GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Shewanella amazonensis SB2B

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 6937577 Sama_1732 phosphoserine aminotransferase (RefSeq)

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__SB2B:6937577
          Length = 364

 Score =  406 bits (1043), Expect = e-118
 Identities = 207/364 (56%), Positives = 262/364 (71%), Gaps = 5/364 (1%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           M+ ++NF +GPAMLPA V+K+AQ EL DWNG G SVMEVSHRG  FIQ+A+++E D R+L
Sbjct: 1   MSAVYNFCAGPAMLPAAVMKKAQAELLDWNGQGVSVMEVSHRGAPFIQLAKDSEADLREL 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           +N+P NY VLF HGGGRGQF+AV  N LGD   A Y+ +G W+ +A +EAKK    N  D
Sbjct: 61  MNIPDNYHVLFMHGGGRGQFSAVVNNFLGDNGKALYLVSGQWSKAATEEAKKLAGDNSID 120

Query: 121 AKVTVDGLRAVKPMREWQLSDNAA---YMHYCPNETIDGIAIDETPDFGADVVVAADFSS 177
               V+ +  +  +    LS N +   Y+HYCPNET+DGI I +  D  +   + AD SS
Sbjct: 121 VINVVEKVNGLNKVVIPALSGNGSEYRYLHYCPNETVDGIEIFD--DIDSPWPIVADMSS 178

Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237
            I+SR IDVSR+ +IYAGAQKNIGP+GL+IVIVR+D+L    +   SI+DY +  +N SM
Sbjct: 179 NIMSREIDVSRFALIYAGAQKNIGPSGLSIVIVRKDMLELPQLTQSSIMDYRLTAENDSM 238

Query: 238 FNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSR 297
           +NTPPTFAWYL+  VFKWLK+ GG+  M ++N +KA  LY  ID+ DFY+N VA  NRS+
Sbjct: 239 YNTPPTFAWYLAAEVFKWLKSVGGIKGMAEVNAEKARRLYACIDSLDFYKNGVAPQNRSQ 298

Query: 298 MNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEF 357
           MNV FQLAD +LDK FL+E+ A GL ALKGHR+VGGMRASIYNAMPLEGV AL  FM  F
Sbjct: 299 MNVTFQLADESLDKDFLKEAEALGLVALKGHRIVGGMRASIYNAMPLEGVDALVSFMRSF 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: 395
Number of extensions: 18
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: 364
Length adjustment: 29
Effective length of query: 333
Effective length of database: 335
Effective search space:   111555
Effective search space used:   111555
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 6937577 Sama_1732 (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.13950.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.8e-148  480.1   0.0   2.1e-148  479.9   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6937577  Sama_1732 phosphoserine aminotra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937577  Sama_1732 phosphoserine aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.9   0.0  2.1e-148  2.1e-148       1     358 []       4     362 ..       4     362 .. 0.94

  Alignments for each domain:
  == domain 1  score: 479.9 bits;  conditional E-value: 2.1e-148
                         TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqf 77 
                                       ++nF+aGPa+lp +v++kaq+elld+ng+g+svme+sHR   f ++++++e dlreL+nipdny+vlf+ GG+++qf
  lcl|FitnessBrowser__SB2B:6937577   4 VYNFCAGPAMLPAAVMKKAQAELLDWNGQGVSVMEVSHRGAPFIQLAKDSEADLRELMNIPDNYHVLFMHGGGRGQF 80 
                                       59*************************************************************************** PP

                         TIGR01364  78 aavplnllkekkvadyivtGawskkalkeakkltk..evkvvase.eekkyskipdeeelelkedaayvylcaneti 151
                                       +av  n+l ++ +a y+v+G+wsk a++eakkl    +++v++   + +  +k+     +    ++ y+++c net+
  lcl|FitnessBrowser__SB2B:6937577  81 SAVVNNFLGDNGKALYLVSGQWSKAATEEAKKLAGdnSIDVINVVeKVNGLNKVVIPALSGNGSEYRYLHYCPNETV 157
                                       *********************************9877444433332334445554446666668899********** PP

                         TIGR01364 152 eGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkila 228
                                       +G+e+ +    +  p+vaD+ss+i+sr+idvs+++liyaGaqKniGp+G+++vivrkd+le  + + +s++dY+ +a
  lcl|FitnessBrowser__SB2B:6937577 158 DGIEIFDDI-DSPWPIVADMSSNIMSREIDVSRFALIYAGAQKNIGPSGLSIVIVRKDMLELPQLTQSSIMDYRLTA 233
                                       ******998.7889*************************************************************** PP

                         TIGR01364 229 endslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkee 305
                                       ends+yntpptfa+y+++ v+kwlk+ GG+k +++ n eKa+ lY +id+  +fykn v++++Rs+mnv+F+l++e 
  lcl|FitnessBrowser__SB2B:6937577 234 ENDSMYNTPPTFAWYLAAEVFKWLKSVGGIKGMAEVNAEKARRLYACIDSL-DFYKNGVAPQNRSQMNVTFQLADES 309
                                       *************************************************77.6************************ PP

                         TIGR01364 306 lekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                       l+k Flkeae+ glv+lkGhr+vGG+RasiYna+ple+v aLv+fm++F++kh
  lcl|FitnessBrowser__SB2B:6937577 310 LDKDFLKEAEALGLVALKGHRIVGGMRASIYNAMPLEGVDALVSFMRSFAAKH 362
                                       **************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (364 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: 11.34
//
[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:

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