Alignments for a candidate for serC in Teredinibacter turnerae T7901

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Teredinibacter turnerae T7901

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_015818676.1 TERTU_RS12145 phosphoserine transaminase

Query= SwissProt::P52878
         (370 letters)



>NCBI__GCF_000023025.1:WP_015818676.1
          Length = 372

 Score =  499 bits (1285), Expect = e-146
 Identities = 232/369 (62%), Positives = 290/369 (78%)

Query: 1   MKPTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLP 60
           M+P   P NP FSSGPC+K PGY + +L     GRSHRS+LGK  LAE  ++T  +LGLP
Sbjct: 1   MQPQVKPQNPNFSSGPCSKRPGYDVSKLALETLGRSHRSSLGKTVLAEVCEETAKVLGLP 60

Query: 61  DDYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAE 120
           + Y VG+VP SDTGA EM +WS+LG RGVDVL WESF  GW TDITKQLKL+DV + EAE
Sbjct: 61  EGYRVGVVPGSDTGAVEMAMWSLLGARGVDVLAWESFGSGWVTDITKQLKLQDVIIREAE 120

Query: 121 YGKLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHK 180
           YG+LP+L +V+F NDVVF +NGTTSGVKVPNGDWIP +R GLT+CDATSA+FAM++P+ K
Sbjct: 121 YGELPNLDEVNFDNDVVFTYNGTTSGVKVPNGDWIPADRNGLTICDATSAVFAMEMPWEK 180

Query: 181 LDVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGS 240
           LDV+T+SWQKVLGGEGAHGMLILSPRAV+RLE+YTP WP+PK+FR+TKGGKL   IF G 
Sbjct: 181 LDVVTYSWQKVLGGEGAHGMLILSPRAVERLETYTPPWPMPKLFRMTKGGKLVDGIFRGE 240

Query: 241 TINTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIR 300
           TINTPSML   D+L  L W +S+GG++  I ++  NLAV E +V +N+WI FLA+   +R
Sbjct: 241 TINTPSMLCVADYLDALNWVKSLGGVEASIAKSQSNLAVIERYVEQNDWIEFLAQDPALR 300

Query: 301 SSTSVCFKVDLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDLQCLCE 360
           S+TSVC  +  + +++K ++K L+KE +AYDIG+YRDAP+GLR+W GATVE  DL+ L  
Sbjct: 301 SNTSVCLTLKATPDQVKAIVKLLDKEGIAYDIGAYRDAPAGLRLWAGATVEAADLEALMP 360

Query: 361 WIEWAYNLV 369
           WI WAY  V
Sbjct: 361 WIGWAYQEV 369


Lambda     K      H
   0.318    0.136    0.429 

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: 489
Number of extensions: 11
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: 372
Length adjustment: 30
Effective length of query: 340
Effective length of database: 342
Effective search space:   116280
Effective search space used:   116280
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_015818676.1 TERTU_RS12145 (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.18269.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-190  618.9   0.1   1.9e-190  618.7   0.1    1.0  1  lcl|NCBI__GCF_000023025.1:WP_015818676.1  TERTU_RS12145 phosphoserine tran


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023025.1:WP_015818676.1  TERTU_RS12145 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  618.7   0.1  1.9e-190  1.9e-190       1     373 [.       6     368 ..       6     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 618.7 bits;  conditional E-value: 1.9e-190
                                 TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 
                                               +p+np+fssgpc+krpgy v +l   +lgrshrs lgk+ l+e  e+t +vl++p+ y++g+v++sdtg
  lcl|NCBI__GCF_000023025.1:WP_015818676.1   6 KPQNPNFSSGPCSKRPGYDVSKLALETLGRSHRSSLGKTVLAEVCEETAKVLGLPEGYRVGVVPGSDTG 74 
                                               599****************************************************************** PP

                                 TIGR01365  70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138
                                               avema+wsllgargvd+la+esfg+gwvtd+tkqlkl+dv + eaeyg+lp+l  v+f++dvvft+ngt
  lcl|NCBI__GCF_000023025.1:WP_015818676.1  75 AVEMAMWSLLGARGVDVLAWESFGSGWVTDITKQLKLQDVIIREAEYGELPNLDEVNFDNDVVFTYNGT 143
                                               ********************************************************************* PP

                                 TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207
                                               tsgv+vpngd+ipadr+glticdatsa+fa+++++ekldvvt+swqkvlggegahg+lilsprav+rle
  lcl|NCBI__GCF_000023025.1:WP_015818676.1 144 TSGVKVPNGDWIPADRNGLTICDATSAVFAMEMPWEKLDVVTYSWQKVLGGEGAHGMLILSPRAVERLE 212
                                               ********************************************************************* PP

                                 TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276
                                               +ytp wp+pk+fr+tkggkl ++if+getintpsml+v d+ldal+w +s+gg++a +a++++nlav+e
  lcl|NCBI__GCF_000023025.1:WP_015818676.1 213 TYTPPWPMPKLFRMTKGGKLVDGIFRGETINTPSMLCVADYLDALNWVKSLGGVEASIAKSQSNLAVIE 281
                                               ********************************************************************* PP

                                 TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345
                                                +v++++w++fla+ +++rsntsvcl +     +a++++     +k +v++l+keg+aydig+yrdapa
  lcl|NCBI__GCF_000023025.1:WP_015818676.1 282 RYVEQNDWIEFLAQDPALRSNTSVCLTL-----KATPDQ-----VKAIVKLLDKEGIAYDIGAYRDAPA 340
                                               **************************99.....555555.....9************************ PP

                                 TIGR01365 346 glriwcgatveksdleallewldwafal 373
                                               glr+w gatve+ dleal++w+ wa++ 
  lcl|NCBI__GCF_000023025.1:WP_015818676.1 341 GLRLWAGATVEAADLEALMPWIGWAYQE 368
                                               **************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (372 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: 12.13
//
[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