GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Phaeobacter inhibens BS107

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate GFF3561 PGA1_c36150 phosphoserine aminotransferase SerC

Query= SwissProt::P52878
         (370 letters)



>FitnessBrowser__Phaeo:GFF3561
          Length = 384

 Score =  462 bits (1189), Expect = e-135
 Identities = 227/372 (61%), Positives = 271/372 (72%), Gaps = 10/372 (2%)

Query: 2   KPTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPD 61
           +P   P NP FSSGPCAK P + + +L   P GRSHR+ +GK+KL  AI+ TR++LG+P 
Sbjct: 5   QPATRPGNPRFSSGPCAKPPAFDLTKLAGAPLGRSHRAAIGKDKLLAAIEGTREILGVPA 64

Query: 62  DYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEY 121
            Y +GIVPASDTGA EM +W++LG RG ++L WESF  GW TD+ KQLKL D  V  A+Y
Sbjct: 65  GYRIGIVPASDTGAVEMAMWNLLGARGAEMLAWESFGAGWVTDVVKQLKL-DAVVKTADY 123

Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKL 181
           G+L DL  VDF NDVVF WNGTTSGV+VPNGDWIP +R GLT+CDATSA FA D+P+ KL
Sbjct: 124 GELVDLASVDFNNDVVFTWNGTTSGVRVPNGDWIPADRAGLTICDATSAAFAQDLPWDKL 183

Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGST 241
           DV TFSWQKVLGGE AHGM+ILSPRAV+RLESYTPAWPLPKIFRLTKGGKL   IF+G+T
Sbjct: 184 DVTTFSWQKVLGGEAAHGMIILSPRAVERLESYTPAWPLPKIFRLTKGGKLIDGIFKGAT 243

Query: 242 INTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRS 301
           INTPSMLA ED+L  L WA SVGGL  L  R + N      F A   WI  LA     RS
Sbjct: 244 INTPSMLAVEDYLLALDWARSVGGLDGLKGRADANAQAIFNFCANRPWIANLATDPATRS 303

Query: 302 STSVCFKVDLSDEKL-------KELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKED 354
           +TSVC K   +D ++       K + K LE E +A DIG+YRDAP+GLRIWCG TVE  D
Sbjct: 304 NTSVCLK--FTDPRIQDGATFAKAIAKRLEAENIALDIGAYRDAPAGLRIWCGGTVETSD 361

Query: 355 LQCLCEWIEWAY 366
           ++ +  W+EWA+
Sbjct: 362 IEAMLPWLEWAF 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: 490
Number of extensions: 19
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 GFF3561 PGA1_c36150 (phosphoserine aminotransferase SerC)
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.30409.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-192  625.9   0.4   1.4e-192  625.7   0.4    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3561  PGA1_c36150 phosphoserine aminot


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3561  PGA1_c36150 phosphoserine aminotransferase SerC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  625.7   0.4  1.4e-192  1.4e-192       1     373 [.       9     375 ..       9     376 .. 0.98

  Alignments for each domain:
  == domain 1  score: 625.7 bits;  conditional E-value: 1.4e-192
                          TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavemalw 76 
                                        rp np fssgpcak p + + +l  a+lgrshr+ +gk+kl +aie tre+l+vpa y+igiv+asdtgavema+w
  lcl|FitnessBrowser__Phaeo:GFF3561   9 RPGNPRFSSGPCAKPPAFDLTKLAGAPLGRSHRAAIGKDKLLAAIEGTREILGVPAGYRIGIVPASDTGAVEMAMW 84 
                                        799************************************************************************* PP

                          TIGR01365  77 sllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpngdfipa 152
                                         llgarg ++la+esfg gwvtdv+kqlkl+ v v  a+yg+l dl+ vdf++dvvftwngttsgvrvpngd+ipa
  lcl|FitnessBrowser__Phaeo:GFF3561  85 NLLGARGAEMLAWESFGAGWVTDVVKQLKLDAV-VKTADYGELVDLASVDFNNDVVFTWNGTTSGVRVPNGDWIPA 159
                                        ******************************887.558*************************************** PP

                          TIGR01365 153 dreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkifrltkggkls 228
                                        dr glticdatsaafaqdl+++kldv tfswqkvlgge ahg++ilsprav+rlesytpawplpkifrltkggkl+
  lcl|FitnessBrowser__Phaeo:GFF3561 160 DRAGLTICDATSAAFAQDLPWDKLDVTTFSWQKVLGGEAAHGMIILSPRAVERLESYTPAWPLPKIFRLTKGGKLI 235
                                        **************************************************************************** PP

                          TIGR01365 229 kdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatkeirsntsvclkv 304
                                        ++if+g+tintpsmlaved+l al wa+s+ggl+ l  rad+n++ + +f a+ +w+  la+ +++rsntsvclk+
  lcl|FitnessBrowser__Phaeo:GFF3561 236 DGIFKGATINTPSMLAVEDYLLALDWARSVGGLDGLKGRADANAQAIFNFCANRPWIANLATDPATRSNTSVCLKF 311
                                        **************************************************************************** PP

                          TIGR01365 305 vdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdleallewldwafal 373
                                        +dp ++    d  a+fak +++ le e++a+dig+yrdapaglriwcg tve+sd+ea+l+wl+waf++
  lcl|FitnessBrowser__Phaeo:GFF3561 312 TDPRIQ----D-GATFAKAIAKRLEAENIALDIGAYRDAPAGLRIWCGGTVETSDIEAMLPWLEWAFET 375
                                        ***985....3.589****************************************************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.66
//
[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:

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:

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:

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:

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