Alignments for a candidate for serC in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Rhodomicrobium vannielii ATCC 17100

Align Phosphoserine aminotransferase; Phosphohydroxythreonine aminotransferase; PSAT; EC 2.6.1.52 (characterized)
to candidate WP_013420529.1 RVAN_RS14850 phosphoserine transaminase

Query= SwissProt::P52878
         (370 letters)



>NCBI__GCF_000166055.1:WP_013420529.1
          Length = 386

 Score =  498 bits (1283), Expect = e-146
 Identities = 239/373 (64%), Positives = 283/373 (75%), Gaps = 8/373 (2%)

Query: 2   KPTRVPNNPCFSSGPCAKHPGYSIEELKDTPFGRSHRSNLGKEKLAEAIKKTRDMLGLPD 61
           KP   PN   FSSGPCAK PGYS++ LK    GRSHRS  GK KL  AI KTR +LG+P 
Sbjct: 5   KPAARPNVAHFSSGPCAKRPGYSLDNLKTAELGRSHRSKPGKAKLKLAIDKTRAILGVPQ 64

Query: 62  DYLVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDVRVFEAEY 121
           DYL+GIV ASDTGAFEM +WS LG RG+DV  WESF K W TDITKQLKLKDVRVF+A Y
Sbjct: 65  DYLIGIVAASDTGAFEMAMWSALGARGIDVFAWESFGKDWVTDITKQLKLKDVRVFDAPY 124

Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNGDWIPENREGLTLCDATSAIFAMDIPYHKL 181
           G+LPDL + DF+NDVVF WNGTTSGV+VP+GD+IP+NREGLT CDATSA FA ++ + KL
Sbjct: 125 GELPDLGQADFRNDVVFTWNGTTSGVRVPSGDFIPDNREGLTFCDATSAAFAQELDWAKL 184

Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKKIFEGST 241
           DV+TFSWQKVLGGE  HG+LILSPRAV+RLESYTPAWP+PK+FR+TKGGKLN++IF+GST
Sbjct: 185 DVVTFSWQKVLGGEAQHGILILSPRAVERLESYTPAWPMPKLFRMTKGGKLNREIFDGST 244

Query: 242 INTPSMLANEDWLATLKWAESVGGLKPLIQRTNDNLAVFEAFVAKNNWIHFLAETKEIRS 301
           INTPSML  ED+L  L WAE +GGL  L  R+N N  V   +V K  W+ FLA     RS
Sbjct: 245 INTPSMLCVEDYLDALNWAEGLGGLTALQARSNANFKVLADWVEKTPWVDFLASVPSTRS 304

Query: 302 STSVCFKV--------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVEKE 353
           +TSVC K+        +      K++  TLEKE VA DIG+YRDAP+GLRIW GAT+E  
Sbjct: 305 NTSVCLKIVDPEIATPEAQAAVAKDIASTLEKEGVALDIGAYRDAPAGLRIWAGATIEAS 364

Query: 354 DLQCLCEWIEWAY 366
           DL+ L  W++WA+
Sbjct: 365 DLEALVPWLDWAF 377


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: 549
Number of extensions: 17
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_013420529.1 RVAN_RS14850 (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.23122.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-210  685.4   0.6   1.2e-210  685.2   0.6    1.0  1  lcl|NCBI__GCF_000166055.1:WP_013420529.1  RVAN_RS14850 phosphoserine trans


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000166055.1:WP_013420529.1  RVAN_RS14850 phosphoserine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.2   0.6  1.2e-210  1.2e-210       1     373 [.       9     379 ..       9     380 .. 0.99

  Alignments for each domain:
  == domain 1  score: 685.2 bits;  conditional E-value: 1.2e-210
                                 TIGR01365   1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtg 69 
                                               rp+  +fssgpcakrpgys+++lk a lgrshrsk gk+klk ai+ktr +l+vp+dyligivaasdtg
  lcl|NCBI__GCF_000166055.1:WP_013420529.1   9 RPNVAHFSSGPCAKRPGYSLDNLKTAELGRSHRSKPGKAKLKLAIDKTRAILGVPQDYLIGIVAASDTG 77 
                                               79999**************************************************************** PP

                                 TIGR01365  70 avemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngt 138
                                               a+ema+ws lgarg+d++a+esfgk+wvtd+tkqlklkdvrv++a+yg+lpdl + df +dvvftwngt
  lcl|NCBI__GCF_000166055.1:WP_013420529.1  78 AFEMAMWSALGARGIDVFAWESFGKDWVTDITKQLKLKDVRVFDAPYGELPDLGQADFRNDVVFTWNGT 146
                                               ********************************************************************* PP

                                 TIGR01365 139 tsgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarle 207
                                               tsgvrvp gdfip++reglt+cdatsaafaq+ld+ kldvvtfswqkvlgge  hg+lilsprav+rle
  lcl|NCBI__GCF_000166055.1:WP_013420529.1 147 TSGVRVPSGDFIPDNREGLTFCDATSAAFAQELDWAKLDVVTFSWQKVLGGEAQHGILILSPRAVERLE 215
                                               ********************************************************************* PP

                                 TIGR01365 208 sytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavle 276
                                               sytpawp+pk+fr+tkggkl+++if+g+tintpsml+ved+ldal+wae +ggl al+ar+++n +vl+
  lcl|NCBI__GCF_000166055.1:WP_013420529.1 216 SYTPAWPMPKLFRMTKGGKLNREIFDGSTINTPSMLCVEDYLDALNWAEGLGGLTALQARSNANFKVLA 284
                                               ********************************************************************* PP

                                 TIGR01365 277 afvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapa 345
                                               ++v+k++wvdfla  + +rsntsvclk+vdp++a+   +aqa +ak+++s+lekegva+dig+yrdapa
  lcl|NCBI__GCF_000166055.1:WP_013420529.1 285 DWVEKTPWVDFLASVPSTRSNTSVCLKIVDPEIATP--EAQAAVAKDIASTLEKEGVALDIGAYRDAPA 351
                                               ********************************9865..458**************************** PP

                                 TIGR01365 346 glriwcgatveksdleallewldwafal 373
                                               glriw gat+e+sdleal++wldwafa 
  lcl|NCBI__GCF_000166055.1:WP_013420529.1 352 GLRIWAGATIEASDLEALVPWLDWAFAN 379
                                               **************************85 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.56
//
[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