Aligments for a candidate for dapC in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Aligments for a candidate for dapC in Phaeobacter inhibens BS107

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate GFF3561 PGA1_c36150 phosphoserine aminotransferase SerC

Query= BRENDA::P52878
         (370 letters)



>lcl|FitnessBrowser__Phaeo:GFF3561 PGA1_c36150 phosphoserine
           aminotransferase SerC
          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.8862.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: 7.20
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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