Alignments for a candidate for dapC in Allochromatium vinosum DSM 180

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Allochromatium vinosum DSM 180

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_012971183.1 ALVIN_RS09870 3-phosphoserine/phosphohydroxythreonine transaminase

Query= BRENDA::P23721
         (362 letters)



>NCBI__GCF_000025485.1:WP_012971183.1
          Length = 360

 Score =  413 bits (1061), Expect = e-120
 Identities = 215/362 (59%), Positives = 262/362 (72%), Gaps = 2/362 (0%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           MA+++NFS+GPAMLP  VL QA+ E+ DW G G  V E+SHRGKEF+ +A EAE D R+L
Sbjct: 1   MARVYNFSAGPAMLPEAVLAQARDEMLDWRGSGMCVAEMSHRGKEFMSIAAEAEADLREL 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           L +P+NYKVLF  GG   QFA +P+N+L     ADY++ G W+  AI EA+ Y T NV  
Sbjct: 61  LAIPANYKVLFLQGGASLQFAMIPMNLLRGAEGADYINTGSWSKKAIAEARHYGTVNVAA 120

Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180
              +    RA     E  LS +AAY+HY PNETI+G+     P+ G D  + AD SSTIL
Sbjct: 121 TTESSKFTRA-PAQDELNLSADAAYVHYTPNETIEGVEFPYVPETG-DKPLVADMSSTIL 178

Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240
           SRPIDVS++G+IYAGAQKNIGPAGLTIVIVREDL+G+     P++LDY I  DN SM+NT
Sbjct: 179 SRPIDVSKFGLIYAGAQKNIGPAGLTIVIVREDLIGQPINGTPTMLDYKIHADNDSMYNT 238

Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV 300
           PPT+AWYL+GLVFKWLK  GG+A M  +N +KA  LY VID S FY N VA  +RS MNV
Sbjct: 239 PPTYAWYLAGLVFKWLKDMGGLAAMADVNARKARKLYDVIDASSFYANPVAPTDRSWMNV 298

Query: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360
           PF LA++ LD++FL+E+ AAGL  LKGHR VGGMRASIYNAMP  GV AL  FM EFERR
Sbjct: 299 PFTLANAELDEVFLKEAKAAGLTTLKGHRSVGGMRASIYNAMPEAGVDALVAFMQEFERR 358

Query: 361 HG 362
           +G
Sbjct: 359 NG 360


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: 397
Number of extensions: 8
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: 360
Length adjustment: 29
Effective length of query: 333
Effective length of database: 331
Effective search space:   110223
Effective search space used:   110223
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 WP_012971183.1 ALVIN_RS09870 (3-phosphoserine/phosphohydroxythreonine transaminase)
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.10742.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.7e-166  537.5   0.0   7.6e-166  537.3   0.0    1.0  1  lcl|NCBI__GCF_000025485.1:WP_012971183.1  ALVIN_RS09870 3-phosphoserine/ph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012971183.1  ALVIN_RS09870 3-phosphoserine/phosphohydroxythreonine transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  537.3   0.0  7.6e-166  7.6e-166       1     357 [.       4     358 ..       4     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 537.3 bits;  conditional E-value: 7.6e-166
                                 TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlfl 69 
                                               ++nFsaGPa+lpe+vl++a++e+ld++g+g+ v+e+sHR kef++++ eae dlreLl ip ny+vlfl
  lcl|NCBI__GCF_000025485.1:WP_012971183.1   4 VYNFSAGPAMLPEAVLAQARDEMLDWRGSGMCVAEMSHRGKEFMSIAAEAEADLRELLAIPANYKVLFL 72 
                                               59******************************************************************* PP

                                 TIGR01364  70 qGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelke 138
                                               qGGa+ qfa++p+nll+  + adyi+tG+wskka++ea+++++ v+v+a++e++k+++ p ++el+l+ 
  lcl|NCBI__GCF_000025485.1:WP_012971183.1  73 QGGASLQFAMIPMNLLRGAEGADYINTGSWSKKAIAEARHYGT-VNVAATTESSKFTRAPAQDELNLSA 140
                                               *****************************************99.************************* PP

                                 TIGR01364 139 daayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivr 207
                                               daayv+++ netieGvef  +pe+ ++plvaD+ss ilsr+idvsk+gliyaGaqKniGpaG+t+vivr
  lcl|NCBI__GCF_000025485.1:WP_012971183.1 141 DAAYVHYTPNETIEGVEFPYVPETGDKPLVADMSSTILSRPIDVSKFGLIYAGAQKNIGPAGLTIVIVR 209
                                               ********************************************************************* PP

                                 TIGR01364 208 kdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeai 276
                                               +dl+++  + +p++ldYki+a+nds+yntppt+a+y++glv+kwlk+ GG++++++ n +Ka+ lY++i
  lcl|NCBI__GCF_000025485.1:WP_012971183.1 210 EDLIGQPINGTPTMLDYKIHADNDSMYNTPPTYAWYLAGLVFKWLKDMGGLAAMADVNARKARKLYDVI 278
                                               ********************************************************************* PP

                                 TIGR01364 277 desegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevq 345
                                               d+s+ fy n+v++++Rs+mnv+Ftl+++el++ Flkea+++gl++lkGhrsvGG+RasiYna+p ++v 
  lcl|NCBI__GCF_000025485.1:WP_012971183.1 279 DASS-FYANPVAPTDRSWMNVPFTLANAELDEVFLKEAKAAGLTTLKGHRSVGGMRASIYNAMPEAGVD 346
                                               *997.**************************************************************** PP

                                 TIGR01364 346 aLvdfmkeFekk 357
                                               aLv+fm+eFe++
  lcl|NCBI__GCF_000025485.1:WP_012971183.1 347 ALVAFMQEFERR 358
                                               *********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (360 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: 8.05
//
[ok]

This GapMind analysis is from Apr 10 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