapqksfasdgglw+a++spaa+er+ 
  lcl|NCBI__GCF_000244975.1:WP_005459498.1 152 TSTGVAVPVRRPEGSDGALVAIDATSGAGGLPVNAADFDVYYFAPQKSFASDGGLWIALMSPAAIERVG 220
                                               ********************************************************************* PP

                                 TIGR01366 208 kiaasgrfvpeflslptavdnslknqtyntpavatlllldeqvdwlngnggldfavartkdsssrlysw 276
                                               +i a++r+vp+flslpta+dns+k+qtyntpavatl+ll++q++w+ g ggl++++art++ss+rly+w
  lcl|NCBI__GCF_000244975.1:WP_005459498.1 221 EIGATDRWVPDFLSLPTALDNSRKDQTYNTPAVATLFLLADQIEWMLGAGGLEWTTARTRESSNRLYEW 289
                                               ********************************************************************* PP

                                 TIGR01366 277 aeereyatpfvadaakrsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidpa 345
                                               ae++ y+tpfv+d+++rsqvvgtidf+d++da+ va+ lrangivd epyrklgrnqlrv+mfpai+p+
  lcl|NCBI__GCF_000244975.1:WP_005459498.1 290 AEKTSYTTPFVSDPGLRSQVVGTIDFDDSVDASLVARTLRANGIVDVEPYRKLGRNQLRVGMFPAIEPD 358
                                               ********************************************************************* PP

                                 TIGR01366 346 dvealteavdfvvek 360
                                               dv alt++v++vve+
  lcl|NCBI__GCF_000244975.1:WP_005459498.1 359 DVTALTRCVEWVVEN 373
                                               *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (377 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: 7.27
//
[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