Alignments for a candidate for dapC in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Marinobacter adhaerens HP15

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate GFF1394 HP15_1361 phosphoserine aminotransferase

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__Marino:GFF1394
          Length = 347

 Score =  380 bits (977), Expect = e-110
 Identities = 192/349 (55%), Positives = 242/349 (69%), Gaps = 2/349 (0%)

Query: 14  LPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVPSNYKVLFCH 73
           +P  VL+QA+ E+ DW G G SVME+SHR  EF+Q+AE AEKD R+L  V  +Y VLF  
Sbjct: 1   MPESVLRQARDEMLDWRGTGMSVMEMSHRSDEFVQIAETAEKDLRELAGVSDDYAVLFMQ 60

Query: 74  GGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVTVDGLRAVKP 133
           GG   QF+ +PLN+LG+K +ADYV+ G W+  AI EA +Y   NV  A     G   +  
Sbjct: 61  GGASSQFSTIPLNLLGEKGSADYVNTGIWSKKAIAEASRYGKVNVV-ASSEDSGFTTIPD 119

Query: 134 MREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPIDVSRYGVIY 193
              WQ S +AAYMHY PNETI G+  D  P+     +VA D SS++LSRP+DVSR+GVIY
Sbjct: 120 QSSWQTSADAAYMHYTPNETIGGLEFDFIPESPTAPLVA-DMSSSMLSRPVDVSRFGVIY 178

Query: 194 AGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTFAWYLSGLVF 253
           AGAQKNIGP+GL +VI+R+DLLGKA    P++++Y ++ DNGSM+NTP T++WYL+GLVF
Sbjct: 179 AGAQKNIGPSGLVVVIIRKDLLGKARKETPTMMNYQVIADNGSMYNTPATYSWYLAGLVF 238

Query: 254 KWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQLADSALDKLF 313
           KWLK  GGV  M +IN +KA  LY  ID ++FY N +    RS MNVPF LAD AL+  F
Sbjct: 239 KWLKEQGGVKAMGEINLRKARKLYDFIDTNEFYANPIDPRFRSWMNVPFTLADDALNGEF 298

Query: 314 LEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
           L+ + A GL  L GHR VGGMRASIYNAMP  GV AL D+M EF +  G
Sbjct: 299 LKGANARGLLNLAGHRSVGGMRASIYNAMPEAGVDALIDYMTEFAKERG 347


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: 380
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: 347
Length adjustment: 29
Effective length of query: 333
Effective length of database: 318
Effective search space:   105894
Effective search space used:   105894
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 GFF1394 HP15_1361 (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.17349.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.7e-156  505.9   0.0     3e-156  505.7   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF1394  HP15_1361 phosphoserine aminotra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1394  HP15_1361 phosphoserine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  505.7   0.0    3e-156    3e-156      11     357 ..       1     345 [.       1     346 [. 0.99

  Alignments for each domain:
  == domain 1  score: 505.7 bits;  conditional E-value: 3e-156
                           TIGR01364  11 lpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqfaavplnll 85 
                                         +pe+vl++a++e+ld++g+g+svme+sHRs+ef +++e+ae+dlreL  ++d+y+vlf+qGGa++qf+++plnll
  lcl|FitnessBrowser__Marino:GFF1394   1 MPESVLRQARDEMLDWRGTGMSVMEMSHRSDEFVQIAETAEKDLRELAGVSDDYAVLFMQGGASSQFSTIPLNLL 75 
                                         89************************************************************************* PP

                           TIGR01364  86 kekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcanetieGvefkelp 160
                                          ek  ady++tG wskka++ea++++k v+vvas+e++ +++ipd+++++++ daay++++ neti G+ef+ +p
  lcl|FitnessBrowser__Marino:GFF1394  76 GEKGSADYVNTGIWSKKAIAEASRYGK-VNVVASSEDSGFTTIPDQSSWQTSADAAYMHYTPNETIGGLEFDFIP 149
                                         *************************99.*********************************************** PP

                           TIGR01364 161 evkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkilaendslyn 235
                                         e+ +aplvaD+ss++lsr++dvs++g+iyaGaqKniGp+G++vvi+rkdll++a+ke+p++++Y+++a+n s+yn
  lcl|FitnessBrowser__Marino:GFF1394 150 ESPTAPLVADMSSSMLSRPVDVSRFGVIYAGAQKNIGPSGLVVVIIRKDLLGKARKETPTMMNYQVIADNGSMYN 224
                                         *************************************************************************** PP

                           TIGR01364 236 tpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeF 310
                                         tp+t+++y++glv+kwlke+GGvk++ + n +Ka+ lY+ id++ +fy n+++++ Rs+mnv+Ftl+++ l+ eF
  lcl|FitnessBrowser__Marino:GFF1394 225 TPATYSWYLAGLVFKWLKEQGGVKAMGEINLRKARKLYDFIDTN-EFYANPIDPRFRSWMNVPFTLADDALNGEF 298
                                         ******************************************77.5***************************** PP

                           TIGR01364 311 lkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekk 357
                                         lk a+++gl++l GhrsvGG+RasiYna+p ++v aL+d+m eF+k+
  lcl|FitnessBrowser__Marino:GFF1394 299 LKGANARGLLNLAGHRSVGGMRASIYNAMPEAGVDALIDYMTEFAKE 345
                                         ********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (347 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.77
//
[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