Alignments for a candidate for serC in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC in Pseudomonas putida KT2440

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate PP_1768 PP_1768 phosphoserine aminotransferase

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__Putida:PP_1768
          Length = 361

 Score =  413 bits (1062), Expect = e-120
 Identities = 206/358 (57%), Positives = 259/358 (72%), Gaps = 2/358 (0%)

Query: 5   FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64
           FNF +GPA LP  VL++AQ E+ DW G G SVME+SHR  +++ +AE+AE+D RDLL+VP
Sbjct: 6   FNFCAGPAALPDAVLQRAQAEMLDWRGKGLSVMEMSHRSDDYVAIAEKAEQDLRDLLSVP 65

Query: 65  SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124
           SNYKVLF  GG   QFA +PLN+L +  TADY++ G W+  AI+EA+++   NV      
Sbjct: 66  SNYKVLFLQGGASQQFAEIPLNLLPENGTADYIETGIWSKKAIEEARRFGNVNVAATAKP 125

Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184
            D L A+    EW L+ NAAY+HY  NETI G+  D  P  G DV +  D SS ILSRPI
Sbjct: 126 YDYL-AIPGQNEWNLTKNAAYVHYASNETIGGLQFDWVPQTG-DVPLVVDMSSDILSRPI 183

Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244
           DVS++G+IYAGAQKNIGP+GL +VIVREDLLG A  +CP++LDY +  DNGSM+NTP T+
Sbjct: 184 DVSQFGLIYAGAQKNIGPSGLVVVIVREDLLGHARSSCPTMLDYKVSADNGSMYNTPATY 243

Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304
           +WYLSGLVF+WLK  GGV  M++ N+ K + LYG ID S+FY N ++   RS MNVPF+L
Sbjct: 244 SWYLSGLVFEWLKEQGGVEAMEQRNRAKKDRLYGFIDRSEFYTNPISVNARSWMNVPFRL 303

Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
           AD  LDK FL  + A GL  LKGHR VGGMRASIYNA+ LE V+AL  +M EFE+ HG
Sbjct: 304 ADERLDKAFLAGADARGLLNLKGHRSVGGMRASIYNALGLEAVEALVGYMAEFEKEHG 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: 410
Number of extensions: 13
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 PP_1768 PP_1768 (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.24429.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     2e-166  539.2   0.0   2.3e-166  539.0   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_1768  PP_1768 phosphoserine aminotrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1768  PP_1768 phosphoserine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  539.0   0.0  2.3e-166  2.3e-166       2     358 .]       6     360 ..       5     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 539.0 bits;  conditional E-value: 2.3e-166
                           TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattq 76 
                                         +nF+aGPaalp++vl++aq+e+ld++g+glsvme+sHRs+++ +++e+ae+dlr+Ll++p+ny+vlflqGGa++q
  lcl|FitnessBrowser__Putida:PP_1768   6 FNFCAGPAALPDAVLQRAQAEMLDWRGKGLSVMEMSHRSDDYVAIAEKAEQDLRDLLSVPSNYKVLFLQGGASQQ 80 
                                         8************************************************************************** PP

                           TIGR01364  77 faavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcaneti 151
                                         fa++plnll e+ +adyi tG wskka++ea+++++ v+v+a+++  +y +ip ++e++l+++aayv++++neti
  lcl|FitnessBrowser__Putida:PP_1768  81 FAEIPLNLLPENGTADYIETGIWSKKAIEEARRFGN-VNVAATAKPYDYLAIPGQNEWNLTKNAAYVHYASNETI 154
                                         **********************************99.************************************** PP

                           TIGR01364 152 eGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYki 226
                                          G++f+++p++ ++plv+D+ssdilsr+idvs++gliyaGaqKniGp+G++vvivr+dll++a++++p++ldYk+
  lcl|FitnessBrowser__Putida:PP_1768 155 GGLQFDWVPQTGDVPLVVDMSSDILSRPIDVSQFGLIYAGAQKNIGPSGLVVVIVREDLLGHARSSCPTMLDYKV 229
                                         *************************************************************************** PP

                           TIGR01364 227 laendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtl 301
                                          a+n s+yntp+t+++y++glv++wlke+GGv+++e++n++K++ lY  id+se fy+n+++ +aRs+mnv+F+l
  lcl|FitnessBrowser__Putida:PP_1768 230 SADNGSMYNTPATYSWYLSGLVFEWLKEQGGVEAMEQRNRAKKDRLYGFIDRSE-FYTNPISVNARSWMNVPFRL 303
                                         ***************************************************996.******************** PP

                           TIGR01364 302 kkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                         ++e+l+k Fl+ a ++gl++lkGhrsvGG+RasiYnal le+v+aLv +m eFek+h
  lcl|FitnessBrowser__Putida:PP_1768 304 ADERLDKAFLAGADARGLLNLKGHRSVGGMRASIYNALGLEAVEALVGYMAEFEKEH 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.00
//
[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