Alignments for a candidate for serC in Polaromonas naphthalenivorans CJ2

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Polaromonas naphthalenivorans CJ2

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_011802171.1 PNAP_RS13945 phosphoserine aminotransferase

Query= BRENDA::Q96255
         (430 letters)



>NCBI__GCF_000015505.1:WP_011802171.1
          Length = 368

 Score =  367 bits (943), Expect = e-106
 Identities = 186/368 (50%), Positives = 253/368 (68%), Gaps = 11/368 (2%)

Query: 72  RVFNFAAGPATLPENVLLKAQADLYNWRGSGMSVMEMSHRGKEFLSIIQKAESDLRQLLE 131
           R FNF+AGPA LPE VL +A A++ +W GSGMSVMEMSHRGKEF+SI + AE+D R+L+E
Sbjct: 3   RPFNFSAGPANLPEEVLRQAAAEMLDWHGSGMSVMEMSHRGKEFISIYEHAEADFRELME 62

Query: 132 IPQEYSVLFLQGGATTQFAALPLNLCKSDDTVDFVVTGSWGDKAVKEAKKYCKTNVIWSG 191
           IP+ + +LF+QGG   + A +PLN+ +     DFVVTGSW DK+ KEA+KYC   +  + 
Sbjct: 63  IPEHFKILFMQGGGLAENAIVPLNISRG-GLADFVVTGSWSDKSQKEARKYCDVQIAATN 121

Query: 192 KSEKYTKVPSFEELEQTPDAKYLHICANETIHGVEFKDYP----VPKNGFLVADMSSNFC 247
           +S  +T +P     +   DA Y+H+C NETIHGVEF++ P    +  +  LV D SS+  
Sbjct: 122 ESSAHTSLPPPATWQLRRDASYVHVCTNETIHGVEFQELPDLKALGSDAPLVIDFSSHVA 181

Query: 248 SKPVDVSKFGVIYGGAQKNVGPSGVTIVIIRKDLIGNAQDITPVMLDYKIHDENSSLYNT 307
           S+PVD SK G+ +GGAQKN+GP+GVT+V++R+DL+G+A  + P   +YK   +N S+YNT
Sbjct: 182 SRPVDWSKVGLAFGGAQKNLGPAGVTLVVVREDLLGHALAVCPSAFNYKTVADNDSMYNT 241

Query: 308 PPCFGIYMCGLVFEDLLEQ-----GGLKEVEKKNQRKADLLYNAIEESNGFFRCPVEKSV 362
           PP + IY+ GL F+ L  Q      G+  +EK N  KA LLY+AI+ S G +   V K  
Sbjct: 242 PPTYAIYIAGLTFQWLKRQKEGEATGIAAMEKHNLAKAKLLYDAIDHS-GLYINKVSKDC 300

Query: 363 RSLMNVPFTLEKSELEAEFIKEAAKEKMVQLKGHRSVGGMRASIYNAMPLAGVEKLVAFM 422
           RS MNVPF L       +F+  A    ++QLKGH+SVGGMRASIYNAMPLAGVE LV+++
Sbjct: 301 RSRMNVPFLLRDESRNEDFLAGAKARGLLQLKGHKSVGGMRASIYNAMPLAGVEALVSYL 360

Query: 423 KDFQAKHA 430
           ++F+ KHA
Sbjct: 361 QEFEQKHA 368


Lambda     K      H
   0.316    0.132    0.381 

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: 439
Number of extensions: 20
Number of successful extensions: 5
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: 368
Length adjustment: 31
Effective length of query: 399
Effective length of database: 337
Effective search space:   134463
Effective search space used:   134463
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_011802171.1 PNAP_RS13945 (phosphoserine aminotransferase)
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.10242.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-149  482.6   0.0   3.6e-149  482.4   0.0    1.0  1  lcl|NCBI__GCF_000015505.1:WP_011802171.1  PNAP_RS13945 phosphoserine amino


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015505.1:WP_011802171.1  PNAP_RS13945 phosphoserine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.4   0.0  3.6e-149  3.6e-149       2     358 .]       5     367 ..       4     367 .. 0.97

  Alignments for each domain:
  == domain 1  score: 482.4 bits;  conditional E-value: 3.6e-149
                                 TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 
                                               +nFsaGPa lpeevl++a++e+ld++g+g+svme+sHR kef ++ e+ae d+reL++ip+++++lf+q
  lcl|NCBI__GCF_000015505.1:WP_011802171.1   5 FNFSAGPANLPEEVLRQAAAEMLDWHGSGMSVMEMSHRGKEFISIYEHAEADFRELMEIPEHFKILFMQ 73 
                                               8******************************************************************** PP

                                 TIGR01364  71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelked 139
                                               GG+  + a vpln+ + +  ad++vtG+ws+k+ kea+k+++ v+++a++e++ ++++p   +++l+ d
  lcl|NCBI__GCF_000015505.1:WP_011802171.1  74 GGGLAENAIVPLNISRGG-LADFVVTGSWSDKSQKEARKYCD-VQIAATNESSAHTSLPPPATWQLRRD 140
                                               **************9988.9*********************9.************************** PP

                                 TIGR01364 140 aayvylcanetieGvefkelpevkk....aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvv 204
                                               a+yv++c+neti+Gvef+elp+ k     aplv D+ss++ sr++d sk gl ++GaqKn+GpaGvt+v
  lcl|NCBI__GCF_000015505.1:WP_011802171.1 141 ASYVHVCTNETIHGVEFQELPDLKAlgsdAPLVIDFSSHVASRPVDWSKVGLAFGGAQKNLGPAGVTLV 209
                                               **********************99888889*************************************** PP

                                 TIGR01364 205 ivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkek..G...GvkklekknqeK 268
                                               +vr+dll++a +++ps ++Yk++a+nds+yntppt+aiy++gl+++wlk++  G   G++++ek+n +K
  lcl|NCBI__GCF_000015505.1:WP_011802171.1 210 VVREDLLGHALAVCPSAFNYKTVADNDSMYNTPPTYAIYIAGLTFQWLKRQkeGeatGIAAMEKHNLAK 278
                                               ************************************************965343444************ PP

                                 TIGR01364 269 akllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYn 337
                                               akllY+aid+s g+y+nkv+k++Rs+mnv+F l++e  ++ Fl+ a+++gl++lkGh+svGG+RasiYn
  lcl|NCBI__GCF_000015505.1:WP_011802171.1 279 AKLLYDAIDHS-GLYINKVSKDCRSRMNVPFLLRDESRNEDFLAGAKARGLLQLKGHKSVGGMRASIYN 346
                                               *********88.7******************************************************** PP

                                 TIGR01364 338 alpleevqaLvdfmkeFekkh 358
                                               a+pl++v+aLv++++eFe+kh
  lcl|NCBI__GCF_000015505.1:WP_011802171.1 347 AMPLAGVEALVSYLQEFEQKH 367
                                               *******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (368 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.19
//
[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