Alignments for a candidate for serC in Rhodospirillum centenum SW; ATCC 51521

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Rhodospirillum centenum SW; ATCC 51521

Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_012566971.1 RC1_RS08575 phosphoserine transaminase

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



>NCBI__GCF_000016185.1:WP_012566971.1
          Length = 386

 Score =  477 bits (1227), Expect = e-139
 Identities = 228/379 (60%), Positives = 280/379 (73%), Gaps = 10/379 (2%)

Query: 2   KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61
           KP   P NP FSSGPCAK PG+++E LK    GRSHRSKPGK KL + I  ++++LG+P 
Sbjct: 6   KPDSRPANPQFSSGPCAKRPGWTIEALKGALVGRSHRSKPGKAKLEQVITLSKEILGIPA 65

Query: 62  DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121
            Y +GIVPASDTGA EM LWS+LG RG+D+L WESF K W TD+ KQL+L D R F+A Y
Sbjct: 66  GYRLGIVPASDTGAVEMALWSLLGARGIDMLAWESFGKDWVTDVVKQLRLTDVREFKAPY 125

Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181
           G LPDL +VDF  DVVF WNGTTSGV+VP+ DWIPDDR+G+T+CDATSA FAMD+P+ KL
Sbjct: 126 GALPDLTQVDFARDVVFTWNGTTSGVRVPDGDWIPDDRQGLTICDATSATFAMDLPWSKL 185

Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGST 241
           DV+T+SWQKVLGGE AHGML+LSPRAV+RLES+ PAWP+PKIFR+TK GK+ + IF G T
Sbjct: 186 DVVTWSWQKVLGGEAAHGMLVLSPRAVERLESHKPAWPMPKIFRMTKDGKIVEGIFKGET 245

Query: 242 INTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRS 301
           INTPSM+A ED L  L WA+S+GGL  LI R+  NL     +VA+ +W+ FL +  E RS
Sbjct: 246 INTPSMIAVEDALDGLTWAKSIGGLPALIGRSEANLKAVTDWVARTDWVDFLPQRPETRS 305

Query: 302 STSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVE 351
            TS+C K+          +   E  K++   LEKE VA D G+YRDAP GLRIW GATVE
Sbjct: 306 CTSICLKIVDPWATGQSAEAQAEIAKKVAALLEKEGVALDAGAYRDAPPGLRIWGGATVE 365

Query: 352 KEDLECLCEWIEWAYNLVK 370
             D++ L  W++WAY  VK
Sbjct: 366 TADIQALLPWLDWAYATVK 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: 535
Number of extensions: 14
Number of successful extensions: 2
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: 386
Length adjustment: 30
Effective length of query: 340
Effective length of database: 356
Effective search space:   121040
Effective search space used:   121040
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_012566971.1 RC1_RS08575 (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.14091.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-202  658.9   1.6   1.3e-202  658.7   1.6    1.0  1  lcl|NCBI__GCF_000016185.1:WP_012566971.1  RC1_RS08575 phosphoserine transa


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016185.1:WP_012566971.1  RC1_RS08575 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  658.7   1.6  1.3e-202  1.3e-202       1     374 []      10     383 ..      10     383 .. 1.00

  Alignments for each domain:
  == domain 1  score: 658.7 bits;  conditional E-value: 1.3e-202
                                 TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 
                                               rpanp+fssgpcakrpg+++e+lk a +grshrsk gk+kl++ i  ++e+l++pa y++giv+asdtg
  lcl|NCBI__GCF_000016185.1:WP_012566971.1  10 RPANPQFSSGPCAKRPGWTIEALKGALVGRSHRSKPGKAKLEQVITLSKEILGIPAGYRLGIVPASDTG 78 
                                               7******************************************************************** PP

                                 TIGR01365  70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138
                                               avemalwsllgarg+d+la+esfgk+wvtdv+kql+l dvr ++a+yg lpdl++vdf++dvvftwngt
  lcl|NCBI__GCF_000016185.1:WP_012566971.1  79 AVEMALWSLLGARGIDMLAWESFGKDWVTDVVKQLRLTDVREFKAPYGALPDLTQVDFARDVVFTWNGT 147
                                               ********************************************************************* PP

                                 TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207
                                               tsgvrvp+gd+ip+dr+glticdatsa fa+dl+++kldvvt+swqkvlgge ahg+l+lsprav+rle
  lcl|NCBI__GCF_000016185.1:WP_012566971.1 148 TSGVRVPDGDWIPDDRQGLTICDATSATFAMDLPWSKLDVVTWSWQKVLGGEAAHGMLVLSPRAVERLE 216
                                               ********************************************************************* PP

                                 TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276
                                               s++pawp+pkifr+tk gk+ ++if+getintpsm+avedald l wa+siggl al+ r+++nl+ + 
  lcl|NCBI__GCF_000016185.1:WP_012566971.1 217 SHKPAWPMPKIFRMTKDGKIVEGIFKGETINTPSMIAVEDALDGLTWAKSIGGLPALIGRSEANLKAVT 285
                                               ********************************************************************* PP

                                 TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345
                                               ++va+++wvdfl +++e+rs ts+clk+vdp  +   ++aqa++ak+++ +lekegva+d g+yrdap+
  lcl|NCBI__GCF_000016185.1:WP_012566971.1 286 DWVARTDWVDFLPQRPETRSCTSICLKIVDPWATGQSAEAQAEIAKKVAALLEKEGVALDAGAYRDAPP 354
                                               ********************************************************************* PP

                                 TIGR01365 346 glriwcgatveksdleallewldwafalv 374
                                               glriw gatve+ d++all+wldwa+a+v
  lcl|NCBI__GCF_000016185.1:WP_012566971.1 355 GLRIWGGATVETADIQALLPWLDWAYATV 383
                                               **************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (374 nodes)
Target sequences:                          1  (386 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: 00:00:00.01
# Mc/sec: 12.61
//
[ok]

This GapMind analysis is from Apr 10 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