Alignments for a candidate for serC in Novosphingobium aromaticivorans DSM 12444

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Novosphingobium aromaticivorans DSM 12444

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_011446321.1 SARO_RS13600 phosphoserine transaminase

Query= metacyc::MONOMER-15918
         (370 letters)



>NCBI__GCF_000013325.1:WP_011446321.1
          Length = 379

 Score =  440 bits (1131), Expect = e-128
 Identities = 213/369 (57%), Positives = 263/369 (71%), Gaps = 2/369 (0%)

Query: 3   PTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPDD 62
           P R P  P FSSGPCAK PGYS E+L     GRSHR+K GK +L   I   R++L LPD 
Sbjct: 6   PARKPARPFFSSGPCAKPPGYSPEKLATESLGRSHRAKIGKTRLQYCIDLMREVLQLPDT 65

Query: 63  YFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEYG 122
           + +GIVP SDTGAFEM +W+MLG R V  L WESF +GW TD  KQLKL D  V  A+YG
Sbjct: 66  HRIGIVPGSDTGAFEMAMWTMLGARPVTTLAWESFGEGWVTDAAKQLKL-DPTVLRADYG 124

Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKLD 182
           ++PDL  +D+ NDV+F WNGTTSGV+VPNAD+IP DREG+   DATSA+FA DI + K+D
Sbjct: 125 QIPDLNAIDWSNDVLFTWNGTTSGVRVPNADFIPADREGLAFADATSAVFAYDIDWSKID 184

Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGSTI 242
           V TFSWQKVLGGEG HG+LIL PRAV+RLE+YTPAWPLPK+FRL   GKL + +F G TI
Sbjct: 185 VATFSWQKVLGGEGGHGVLILGPRAVERLETYTPAWPLPKVFRLVSKGKLAEGVFKGETI 244

Query: 243 NTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRSS 302
           NTPSMLA ED +  L+WA+ +GGL+ L  R++ N A     V + +W+  LA  +  RS 
Sbjct: 245 NTPSMLAVEDAIFALEWAKGLGGLEGLQARSDANAAALNKIVEERSWLSHLAADEATRSK 304

Query: 303 TSVCFKVDLSD-EKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLECLCEW 361
           TSVC  V+ +D + +K+    LEK+  AYDI  YRDAP+GLRIWCGATV  ED+  L  W
Sbjct: 305 TSVCLSVEGADADFIKKFAGLLEKQGAAYDIAGYRDAPAGLRIWCGATVNAEDIADLGPW 364

Query: 362 IEWAYNLVK 370
           ++WAY   +
Sbjct: 365 LDWAYETTR 373


Lambda     K      H
   0.319    0.136    0.430 

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: 495
Number of extensions: 14
Number of successful extensions: 3
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: 370
Length of database: 379
Length adjustment: 30
Effective length of query: 340
Effective length of database: 349
Effective search space:   118660
Effective search space used:   118660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_011446321.1 SARO_RS13600 (phosphoserine transaminase)
to HMM TIGR01365 (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/TIGR01365.hmm
# target sequence database:        /tmp/gapView.128292.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01365  [M=374]
Accession:   TIGR01365
Description: serC_2: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.3e-181  588.3   0.2   3.9e-181  588.1   0.2    1.0  1  NCBI__GCF_000013325.1:WP_011446321.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013325.1:WP_011446321.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  588.1   0.2  3.9e-181  3.9e-181       1     373 [.       9     371 ..       9     372 .. 0.99

  Alignments for each domain:
  == domain 1  score: 588.1 bits;  conditional E-value: 3.9e-181
                             TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 
                                           +pa+p fssgpcak pgys+e+l   +lgrshr+k+gk++l+ +i+  revl++p+ ++igiv++sdtga+em
  NCBI__GCF_000013325.1:WP_011446321.1   9 KPARPFFSSGPCAKPPGYSPEKLATESLGRSHRAKIGKTRLQYCIDLMREVLQLPDTHRIGIVPGSDTGAFEM 81 
                                           69*********************************************************************** PP

                             TIGR01365  74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146
                                           a+w++lgar+v  la+esfg+gwvtd +kqlkl d  vl a+yg++pdl+ +d ++dv+ftwngttsgvrvpn
  NCBI__GCF_000013325.1:WP_011446321.1  82 AMWTMLGARPVTTLAWESFGEGWVTDAAKQLKL-DPTVLRADYGQIPDLNAIDWSNDVLFTWNGTTSGVRVPN 153
                                           ********************************9.678************************************ PP

                             TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219
                                           +dfipadregl++ datsa+fa d+d++k+dv tfswqkvlggeg hgvlil prav+rle+ytpawplpk+f
  NCBI__GCF_000013325.1:WP_011446321.1 154 ADFIPADREGLAFADATSAVFAYDIDWSKIDVATFSWQKVLGGEGGHGVLILGPRAVERLETYTPAWPLPKVF 226
                                           ************************************************************************* PP

                             TIGR01365 220 rltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatk 292
                                           rl + gkl++++f+getintpsmlaveda+ al+wa+ +ggl+ l+ar+d+n+a l++ v+  sw+++laa +
  NCBI__GCF_000013325.1:WP_011446321.1 227 RLVSKGKLAEGVFKGETINTPSMLAVEDAIFALEWAKGLGGLEGLQARSDANAAALNKIVEERSWLSHLAADE 299
                                           ************************************************************************* PP

                             TIGR01365 293 eirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdlealle 365
                                           ++rs+tsvcl+v         e a+adf+k+++ +lek+g+aydi +yrdapaglriwcgatv+++d+  l +
  NCBI__GCF_000013325.1:WP_011446321.1 300 ATRSKTSVCLSV---------EGADADFIKKFAGLLEKQGAAYDIAGYRDAPAGLRIWCGATVNAEDIADLGP 363
                                           ************.........667799********************************************** PP

                             TIGR01365 366 wldwafal 373
                                           wldwa+++
  NCBI__GCF_000013325.1:WP_011446321.1 364 WLDWAYET 371
                                           ******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (379 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: 16.30
//
[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