GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Pseudomonas simiae WCS417

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate GFF1596 PS417_08120 MFS transporter

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__WCS417:GFF1596
          Length = 361

 Score =  405 bits (1042), Expect = e-118
 Identities = 201/358 (56%), Positives = 253/358 (70%), Gaps = 2/358 (0%)

Query: 5   FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64
           +NF +GPA LP  VL++AQ EL DW+G G SVME+SHR  EF+ +A +AE+D RDLL++P
Sbjct: 6   YNFCAGPAALPEAVLQRAQGELLDWHGKGLSVMEMSHRSDEFVSIATKAEQDLRDLLDIP 65

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

Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184
            D   A+    EW+LS +AAY+HY  NETI G+  D  P+ G DV +  D SS ILSRPI
Sbjct: 126 YDYF-AIPGQNEWKLSKDAAYVHYVANETIGGLEFDWVPEVG-DVPLVCDMSSDILSRPI 183

Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244
           DVS+YG+IYAGAQKNIGP+G+ + I+REDLLG+A   CP++L+Y +  DNGSM+NTPP F
Sbjct: 184 DVSKYGMIYAGAQKNIGPSGILVNIIREDLLGRARSLCPTMLNYKVAADNGSMYNTPPAF 243

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

Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
           AD  LDK FL  +   GL  LKGHR VGGMRASIYNA+ +  + AL ++M  FE+ HG
Sbjct: 304 ADDRLDKPFLVGAEERGLLNLKGHRSVGGMRASIYNAVDIHAINALVEYMAAFEKEHG 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: 422
Number of extensions: 14
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 GFF1596 PS417_08120 (MFS transporter)
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.25701.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.3e-163  530.0   0.0   1.5e-163  529.8   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF1596  PS417_08120 MFS transporter


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF1596  PS417_08120 MFS transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  529.8   0.0  1.5e-163  1.5e-163       2     358 .]       6     360 ..       5     360 .. 0.99

  Alignments for each domain:
  == domain 1  score: 529.8 bits;  conditional E-value: 1.5e-163
                           TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattq 76 
                                         +nF+aGPaalpe+vl++aq elld++g+glsvme+sHRs+ef +++++ae+dlr+Ll+ip+ny+vlflqGGa++q
  lcl|FitnessBrowser__WCS417:GFF1596   6 YNFCAGPAALPEAVLQRAQGELLDWHGKGLSVMEMSHRSDEFVSIATKAEQDLRDLLDIPSNYKVLFLQGGASQQ 80 
                                         8************************************************************************** PP

                           TIGR01364  77 faavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcaneti 151
                                         fa++plnll e+ +adyi tG w++ka++ea+++++ v+v+ +++  +y +ip ++e++l++daayv++ aneti
  lcl|FitnessBrowser__WCS417:GFF1596  81 FAQIPLNLLPEDGTADYIDTGIWGQKAIEEASRYGH-VNVAGTAKPYDYFAIPGQNEWKLSKDAAYVHYVANETI 154
                                         **********************************99.************************************** PP

                           TIGR01364 152 eGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYki 226
                                          G+ef+++pev ++plv+D+ssdilsr+idvskyg+iyaGaqKniGp+G+ v i+r+dll+ra++ +p++l+Yk+
  lcl|FitnessBrowser__WCS417:GFF1596 155 GGLEFDWVPEVGDVPLVCDMSSDILSRPIDVSKYGMIYAGAQKNIGPSGILVNIIREDLLGRARSLCPTMLNYKV 229
                                         *************************************************************************** PP

                           TIGR01364 227 laendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtl 301
                                         +a+n s+yntpp fa+y++glv++wlke+GGv+++ k n+eK+++lY+ id+s g+y n+++ ++Rs+mnv+F+l
  lcl|FitnessBrowser__WCS417:GFF1596 230 AADNGSMYNTPPAFAWYLSGLVFEWLKEQGGVAAMGKLNEEKKRVLYDFIDAS-GLYSNPINLTDRSWMNVPFRL 303
                                         ***************************************************99.6******************** PP

                           TIGR01364 302 kkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                         ++++l+k Fl  aee+gl++lkGhrsvGG+RasiYna+ +++++aLv++m  Fek+h
  lcl|FitnessBrowser__WCS417:GFF1596 304 ADDRLDKPFLVGAEERGLLNLKGHRSVGGMRASIYNAVDIHAINALVEYMAAFEKEH 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: 10.46
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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:

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:

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:

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