Alignments for a candidate for serC in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Haloechinothrix alba DSM 45207

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_089301521.1 CHB84_RS11310 phosphoserine transaminase

Query= BRENDA::P9WQ73
         (376 letters)



>NCBI__GCF_900188115.1:WP_089301521.1
          Length = 375

 Score =  515 bits (1327), Expect = e-151
 Identities = 244/367 (66%), Positives = 295/367 (80%)

Query: 9   LEIPTAIKPRDGRFGSGPSKVRLEQLQTLTTTAAALFGTSHRQAPVKNLVGRVRSGLAEL 68
           L +P  IKP DGRFG GPSKVR EQL  L +  AA+ GTSHRQ PVK+LVGRVR+GL +L
Sbjct: 7   LTLPDDIKPADGRFGCGPSKVRTEQLAHLASGGAAVMGTSHRQKPVKDLVGRVRTGLRDL 66

Query: 69  FSLPDGYEVILGNGGATAFWDAAAFGLIDKRSLHLTYGEFSAKFASAVSKNPFVGEPIII 128
           F+LPDGYEV+LGNGG TAFWDAAAFGL+ +R+   TYGEFS+KFA      PF+ +PI++
Sbjct: 67  FNLPDGYEVLLGNGGTTAFWDAAAFGLVRERAQLFTYGEFSSKFAKVAEGAPFLSDPIVV 126

Query: 129 TSDPGSAPEPQTDPSVDVIAWAHNETSTGVAVAVRRPEGSDDALVVIDATSGAGGLPVDI 188
            S+PG+APE    P  D++ WAHNETSTGVAV VRRP GS+ ALV IDATSGAGGLPV  
Sbjct: 127 ASEPGTAPEITYQPGADIVGWAHNETSTGVAVPVRRPAGSEGALVTIDATSGAGGLPVAA 186

Query: 189 AETDAYYFAPQKNFASDGGLWLAIMSPAALSRIEAIAATGRWVPDFLSLPIAVENSLKNQ 248
            + D YYFAPQK FA+DGGLW+A+ SPAA+ RIE I  +GRWVP+FLSL  A++NS KNQ
Sbjct: 187 EDFDVYYFAPQKCFAADGGLWVALASPAAVERIEEIGNSGRWVPEFLSLTTALDNSRKNQ 246

Query: 249 TYNTPAIATLALLAEQIDWLVGNGGLDWAVKRTADSSQRLYSWAQERPYTTPFVTDPGLR 308
           TYNTPA+ TL LLA+QI+W++  GGL+W  KRTA+S++RLY WA++  YT+P+V++P LR
Sbjct: 247 TYNTPAVGTLLLLADQIEWMLEGGGLEWTTKRTAESARRLYEWAEKTSYTSPYVSEPELR 306

Query: 309 SQVVGTIDFVDDVDAGTVAKILRANGIVDTEPYRKLGRNQLRVAMFPAVEPDDVSALTEC 368
           S VVGT+DF DDVDA  +A  LRANGIVD EPYRKLGRNQLRV MFPA+EPDD+SAL + 
Sbjct: 307 SHVVGTVDFADDVDATQLAATLRANGIVDVEPYRKLGRNQLRVGMFPAIEPDDISALIQS 366

Query: 369 VDWVVER 375
           VDW+VER
Sbjct: 367 VDWIVER 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: 586
Number of extensions: 20
Number of successful extensions: 1
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: 375
Length adjustment: 30
Effective length of query: 346
Effective length of database: 345
Effective search space:   119370
Effective search space used:   119370
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_089301521.1 CHB84_RS11310 (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.10309.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-190  619.1   0.1   1.5e-190  618.9   0.1    1.0  1  lcl|NCBI__GCF_900188115.1:WP_089301521.1  CHB84_RS11310 phosphoserine tran


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188115.1:WP_089301521.1  CHB84_RS11310 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.9   0.1  1.5e-190  1.5e-190       1     360 [.      14     373 ..      14     374 .. 1.00

  Alignments for each domain:
  == domain 1  score: 618.9 bits;  conditional E-value: 1.5e-190
                                 TIGR01366   1 kpadgrfgagpskvrleqlqalvataasllgtshrqaavknlvgkvreglaelfslpdgyevilgngga 69 
                                               kpadgrfg+gpskvr+eql  l++++a+++gtshrq +vk+lvg+vr gl++lf+lpdgyev+lgngg+
  lcl|NCBI__GCF_900188115.1:WP_089301521.1  14 KPADGRFGCGPSKVRTEQLAHLASGGAAVMGTSHRQKPVKDLVGRVRTGLRDLFNLPDGYEVLLGNGGT 82 
                                               7******************************************************************** PP

                                 TIGR01366  70 tafwdaatfgliekkslhlsfgefsskfakaaklapfldepeivtadpgsapeaqaeegvdvialahne 138
                                               tafwdaa+fgl+ ++++ +++gefsskfak a+ apfl++p++v+++pg+ape   ++g+d++++ahne
  lcl|NCBI__GCF_900188115.1:WP_089301521.1  83 TAFWDAAAFGLVRERAQLFTYGEFSSKFAKVAEGAPFLSDPIVVASEPGTAPEITYQPGADIVGWAHNE 151
                                               ********************************************************************* PP

                                 TIGR01366 139 tstgvavavrrpegsdealvvidatsgagglpvdiketdvyyfapqksfasdgglwlavlspaalerie 207
                                               tstgvav+vrrp+gs++alv idatsgagglpv  ++ dvyyfapqk+fa+dgglw+a+ spaa+erie
  lcl|NCBI__GCF_900188115.1:WP_089301521.1 152 TSTGVAVPVRRPAGSEGALVTIDATSGAGGLPVAAEDFDVYYFAPQKCFAADGGLWVALASPAAVERIE 220
                                               ********************************************************************* PP

                                 TIGR01366 208 kiaasgrfvpeflslptavdnslknqtyntpavatlllldeqvdwlngnggldfavartkdsssrlysw 276
                                               +i  sgr+vpeflsl ta+dns+knqtyntpav tllll++q++w+   ggl+++++rt++s++rly+w
  lcl|NCBI__GCF_900188115.1:WP_089301521.1 221 EIGNSGRWVPEFLSLTTALDNSRKNQTYNTPAVGTLLLLADQIEWMLEGGGLEWTTKRTAESARRLYEW 289
                                               ********************************************************************* PP

                                 TIGR01366 277 aeereyatpfvadaakrsqvvgtidfsddidaavvakilrangivdtepyrklgrnqlrvamfpaidpa 345
                                               ae++ y++p+v+++ +rs+vvgt+df+dd+da+ +a  lrangivd epyrklgrnqlrv+mfpai+p+
  lcl|NCBI__GCF_900188115.1:WP_089301521.1 290 AEKTSYTSPYVSEPELRSHVVGTVDFADDVDATQLAATLRANGIVDVEPYRKLGRNQLRVGMFPAIEPD 358
                                               ********************************************************************* PP

                                 TIGR01366 346 dvealteavdfvvek 360
                                               d++al ++vd++ve+
  lcl|NCBI__GCF_900188115.1:WP_089301521.1 359 DISALIQSVDWIVER 373
                                               *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (361 nodes)
Target sequences:                          1  (375 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: 9.11
//
[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