Alignments for a candidate for serC in Methanosarcina mazei Go1

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Methanosarcina mazei Go1

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_011034813.1 MM_RS15105 phosphoserine transaminase

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



>NCBI__GCF_000007065.1:WP_011034813.1
          Length = 370

 Score =  732 bits (1890), Expect = 0.0
 Identities = 348/370 (94%), Positives = 359/370 (97%)

Query: 1   MKPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLP 60
           MKPTRVPKNPCFSSGPCAKHPGYS+E+L D PFGRSHRSKPGKEKLAEAIKRTRDMLGLP
Sbjct: 1   MKPTRVPKNPCFSSGPCAKHPGYSIEDLNDAPFGRSHRSKPGKEKLAEAIKRTRDMLGLP 60

Query: 61  DDYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAE 120
            DY VGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSK WATDITKQLKLKDTRVFEAE
Sbjct: 61  SDYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKEWATDITKQLKLKDTRVFEAE 120

Query: 121 YGKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHK 180
           YGKLPDL+ VDFKNDVVFVWNGTTSGVKVPN DWIPD REG+TLCDATSA+FAMDIPYHK
Sbjct: 121 YGKLPDLENVDFKNDVVFVWNGTTSGVKVPNGDWIPDSREGLTLCDATSAVFAMDIPYHK 180

Query: 181 LDVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGS 240
           LDV+TFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNK+IF GS
Sbjct: 181 LDVLTFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKEIFEGS 240

Query: 241 TINTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIR 300
           TINTPSMLANEDWLATLKWAESVGGLKQLI+RTNENLAVFEAFVAKNNWIHFLAETKEIR
Sbjct: 241 TINTPSMLANEDWLATLKWAESVGGLKQLIQRTNENLAVFEAFVAKNNWIHFLAETKEIR 300

Query: 301 SSTSVCFKVDLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLECLCE 360
           SSTSVCFKVDLS+EKLKELIK LE EKVAYDIGSYRDAPSGLRIWCGAT+EKEDLECLCE
Sbjct: 301 SSTSVCFKVDLSEEKLKELIKMLENEKVAYDIGSYRDAPSGLRIWCGATIEKEDLECLCE 360

Query: 361 WIEWAYNLVK 370
           WIEWAY+LVK
Sbjct: 361 WIEWAYDLVK 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: 652
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_011034813.1 MM_RS15105 (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.497692.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-221  719.6   0.1   4.7e-221  719.4   0.1    1.0  1  NCBI__GCF_000007065.1:WP_011034813.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007065.1:WP_011034813.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  719.4   0.1  4.7e-221  4.7e-221       1     373 [.       6     368 ..       6     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 719.4 bits;  conditional E-value: 4.7e-221
                             TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 
                                           +p+np+fssgpcak+pgys+e+l++a++grshrsk gkekl+eai++tr++l++p+dyl+giv+asdtga+em
  NCBI__GCF_000007065.1:WP_011034813.1   6 VPKNPCFSSGPCAKHPGYSIEDLNDAPFGRSHRSKPGKEKLAEAIKRTRDMLGLPSDYLVGIVPASDTGAFEM 78 
                                           699********************************************************************** PP

                             TIGR01365  74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146
                                           +lws+lg+rgvd+l++esf+k+w+td+tkqlklkd rv+eaeygklpdl++vdfk+dvvf+wngttsgv+vpn
  NCBI__GCF_000007065.1:WP_011034813.1  79 CLWSMLGCRGVDVLVWESFSKEWATDITKQLKLKDTRVFEAEYGKLPDLENVDFKNDVVFVWNGTTSGVKVPN 151
                                           ************************************************************************* PP

                             TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219
                                           gd+ip+ reglt+cdatsa+fa+d++y+kldv+tfswqkvlggegahg+lilsprav+rlesytpawplpkif
  NCBI__GCF_000007065.1:WP_011034813.1 152 GDWIPDSREGLTLCDATSAVFAMDIPYHKLDVLTFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIF 224
                                           ************************************************************************* PP

                             TIGR01365 220 rltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatk 292
                                           rltkggkl+k+ifeg+tintpsmla+ed+l++lkwaes+gglk l++r+++nlav+eafvak++w++fla+tk
  NCBI__GCF_000007065.1:WP_011034813.1 225 RLTKGGKLNKEIFEGSTINTPSMLANEDWLATLKWAESVGGLKQLIQRTNENLAVFEAFVAKNNWIHFLAETK 297
                                           ************************************************************************* PP

                             TIGR01365 293 eirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdlealle 365
                                           eirs+tsvc+kv     ++++e+     +kel+++le+e+vaydigsyrdap+glriwcgat+ek+dle+l+e
  NCBI__GCF_000007065.1:WP_011034813.1 298 EIRSSTSVCFKV-----DLSEEK-----LKELIKMLENEKVAYDIGSYRDAPSGLRIWCGATIEKEDLECLCE 360
                                           ***********9.....889999.....9******************************************** PP

                             TIGR01365 366 wldwafal 373
                                           w++wa++l
  NCBI__GCF_000007065.1:WP_011034813.1 361 WIEWAYDL 368
                                           ******87 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 20.92
//
[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