Alignments for a candidate for serC in Sinorhizobium medicae WSM419

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Sinorhizobium medicae WSM419

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_012066838.1 SMED_RS13120 phosphoserine transaminase

Query= metacyc::MONOMER-15918
         (370 letters)



>NCBI__GCF_000017145.1:WP_012066838.1
          Length = 392

 Score =  481 bits (1238), Expect = e-140
 Identities = 235/379 (62%), Positives = 279/379 (73%), Gaps = 10/379 (2%)

Query: 2   KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61
           KP + P N  FSSGPCAK PG+++E L D P GRSHR+K GK KL +AI  TR++L +P 
Sbjct: 6   KPAQRPANTHFSSGPCAKRPGWTLEALSDAPLGRSHRAKIGKTKLKQAIDLTREILEVPA 65

Query: 62  DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121
           DY +GIVPASDTGA EM LWSMLG RGVD+L WESF  GW TD+ KQLKL D R  EA+Y
Sbjct: 66  DYRIGIVPASDTGAVEMALWSMLGARGVDMLAWESFGSGWVTDVVKQLKLADVRRLEADY 125

Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181
           G+LPDL +VDF  DVVF WNGTTSGV+VP+AD+IP  R+G+T+CDATSA FA  + + KL
Sbjct: 126 GELPDLSRVDFDRDVVFTWNGTTSGVRVPDADFIPSGRKGLTICDATSAAFAQALDFAKL 185

Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGST 241
           DV+TFSWQKVLGGEGAHG+LILSPRAV+RLE+Y PAWPLPKIFR+TKGGKL + IF G T
Sbjct: 186 DVVTFSWQKVLGGEGAHGVLILSPRAVERLETYVPAWPLPKIFRMTKGGKLIEGIFTGET 245

Query: 242 INTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRS 301
           INTPSML  ED++  L WA+SVGGLK L  R + N  V   FVA N+WI  LA   E RS
Sbjct: 246 INTPSMLCVEDYIDALLWAKSVGGLKGLTARADANAEVIHRFVAANDWIVNLAVKPETRS 305

Query: 302 STSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVE 351
           +TSVC ++          D      K ++  LEKE VA+DIG YRDAPSGLRIW GAT+E
Sbjct: 306 NTSVCLRIVDGDVSALDADAQGAFAKGVVALLEKEGVAFDIGHYRDAPSGLRIWAGATIE 365

Query: 352 KEDLECLCEWIEWAYNLVK 370
             D+E L  W+ WA+   K
Sbjct: 366 TSDMEALMPWLAWAFETQK 384


Lambda     K      H
   0.319    0.136    0.430 

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: 496
Number of extensions: 20
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: 392
Length adjustment: 30
Effective length of query: 340
Effective length of database: 362
Effective search space:   123080
Effective search space used:   123080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_012066838.1 SMED_RS13120 (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.3894965.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     3e-216  703.6   0.8   3.4e-216  703.4   0.8    1.0  1  NCBI__GCF_000017145.1:WP_012066838.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017145.1:WP_012066838.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  703.4   0.8  3.4e-216  3.4e-216       1     373 [.      10     382 ..      10     383 .. 1.00

  Alignments for each domain:
  == domain 1  score: 703.4 bits;  conditional E-value: 3.4e-216
                             TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 
                                           rpan +fssgpcakrpg+++e+l +a+lgrshr+k+gk+klk+ai+ tre+levpady+igiv+asdtgavem
  NCBI__GCF_000017145.1:WP_012066838.1  10 RPANTHFSSGPCAKRPGWTLEALSDAPLGRSHRAKIGKTKLKQAIDLTREILEVPADYRIGIVPASDTGAVEM 82 
                                           79*********************************************************************** PP

                             TIGR01365  74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146
                                           alws+lgargvd+la+esfg+gwvtdv+kqlkl dvr+lea+yg+lpdl++vdf++dvvftwngttsgvrvp+
  NCBI__GCF_000017145.1:WP_012066838.1  83 ALWSMLGARGVDMLAWESFGSGWVTDVVKQLKLADVRRLEADYGELPDLSRVDFDRDVVFTWNGTTSGVRVPD 155
                                           ************************************************************************* PP

                             TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219
                                           +dfip+ r+glticdatsaafaq ld+ kldvvtfswqkvlggegahgvlilsprav+rle+y pawplpkif
  NCBI__GCF_000017145.1:WP_012066838.1 156 ADFIPSGRKGLTICDATSAAFAQALDFAKLDVVTFSWQKVLGGEGAHGVLILSPRAVERLETYVPAWPLPKIF 228
                                           ************************************************************************* PP

                             TIGR01365 220 rltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatk 292
                                           r+tkggkl+++if getintpsml+ved++dal wa+s+gglk l arad+n++v++ fva ++w+  la+++
  NCBI__GCF_000017145.1:WP_012066838.1 229 RMTKGGKLIEGIFTGETINTPSMLCVEDYIDALLWAKSVGGLKGLTARADANAEVIHRFVAANDWIVNLAVKP 301
                                           ************************************************************************* PP

                             TIGR01365 293 eirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdlealle 365
                                           e+rsntsvcl++vd dv+ald+daq  fak++v +lekegva+dig yrdap+glriw gat+e+sd+eal++
  NCBI__GCF_000017145.1:WP_012066838.1 302 ETRSNTSVCLRIVDGDVSALDADAQGAFAKGVVALLEKEGVAFDIGHYRDAPSGLRIWAGATIETSDMEALMP 374
                                           ************************************************************************* PP

                             TIGR01365 366 wldwafal 373
                                           wl waf++
  NCBI__GCF_000017145.1:WP_012066838.1 375 WLAWAFET 382
                                           ******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (392 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.93
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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