Alignments for a candidate for dapC in Roseburia faecis M72

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Roseburia faecis M72

Align Phosphoserine aminotransferase, chloroplastic; PSAT; Phosphohydroxythreonine aminotransferase; EC 2.6.1.52 (characterized)
to candidate WP_055068250.1 M72_RS11030 3-phosphoserine/phosphohydroxythreonine transaminase

Query= SwissProt::P52877
         (430 letters)



>NCBI__GCF_001406815.1:WP_055068250.1
          Length = 360

 Score =  377 bits (968), Expect = e-109
 Identities = 205/365 (56%), Positives = 251/365 (68%), Gaps = 9/365 (2%)

Query: 68  RVFNFAAGPAVLPENVLQKAQSELLNWRGSGMSVMEMSHRGKEFTSIIDKAEADLRTLLN 127
           RV+NF+AGPAVLPE VLQ+A  E+L++RG GMSVMEMSHR K F  II  AE DLR L+N
Sbjct: 3   RVYNFSAGPAVLPEEVLQEAADEMLDYRGCGMSVMEMSHRSKVFDDIIKDAEKDLRELMN 62

Query: 128 IPSDYTVLFLQGGASTQFSAIPLNLCTPDSAVDYIVTGSWGDKAAKEAAKYAAVSSIWSG 187
           IP +Y VLFLQGGAS QF+A+P+NL     A  YIVTG W  KA +EA  Y     + S 
Sbjct: 63  IPDNYKVLFLQGGASQQFAAVPMNLMKNKKA-GYIVTGQWAKKAYQEAQMYGEAIELASS 121

Query: 188 KSDNYVRIPNFDGSEFVQNSQARYLHICANETIYGVEFKKYPVPANPDG-FLVADMSSNF 246
               +  IP  D S+        Y++IC N TIYG ++KK P   N  G  LVAD+SS F
Sbjct: 122 ADQTFSYIP--DCSDLDIPDDLDYVYICENNTIYGTKYKKLP---NTKGKTLVADVSSCF 176

Query: 247 CSKPVDVTKFGLIYAGAQKNVGPSGVTIVIVRNDLI-GNAQKMTPVMLDYKIHADNKSLY 305
            S+PVDVTK+G+IY G QKN+GP+GV IVI R DLI  +    TP ML +K  AD  SLY
Sbjct: 177 LSEPVDVTKYGVIYGGVQKNIGPAGVVIVIAREDLITDDVLPGTPTMLKWKTQADKDSLY 236

Query: 306 NTPPCYGIYMCGLVFEDLLNQGGLVEVEKKNKAKAQVLYDAIDESNGFYKCPVEKSVRSL 365
           NTPPCYGIY+CG VFE L   GGL E++++N  KA++LYD +DES   +K  V K  RSL
Sbjct: 237 NTPPCYGIYICGKVFEWLKKMGGLEEMQRRNIEKAKILYDFLDESK-LFKGTVRKEDRSL 295

Query: 366 MNVPFTLEKSELEGDFIKEAAKEKMVALKGHRSVGGMRASIYNAMPLAGVEKLVAFMKEF 425
           MNVPF     +++  F+KEA +   V LKGHR+VGGMRASIYNAMP  GVEKLVAFMK+F
Sbjct: 296 MNVPFVTGDKDMDAKFVKEATEAGFVNLKGHRTVGGMRASIYNAMPKEGVEKLVAFMKKF 355

Query: 426 QAKHA 430
           + ++A
Sbjct: 356 EKENA 360


Lambda     K      H
   0.317    0.132    0.383 

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: 443
Number of extensions: 18
Number of successful extensions: 8
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: 430
Length of database: 360
Length adjustment: 31
Effective length of query: 399
Effective length of database: 329
Effective search space:   131271
Effective search space used:   131271
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 WP_055068250.1 M72_RS11030 (3-phosphoserine/phosphohydroxythreonine transaminase)
to HMM TIGR01364 (serC: phosphoserine transaminase (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/TIGR01364.hmm
# target sequence database:        /tmp/gapView.3123160.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01364  [M=358]
Accession:   TIGR01364
Description: serC_1: phosphoserine transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-159  517.1   0.0   1.2e-159  516.9   0.0    1.0  1  NCBI__GCF_001406815.1:WP_055068250.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001406815.1:WP_055068250.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.9   0.0  1.2e-159  1.2e-159       1     357 [.       4     358 ..       4     359 .. 0.97

  Alignments for each domain:
  == domain 1  score: 516.9 bits;  conditional E-value: 1.2e-159
                             TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGa 73 
                                           ++nFsaGPa+lpeevl++a++e+ld++g g+svme+sHRsk f++++++ae+dlreL+nipdny+vlflqGGa
  NCBI__GCF_001406815.1:WP_055068250.1   4 VYNFSAGPAVLPEEVLQEAADEMLDYRGCGMSVMEMSHRSKVFDDIIKDAEKDLRELMNIPDNYKVLFLQGGA 76 
                                           59*********************************************************************** PP

                             TIGR01364  74 ttqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylc 146
                                           ++qfaavp+nl+k+k +a yivtG+w+kka++ea+ +++ ++ +as++++ +s ipd ++l++ +d +yvy+c
  NCBI__GCF_001406815.1:WP_055068250.1  77 SQQFAAVPMNLMKNK-KAGYIVTGQWAKKAYQEAQMYGEAIE-LASSADQTFSYIPDCSDLDIPDDLDYVYIC 147
                                           ************998.9********************99555.55556899********************** PP

                             TIGR01364 147 anetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakk.el 218
                                           +n+ti+G+++k+lp++k ++lvaD+ss +ls+++dv+kyg+iy+G+qKniGpaGv++vi r+dl+       +
  NCBI__GCF_001406815.1:WP_055068250.1 148 ENNTIYGTKYKKLPNTKGKTLVADVSSCFLSEPVDVTKYGVIYGGVQKNIGPAGVVIVIAREDLITDDVLpGT 220
                                           *****************************************************************9765559* PP

                             TIGR01364 219 psvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekka 291
                                           p++l++k++a++dslyntpp+++iy++g+v++wlk+ GG+++++++n eKak+lY+ +des+ ++k++v+k++
  NCBI__GCF_001406815.1:WP_055068250.1 221 PTMLKWKTQADKDSLYNTPPCYGIYICGKVFEWLKKMGGLEEMQRRNIEKAKILYDFLDESK-LFKGTVRKED 292
                                           ***********************************************************995.********** PP

                             TIGR01364 292 RslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekk 357
                                           Rslmnv+F + +++++++F+kea+e+g+v+lkGhr+vGG+RasiYna+p e+v++Lv+fmk+Fek+
  NCBI__GCF_001406815.1:WP_055068250.1 293 RSLMNVPFVTGDKDMDAKFVKEATEAGFVNLKGHRTVGGMRASIYNAMPKEGVEKLVAFMKKFEKE 358
                                           ****************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (360 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: 12.26
//
[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