Alignments for a candidate for serC in Methylocystis bryophila S285

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Methylocystis bryophila S285

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_085771168.1 B1812_RS08285 phosphoserine transaminase

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



>NCBI__GCF_002117405.1:WP_085771168.1
          Length = 390

 Score =  446 bits (1146), Expect = e-130
 Identities = 223/375 (59%), Positives = 267/375 (71%), Gaps = 10/375 (2%)

Query: 2   KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61
           KP  +PKNP FSSGPCAK PG+S + L     GRSHR+K GKEKL  AI  TR++L +PD
Sbjct: 7   KPAGLPKNPSFSSGPCAKRPGWSPQNLSAAALGRSHRAKAGKEKLERAIALTREVLRVPD 66

Query: 62  DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121
           DY +GIVPASDTGA EM LWSMLG R VDVL +ESFS GWATD+ KQLKL   RV  A Y
Sbjct: 67  DYRIGIVPASDTGAVEMALWSMLGPRPVDVLAFESFSSGWATDVQKQLKLPQARVLTAPY 126

Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181
           G+LPDL +V+  +D+VF WNGTTSGV+VPNA +I  DR+G+T+CDATS  FA  + + KL
Sbjct: 127 GELPDLAQVNGDHDLVFAWNGTTSGVRVPNAAFIAADRKGLTICDATSGAFAQPLDFAKL 186

Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGST 241
           DV TFSWQK LGGE AHGMLILSPRAV+RLESY P WPLPKIFRLTKG KL + +FAG T
Sbjct: 187 DVTTFSWQKCLGGEAAHGMLILSPRAVERLESYVPPWPLPKIFRLTKGSKLIEGVFAGET 246

Query: 242 INTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRS 301
           INTPS+L  ED+L  L+WA S+GGL  L  R + N AV   +  +     FLA+  + RS
Sbjct: 247 INTPSLLCVEDYLDALQWARSIGGLDALCARADANAAVVAEWTLRQPAFAFLAKQPQTRS 306

Query: 302 STSVCF-----KVDLSDEK-----LKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVE 351
           +TSVC      +V   D K      K L+  +EKE   +D G+YRDAP GLRIWCG TVE
Sbjct: 307 NTSVCLEFADPRVIAMDPKARSGLAKALVSLVEKEGAGFDFGAYRDAPPGLRIWCGPTVE 366

Query: 352 KEDLECLCEWIEWAY 366
             D+  L +WI+WA+
Sbjct: 367 PADVSLLTDWIDWAF 381


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: 488
Number of extensions: 16
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: 370
Length of database: 390
Length adjustment: 30
Effective length of query: 340
Effective length of database: 360
Effective search space:   122400
Effective search space used:   122400
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_085771168.1 B1812_RS08285 (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.29678.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-197  641.0   0.0   3.7e-197  640.8   0.0    1.0  1  lcl|NCBI__GCF_002117405.1:WP_085771168.1  B1812_RS08285 phosphoserine tran


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002117405.1:WP_085771168.1  B1812_RS08285 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  640.8   0.0  3.7e-197  3.7e-197       2     372 ..      12     382 ..      11     384 .. 1.00

  Alignments for each domain:
  == domain 1  score: 640.8 bits;  conditional E-value: 3.7e-197
                                 TIGR01365   2 panpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtga 70 
                                               p+np+fssgpcakrpg+s+++l  aalgrshr+k gkekl++ai  trevl+vp+dy+igiv+asdtga
  lcl|NCBI__GCF_002117405.1:WP_085771168.1  12 PKNPSFSSGPCAKRPGWSPQNLSAAALGRSHRAKAGKEKLERAIALTREVLRVPDDYRIGIVPASDTGA 80 
                                               99******************************************************************* PP

                                 TIGR01365  71 vemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngtt 139
                                               vemalws+lg r+vd+lafesf++gw+tdv kqlkl++ rvl a+yg+lpdl++v+ ++d+vf+wngtt
  lcl|NCBI__GCF_002117405.1:WP_085771168.1  81 VEMALWSMLGPRPVDVLAFESFSSGWATDVQKQLKLPQARVLTAPYGELPDLAQVNGDHDLVFAWNGTT 149
                                               ********************************************************************* PP

                                 TIGR01365 140 sgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarles 208
                                               sgvrvpn+ fi+adr+glticdats afaq ld+ kldv tfswqk lgge ahg+lilsprav+rles
  lcl|NCBI__GCF_002117405.1:WP_085771168.1 150 SGVRVPNAAFIAADRKGLTICDATSGAFAQPLDFAKLDVTTFSWQKCLGGEAAHGMLILSPRAVERLES 218
                                               ********************************************************************* PP

                                 TIGR01365 209 ytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavlea 277
                                               y p wplpkifrltkg+kl++++f getintps+l+ved+ldal+wa+siggl+al arad+n+av+++
  lcl|NCBI__GCF_002117405.1:WP_085771168.1 219 YVPPWPLPKIFRLTKGSKLIEGVFAGETINTPSLLCVEDYLDALQWARSIGGLDALCARADANAAVVAE 287
                                               ********************************************************************* PP

                                 TIGR01365 278 fvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapag 346
                                               +  +++   fla+++++rsntsvcl+++dp v a+d +a++ +ak lvs++ekeg+ +d g+yrdap+g
  lcl|NCBI__GCF_002117405.1:WP_085771168.1 288 WTLRQPAFAFLAKQPQTRSNTSVCLEFADPRVIAMDPKARSGLAKALVSLVEKEGAGFDFGAYRDAPPG 356
                                               ********************************************************************* PP

                                 TIGR01365 347 lriwcgatveksdleallewldwafa 372
                                               lriwcg tve  d+  l++w+dwaf+
  lcl|NCBI__GCF_002117405.1:WP_085771168.1 357 LRIWCGPTVEPADVSLLTDWIDWAFE 382
                                               *************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (390 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: 8.89
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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