Alignments for a candidate for dapC in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Dinoroseobacter shibae DFL-12

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate 3609935 Dshi_3317 phosphoserine aminotransferase (RefSeq)

Query= SwissProt::P52878
         (370 letters)



>FitnessBrowser__Dino:3609935
          Length = 384

 Score =  462 bits (1188), Expect = e-135
 Identities = 229/371 (61%), Positives = 270/371 (72%), Gaps = 10/371 (2%)

Query: 3   PTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPDD 62
           P   P NP FSSGPCAK P ++++ L D   GRSHR+ +GK+KL  AI+ TR++LG+P D
Sbjct: 6   PVTRPANPRFSSGPCAKPPTWTLDTLGDAALGRSHRATVGKDKLKAAIETTREVLGVPAD 65

Query: 63  YLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEYG 122
           Y +GIVPASDTGA+EM +WS+LG R V++L WESF  GW TD  KQLKL D     AEYG
Sbjct: 66  YKIGIVPASDTGAYEMAMWSLLGERPVEMLAWESFGSGWVTDAIKQLKL-DATTRTAEYG 124

Query: 123 KLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKLD 182
           ++ DL  VDF  DV F WNGTTSGV+VP+GDWIP +R GLTLCDATSA FAMD+ + KLD
Sbjct: 125 EIVDLAAVDFDKDVCFTWNGTTSGVRVPDGDWIPADRAGLTLCDATSAAFAMDLAWDKLD 184

Query: 183 VITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGSTI 242
             TFSWQKVLGGE AHG+LILSPRAV RLESYTP WPLPKIFRLTKGGKL   IF G TI
Sbjct: 185 ATTFSWQKVLGGEAAHGILILSPRAVARLESYTPPWPLPKIFRLTKGGKLIDGIFRGETI 244

Query: 243 NTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRSS 302
           NTPSML  ED+L  L WA+SVGGL  LI R   N A   AFVA N+WI FLA     RS+
Sbjct: 245 NTPSMLCVEDYLFALDWAKSVGGLPGLIARAEANTAAIAAFVAANDWIDFLAADPATRST 304

Query: 303 TSVCFKVDLSDEKL-------KELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKEDL 355
           TSVC K   +D+++       K + K LE E +A+DIG+YRDAP GLRIWCG TVE  D+
Sbjct: 305 TSVCLK--FTDDRIADGAAFAKAVAKRLEAEGIAFDIGAYRDAPPGLRIWCGGTVETSDV 362

Query: 356 QCLCEWIEWAY 366
           + L  W+ WA+
Sbjct: 363 EALLPWLSWAF 373


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: 477
Number of extensions: 18
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: 384
Length adjustment: 30
Effective length of query: 340
Effective length of database: 354
Effective search space:   120360
Effective search space used:   120360
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: 50 (23.9 bits)

Align candidate 3609935 Dshi_3317 (phosphoserine aminotransferase (RefSeq))
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.28913.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.2e-194  632.5   1.4   1.4e-194  632.3   1.4    1.0  1  lcl|FitnessBrowser__Dino:3609935  Dshi_3317 phosphoserine aminotra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609935  Dshi_3317 phosphoserine aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  632.3   1.4  1.4e-194  1.4e-194       1     373 [.       9     375 ..       9     376 .. 0.98

  Alignments for each domain:
  == domain 1  score: 632.3 bits;  conditional E-value: 1.4e-194
                         TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavemalws 77 
                                       rpanp fssgpcak p ++++ l +aalgrshr+ +gk+klk+aie trevl+vpady+igiv+asdtga+ema+ws
  lcl|FitnessBrowser__Dino:3609935   9 RPANPRFSSGPCAKPPTWTLDTLGDAALGRSHRATVGKDKLKAAIETTREVLGVPADYKIGIVPASDTGAYEMAMWS 85 
                                       7**************************************************************************** PP

                         TIGR01365  78 llgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpngdfipadr 154
                                       llg+r+v++la+esfg+gwvtd +kqlkl d     aeyg++ dl+ vdf+kdv ftwngttsgvrvp+gd+ipadr
  lcl|FitnessBrowser__Dino:3609935  86 LLGERPVEMLAWESFGSGWVTDAIKQLKL-DATTRTAEYGEIVDLAAVDFDKDVCFTWNGTTSGVRVPDGDWIPADR 161
                                       ****************************9.566779***************************************** PP

                         TIGR01365 155 eglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkifrltkggklskdi 231
                                        glt+cdatsaafa+dl ++kld  tfswqkvlgge ahg+lilspravarlesytp wplpkifrltkggkl+++i
  lcl|FitnessBrowser__Dino:3609935 162 AGLTLCDATSAAFAMDLAWDKLDATTFSWQKVLGGEAAHGILILSPRAVARLESYTPPWPLPKIFRLTKGGKLIDGI 238
                                       ***************************************************************************** PP

                         TIGR01365 232 fegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatkeirsntsvclkvvdpd 308
                                       f+getintpsml+ved+l al wa+s+ggl  l+ara++n a ++afva ++w+dflaa +++rs+tsvclk++d  
  lcl|FitnessBrowser__Dino:3609935 239 FRGETINTPSMLCVEDYLFALDWAKSVGGLPGLIARAEANTAAIAAFVAANDWIDFLAADPATRSTTSVCLKFTDDR 315
                                       *************************************************************************9998 PP

                         TIGR01365 309 vaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdleallewldwafal 373
                                       +a    d  a fak +++ le eg+a+dig+yrdap+glriwcg tve+sd+eall+wl waf++
  lcl|FitnessBrowser__Dino:3609935 316 IA----D-GAAFAKAVAKRLEAEGIAFDIGAYRDAPPGLRIWCGGTVETSDVEALLPWLSWAFEA 375
                                       85....3.478****************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (384 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.60
//
[ok]

This GapMind analysis is from Apr 09 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