Alignments for a candidate for dapC in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Methanosarcina acetivorans C2A

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_011022283.1 MA_RS11965 phosphoserine aminotransferase

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



>NCBI__GCF_000007345.1:WP_011022283.1
          Length = 370

 Score =  768 bits (1983), Expect = 0.0
 Identities = 370/370 (100%), Positives = 370/370 (100%)

Query: 1   MKPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLP 60
           MKPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLP
Sbjct: 1   MKPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLP 60

Query: 61  DDYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAE 120
           DDYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAE
Sbjct: 61  DDYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAE 120

Query: 121 YGKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHK 180
           YGKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHK
Sbjct: 121 YGKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHK 180

Query: 181 LDVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGS 240
           LDVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGS
Sbjct: 181 LDVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGS 240

Query: 241 TINTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIR 300
           TINTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIR
Sbjct: 241 TINTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIR 300

Query: 301 SSTSVCFKVDLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLECLCE 360
           SSTSVCFKVDLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLECLCE
Sbjct: 301 SSTSVCFKVDLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLECLCE 360

Query: 361 WIEWAYNLVK 370
           WIEWAYNLVK
Sbjct: 361 WIEWAYNLVK 370


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: 665
Number of extensions: 17
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: 370
Length of database: 370
Length adjustment: 30
Effective length of query: 340
Effective length of database: 340
Effective search space:   115600
Effective search space used:   115600
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: 49 (23.5 bits)

Align candidate WP_011022283.1 MA_RS11965 (phosphoserine aminotransferase)
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.22330.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     4e-225  732.8   0.4   4.6e-225  732.6   0.4    1.0  1  lcl|NCBI__GCF_000007345.1:WP_011022283.1  MA_RS11965 phosphoserine aminotr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007345.1:WP_011022283.1  MA_RS11965 phosphoserine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  732.6   0.4  4.6e-225  4.6e-225       1     374 []       6     369 ..       6     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 732.6 bits;  conditional E-value: 4.6e-225
                                 TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 
                                               +p+np+fssgpcak+pgysveelk++++grshrsk gkekl+eai++tr++l++p+dy +giv+asdtg
  lcl|NCBI__GCF_000007345.1:WP_011022283.1   6 VPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPDDYFVGIVPASDTG 74 
                                               699****************************************************************** PP

                                 TIGR01365  70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138
                                               a+em+lws+lg+rgvd+l++esf+kgw+td+tkqlklkd rv+eaeygklpdlkkvdfk+dvvf+wngt
  lcl|NCBI__GCF_000007345.1:WP_011022283.1  75 AFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEYGKLPDLKKVDFKNDVVFVWNGT 143
                                               ********************************************************************* PP

                                 TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207
                                               tsgv+vpn+d+ip+dreg+t+cdatsa+fa+d++y+kldv+tfswqkvlggegahg+lilsprav+rle
  lcl|NCBI__GCF_000007345.1:WP_011022283.1 144 TSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKLDVITFSWQKVLGGEGAHGMLILSPRAVQRLE 212
                                               ********************************************************************* PP

                                 TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276
                                               sytpawplpkifrltkggkl+kdif g+tintpsmla+ed+l++lkwaes+gglk l+ r+++nlav+e
  lcl|NCBI__GCF_000007345.1:WP_011022283.1 213 SYTPAWPLPKIFRLTKGGKLNKDIFAGSTINTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFE 281
                                               ********************************************************************* PP

                                 TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345
                                               afvak++w++fla+tkeirs+tsvc+kv     +++de+     +kel+++leke+vaydigsyrdap+
  lcl|NCBI__GCF_000007345.1:WP_011022283.1 282 AFVAKNNWIHFLAETKEIRSSTSVCFKV-----DLSDEK-----LKELIKTLEKEKVAYDIGSYRDAPS 340
                                               ***************************9.....899*99.....9************************ PP

                                 TIGR01365 346 glriwcgatveksdleallewldwafalv 374
                                               glriwcgatvek+dle+l+ew++wa++lv
  lcl|NCBI__GCF_000007345.1:WP_011022283.1 341 GLRIWCGATVEKEDLECLCEWIEWAYNLV 369
                                               **************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.25
//
[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