GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Shewanella sp. ANA-3

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 7024795 Shewana3_1973 phosphoserine aminotransferase (RefSeq)

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__ANA3:7024795
          Length = 363

 Score =  418 bits (1075), Expect = e-121
 Identities = 215/364 (59%), Positives = 272/364 (74%), Gaps = 5/364 (1%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           M+ I+NF +GPAMLPA V+K+AQQEL DWNGLG SVMEVSHRGKEFI + ++AE D R+L
Sbjct: 1   MSAIYNFCAGPAMLPAAVMKKAQQELLDWNGLGVSVMEVSHRGKEFIALTKQAEADLREL 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           +++P NY VLF HGGGRGQF+AV  N LG++  A Y+ +G W+++A+ EA+K       D
Sbjct: 61  MHIPQNYHVLFMHGGGRGQFSAVVNNFLGNQGRALYLVSGQWSSAALAEAQKLAGDTQID 120

Query: 121 AKVTVD---GLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSS 177
           +   V+   GL AV      ++  +  Y+HYCPNET+DGI I +  D    +V  AD SS
Sbjct: 121 SLNIVEKHNGLNAVVLPELHKIDADYRYVHYCPNETVDGIEIFDELDSPWPIV--ADLSS 178

Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237
           TI+SR IDVSRYG+IYAGAQKNIGP+GL+IVIVR+D+L   ++   SI+DY +  ++ SM
Sbjct: 179 TIMSREIDVSRYGLIYAGAQKNIGPSGLSIVIVRDDMLKLPSLTQSSIMDYRLAVEHDSM 238

Query: 238 FNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSR 297
           FNTPPTFAWYL+  VF WLK+ GGVA + KINQQKA++LY  ID + FY+N V  ANRS+
Sbjct: 239 FNTPPTFAWYLAAEVFAWLKSLGGVASIAKINQQKAQMLYACIDANPFYKNGVVAANRSQ 298

Query: 298 MNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEF 357
           MNV FQLAD +LD  FL+E+ AAGL ALKGHR+VGGMRAS+YNAMPLEGV AL  FM EF
Sbjct: 299 MNVTFQLADESLDGAFLKEAEAAGLVALKGHRIVGGMRASLYNAMPLEGVAALVSFMNEF 358

Query: 358 ERRH 361
             +H
Sbjct: 359 AAKH 362


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: 384
Number of extensions: 7
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: 363
Length adjustment: 29
Effective length of query: 333
Effective length of database: 334
Effective search space:   111222
Effective search space used:   111222
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 7024795 Shewana3_1973 (phosphoserine aminotransferase (RefSeq))
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.3629254.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.4e-149  483.0   0.0   2.7e-149  482.8   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7024795  Shewana3_1973 phosphoserine amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7024795  Shewana3_1973 phosphoserine aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.8   0.0  2.7e-149  2.7e-149       1     358 []       4     362 ..       4     362 .. 0.96

  Alignments for each domain:
  == domain 1  score: 482.8 bits;  conditional E-value: 2.7e-149
                         TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqf 77 
                                       i+nF+aGPa+lp +v++kaq+elld+nglg+svme+sHR kef +++++ae dlreL++ip+ny+vlf+ GG+++qf
  lcl|FitnessBrowser__ANA3:7024795   4 IYNFCAGPAMLPAAVMKKAQQELLDWNGLGVSVMEVSHRGKEFIALTKQAEADLRELMHIPQNYHVLFMHGGGRGQF 80 
                                       69*************************************************************************** PP

                         TIGR01364  78 aavplnllkekkvadyivtGawskkalkeakkltk..evkvvase.eekkyskipdeeelelkedaayvylcaneti 151
                                       +av  n+l ++  a y+v+G+ws+ al+ea+kl    ++++++   +++  +++   e  +++ d+ yv++c net+
  lcl|FitnessBrowser__ANA3:7024795  81 SAVVNNFLGNQGRALYLVSGQWSSAALAEAQKLAGdtQIDSLNIVeKHNGLNAVVLPELHKIDADYRYVHYCPNETV 157
                                       *********************************986645444433366777778778999999************** PP

                         TIGR01364 152 eGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkila 228
                                       +G+e+ ++   +  p+vaDlss i+sr+idvs+ygliyaGaqKniGp+G+++vivr+d+l+  + + +s++dY+ ++
  lcl|FitnessBrowser__ANA3:7024795 158 DGIEIFDEL-DSPWPIVADLSSTIMSREIDVSRYGLIYAGAQKNIGPSGLSIVIVRDDMLKLPSLTQSSIMDYRLAV 233
                                       ******998.7889*************************************************************** PP

                         TIGR01364 229 endslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkee 305
                                       e+ds++ntpptfa+y+++ v+ wlk+ GGv++++k nq+Ka++lY +id++  fykn v +++Rs+mnv+F+l++e 
  lcl|FitnessBrowser__ANA3:7024795 234 EHDSMFNTPPTFAWYLAAEVFAWLKSLGGVASIAKINQQKAQMLYACIDANP-FYKNGVVAANRSQMNVTFQLADES 309
                                       *************************************************886.************************ PP

                         TIGR01364 306 lekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                       l+  Flkeae++glv+lkGhr+vGG+Ras+Yna+ple+v aLv+fm+eF++kh
  lcl|FitnessBrowser__ANA3:7024795 310 LDGAFLKEAEAAGLVALKGHRIVGGMRASLYNAMPLEGVAALVSFMNEFAAKH 362
                                       **************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (363 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 15.26
//
[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