Alignments for a candidate for dapC in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Pseudomonas fluorescens FW300-N2C3

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate AO356_03470 AO356_03470 3-phosphoserine/phosphohydroxythreonine aminotransferase

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_03470
          Length = 361

 Score =  406 bits (1043), Expect = e-118
 Identities = 202/358 (56%), Positives = 252/358 (70%), Gaps = 2/358 (0%)

Query: 5   FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64
           +NF +GPA LP  VLK+AQ EL DW+G G SVME+SHR  EF+ +A +AE+D RDLLN+P
Sbjct: 6   YNFCAGPAALPEAVLKRAQGELLDWHGKGLSVMEMSHRSDEFVSIATKAEQDLRDLLNIP 65

Query: 65  SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124
           SNYKVLF  GG   QFA +PLN+L +   ADY+D G W+  AI+EA +Y   NV      
Sbjct: 66  SNYKVLFLQGGASQQFAQIPLNLLPENGKADYIDTGIWSQKAIEEASRYGHVNVAATAKP 125

Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184
            D   A+    EW LS +AAY+HY PNETI G+  +  P+ G DV + AD SS ILSRP+
Sbjct: 126 YDYF-AIPGQNEWNLSKDAAYVHYAPNETIGGLEFNWIPETG-DVPLVADMSSDILSRPV 183

Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244
           D+SR+G+IYAGAQKNIGP+G+ + I+REDLLG+A   CP++L+Y +  DNGSM+NTPPT 
Sbjct: 184 DISRFGMIYAGAQKNIGPSGILVSIIREDLLGRARSLCPTMLNYKVAADNGSMYNTPPTL 243

Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304
           AWYLSGLVF+WLK  GGV  + K+N+ K   LY  ID S  Y N + K +RS MNVPF+L
Sbjct: 244 AWYLSGLVFEWLKEQGGVEAIGKLNEVKQRTLYDFIDASGLYSNPINKTDRSWMNVPFRL 303

Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
           AD  LDK FL  +   GL  LKGHR VGGMRASIYNA+ +  V AL  +M EFE+ HG
Sbjct: 304 ADDRLDKPFLAGADERGLLNLKGHRSVGGMRASIYNAVDINAVNALIAYMAEFEKEHG 361


Lambda     K      H
   0.319    0.136    0.405 

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: 419
Number of extensions: 12
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: 362
Length of database: 361
Length adjustment: 29
Effective length of query: 333
Effective length of database: 332
Effective search space:   110556
Effective search space used:   110556
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate AO356_03470 AO356_03470 (3-phosphoserine/phosphohydroxythreonine 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.6801.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-164  533.5   0.0   1.2e-164  533.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470  AO356_03470 3-phosphoserine/phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470  AO356_03470 3-phosphoserine/phosphohydroxythreonine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  533.3   0.0  1.2e-164  1.2e-164       2     358 .]       6     360 ..       5     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 533.3 bits;  conditional E-value: 1.2e-164
                                       TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdny 64 
                                                     +nF+aGPaalpe+vl++aq elld++g+glsvme+sHRs+ef +++++ae+dlr+Llnip+ny
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470   6 YNFCAGPAALPEAVLKRAQGELLDWHGKGLSVMEMSHRSDEFVSIATKAEQDLRDLLNIPSNY 68 
                                                     8************************************************************** PP

                                       TIGR01364  65 evlflqGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkysk 127
                                                     +vlflqGGa++qfa++plnll e+ +adyi tG ws+ka++ea+++++ v+v+a+++  +y +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470  69 KVLFLQGGASQQFAQIPLNLLPENGKADYIDTGIWSQKAIEEASRYGH-VNVAATAKPYDYFA 130
                                                     **********************************************99.************** PP

                                       TIGR01364 128 ipdeeelelkedaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliya 190
                                                     ip ++e++l++daayv+++ neti G+ef+++pe+ ++plvaD+ssdilsr++d+s++g+iya
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 131 IPGQNEWNLSKDAAYVHYAPNETIGGLEFNWIPETGDVPLVADMSSDILSRPVDISRFGMIYA 193
                                                     *************************************************************** PP

                                       TIGR01364 191 GaqKniGpaGvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlk 253
                                                     GaqKniGp+G+ v i+r+dll+ra++ +p++l+Yk++a+n s+yntppt a+y++glv++wlk
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 194 GAQKNIGPSGILVSIIREDLLGRARSLCPTMLNYKVAADNGSMYNTPPTLAWYLSGLVFEWLK 256
                                                     *************************************************************** PP

                                       TIGR01364 254 ekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaee 316
                                                     e+GGv+++ k n+ K + lY+ id+s g+y n+++k++Rs+mnv+F+l++++l+k Fl+ a e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 257 EQGGVEAIGKLNEVKQRTLYDFIDAS-GLYSNPINKTDRSWMNVPFRLADDRLDKPFLAGADE 318
                                                     ************************99.6*********************************** PP

                                       TIGR01364 317 kglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                                     +gl++lkGhrsvGG+RasiYna+ +++v+aL+++m eFek+h
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_03470 319 RGLLNLKGHRSVGGMRASIYNAVDINAVNALIAYMAEFEKEH 360
                                                     ***************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (361 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: 8.41
//
[ok]

This GapMind analysis is from Apr 09 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