Alignments for a candidate for serC in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Malonomonas rubra DSM 5091

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_072909464.1 BUB13_RS14345 3-phosphoserine/phosphohydroxythreonine transaminase

Query= BRENDA::Q9SHP0
         (422 letters)



>NCBI__GCF_900142125.1:WP_072909464.1
          Length = 362

 Score =  327 bits (838), Expect = 4e-94
 Identities = 171/363 (47%), Positives = 236/363 (65%), Gaps = 5/363 (1%)

Query: 62  RVINFAAGPAALPENVLLKAQSDLYNWRGSGMSVMEMSHRGKEFLSIIQKAESDLRQLLE 121
           +V NF AGPA LPE+V+ + + +  ++ G G+S++E+SHR KEF  ++ KA+ D R+L  
Sbjct: 3   KVFNFGAGPAMLPESVMQQIREEWLDFSGMGVSIIEISHRAKEFEQVLLKAQDDFRKLTN 62

Query: 122 IPSEYSVLFLQGGATTQFAALPLNLCKSDDSVD--YIVTGSWGDKAFKEAKKYCNPKVIW 179
           +P  Y +LF+ GGA  QF+ALPLNL +  +S    Y+ TG++   A K+A  +C+ KVI 
Sbjct: 63  LPENYKILFIHGGARMQFSALPLNLARRSESKKCLYVETGNFAKLANKDAAAFCDVKVIA 122

Query: 180 SGKSEKYTKVPTFDGLEQSSDAKYLHICANETIHGVEFKDYPLVENPDGVLIADMSSNFC 239
           S     Y ++P         DA YLHI  N TI+G  +  +P  E     LIAD +S   
Sbjct: 123 SSADTNYDRIPEITPEMVDQDAAYLHITTNNTIYGSRYNSFP--ETGAVPLIADQTSEIL 180

Query: 240 SKPVDVSKFGVIYAGAQKNVGPSGVTIVIIRKDLIGNARDITPVMLDYKIHDENSSLYNT 299
           S+ VD SKFG IYAG QKN+GPSG  IV+IR+DL+G A + TP +L+Y   D+++SL NT
Sbjct: 181 SRVVDYSKFGCIYAGLQKNLGPSGTAIVVIREDLLGQAAEKTPTLLNYTQADKDNSLTNT 240

Query: 300 PPCFGIYMCGLVFDDLLEQGGLKEVEKKNQRKAELLYNAIDESRGFFRCPVEKSVRSLMN 359
              F IY  GLV   LL+QGG+  +EK+N+ KA++LY+ ID S  +FR  +    R  MN
Sbjct: 241 ANTFAIYTTGLVLQWLLDQGGVAAIEKQNEAKAKVLYDLIDSS-DYFRGVILPEFRGTMN 299

Query: 360 VPFTLEKSELEAEFIKEAAKEKMVQLKGHRSVGGMRASIYNAMPLAGVEKLVAFMKDFQA 419
           V F L  +ELEA+F+KEA    +  LKGHRSVGG+RASIYNAMP+AGVE L  FM+DF  
Sbjct: 300 VSFNLPTAELEAQFLKEAGAANLYALKGHRSVGGIRASIYNAMPMAGVEALANFMQDFAK 359

Query: 420 RHA 422
           +++
Sbjct: 360 KNS 362


Lambda     K      H
   0.317    0.133    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: 367
Number of extensions: 16
Number of successful extensions: 4
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: 422
Length of database: 362
Length adjustment: 31
Effective length of query: 391
Effective length of database: 331
Effective search space:   129421
Effective search space used:   129421
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_072909464.1 BUB13_RS14345 (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.22769.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-141  457.8   0.0   1.2e-141  457.7   0.0    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072909464.1  BUB13_RS14345 3-phosphoserine/ph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072909464.1  BUB13_RS14345 3-phosphoserine/phosphohydroxythreonine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.7   0.0  1.2e-141  1.2e-141       1     358 []       4     361 ..       4     361 .. 0.99

  Alignments for each domain:
  == domain 1  score: 457.7 bits;  conditional E-value: 1.2e-141
                                 TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 
                                               ++nF+aGPa+lpe+v++++++e ldf+g+g+s++eisHR+kefe+v+ +a++d+r+L n+p+ny++lf+
  lcl|NCBI__GCF_900142125.1:WP_072909464.1   4 VFNFGAGPAMLPESVMQQIREEWLDFSGMGVSIIEISHRAKEFEQVLLKAQDDFRKLTNLPENYKILFI 72 
                                               58******************************************************************* PP

                                 TIGR01364  70 qGGattqfaavplnllk..ekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelel 136
                                                GGa+ qf+a+plnl++  e+k++ y+ tG+++k a k+a  +++ vkv+as+++++y++ip+     +
  lcl|NCBI__GCF_900142125.1:WP_072909464.1  73 HGGARMQFSALPLNLARrsESKKCLYVETGNFAKLANKDAAAFCD-VKVIASSADTNYDRIPEITPEMV 140
                                               ****************977778**********************9.*********************** PP

                                 TIGR01364 137 kedaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvi 205
                                               ++daay+++++n+ti+G  +++ pe+  +pl+aD  s+ilsr +d sk+g iyaG qKn+Gp+G ++v+
  lcl|NCBI__GCF_900142125.1:WP_072909464.1 141 DQDAAYLHITTNNTIYGSRYNSFPETGAVPLIADQTSEILSRVVDYSKFGCIYAGLQKNLGPSGTAIVV 209
                                               ********************************************************************* PP

                                 TIGR01364 206 vrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYe 274
                                               +r+dll++a +++p++l+Y+ + + +sl nt  tfaiy++glvl+wl+++GGv+++ek+n++Kak+lY+
  lcl|NCBI__GCF_900142125.1:WP_072909464.1 210 IREDLLGQAAEKTPTLLNYTQADKDNSLTNTANTFAIYTTGLVLQWLLDQGGVAAIEKQNEAKAKVLYD 278
                                               ********************************************************************* PP

                                 TIGR01364 275 aidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalplee 343
                                               +id+s+ ++++ + ++ R +mnv+F+l+ +ele++Flkea +++l +lkGhrsvGGiRasiYna+p+++
  lcl|NCBI__GCF_900142125.1:WP_072909464.1 279 LIDSSD-YFRGVILPEFRGTMNVSFNLPTAELEAQFLKEAGAANLYALKGHRSVGGIRASIYNAMPMAG 346
                                               ***885.************************************************************** PP

                                 TIGR01364 344 vqaLvdfmkeFekkh 358
                                               v+aL++fm++F+kk+
  lcl|NCBI__GCF_900142125.1:WP_072909464.1 347 VEALANFMQDFAKKN 361
                                               ************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (362 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.59
//
[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