Aligments for a candidate for serA in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Aligments for a candidate for serA in Caulobacter crescentus NA1000

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate CCNA_03322 CCNA_03322 D-3-phosphoglycerate dehydrogenase

Query= BRENDA::Q9Z564
         (529 letters)



>FitnessBrowser__Caulo:CCNA_03322
          Length = 526

 Score =  378 bits (971), Expect = e-109
 Identities = 214/528 (40%), Positives = 322/528 (60%), Gaps = 13/528 (2%)

Query: 5   PVVLIAEELSPATVDAL---GPDFEIRHCNGADRAELLPAIADVDAILVRSATKVDAEAV 61
           P VLIA++LSPA V+     G  F+I+   G  + EL+  I D D I +RS  K+D + +
Sbjct: 4   PRVLIADKLSPAAVEIFKNRGLAFDIK--TGLSKDELIAVIGDYDGIAIRSGAKLDKDVI 61

Query: 62  AAAKKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNIPQA 121
           AAA KL+V+ARAG+G+DNVD+ AAT  G++V+N P  N +T AE A  ++ A AR IP A
Sbjct: 62  AAANKLRVIARAGIGVDNVDIPAATAKGIVVMNTPFGNSITTAEHAIAMMFALARQIPAA 121

Query: 122 NAALKNGEWKRSKYTGVELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYVQPARAA 181
           + + + G+W+++++ GVEL  KTLG++G G IG +VA R     MKVVAYDP++ P RA 
Sbjct: 122 DVSTQGGKWEKNRFMGVELYAKTLGLIGAGNIGGIVADRALGLKMKVVAYDPFLSPERAV 181

Query: 182 QMGVKVLSLDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGIVDEEA 241
           +MGV+ + LDELL  +D IT+H P T +T  ++  E L K K  V IVN ARGG+VDE A
Sbjct: 182 EMGVEKVELDELLARADVITLHTPLTDKTRNILSAENLAKTKKGVMIVNCARGGLVDEAA 241

Query: 242 LYSALKEGRVAGAGLDVYAKEPCTDSPLFEFDQVVATPHLGASTDEAQEKAGIAVAKSVR 301
           L   L EG V GA  DV+  EP  ++PLF  D+VVATPHLGAST+EAQE   + VA+ V 
Sbjct: 242 LRKLLDEGHVGGAAFDVFTVEPAKENPLFGSDKVVATPHLGASTNEAQENVALQVAEQVS 301

Query: 302 LALAGELVPDAVNVQGGVIAED---VKPGLPLAERLGRIFTALAGEVAVRLDVEVYGEIT 358
             L    V +A+N    + AE+   +KP + LAE++G     +       +D+   GE++
Sbjct: 302 DYLLTGAVTNALN-SPSITAEEAPKLKPFVALAEKIGAFAGQMVDFGVKAIDIAYEGEVS 360

Query: 359 QHDVKVLELSALKGVFEDVVDETVSYVNAPLFAQERGVEVRLTTSSESPEHRNVVIVRGT 418
             +VK +  +AL GV + ++ E ++ V+AP  A+ERG+ V  +    SP + +++ V  T
Sbjct: 361 NLNVKPMTSAALAGVLKPMLAE-INMVSAPAIAKERGITVSESRQEVSPTYDSLMRVTIT 419

Query: 419 LSDGEEVSVSGTLAGPKHLQKIVAIGEYDVDLALADHMVVLRYEDRPGVVGTVGRIIGEA 478
              G+       +AG     +IV +   ++D A +  M+ +   D+PG +G +G ++GEA
Sbjct: 420 TEKGKRAFAGTVIAG---APRIVEVKGMELDAAFSPAMLYVNNLDKPGFIGALGMLLGEA 476

Query: 479 GLNIAGMQVARATVGGEALAVLTVDDTVPSGVLAEVAAEIGATSARSV 526
           G+NIA   + R +   +A+A++ VD    +G+LA++ A      AR++
Sbjct: 477 GVNIATFNLGRVSADEDAIALVGVDQAPDAGLLAKIQALPHVKEARAL 524


Lambda     K      H
   0.315    0.133    0.362 

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: 740
Number of extensions: 39
Number of successful extensions: 6
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: 529
Length of database: 526
Length adjustment: 35
Effective length of query: 494
Effective length of database: 491
Effective search space:   242554
Effective search space used:   242554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate CCNA_03322 CCNA_03322 (D-3-phosphoglycerate dehydrogenase)
to HMM TIGR01327 (serA: phosphoglycerate dehydrogenase (EC 1.1.1.95))

# 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/TIGR01327.hmm
# target sequence database:        /tmp/gapView.13956.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01327  [M=525]
Accession:   TIGR01327
Description: PGDH: phosphoglycerate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-223  729.1   6.7   1.8e-223  729.0   6.7    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_03322  CCNA_03322 D-3-phosphoglycerate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_03322  CCNA_03322 D-3-phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  729.0   6.7  1.8e-223  1.8e-223       1     523 [.       5     524 ..       5     526 .] 0.99

  Alignments for each domain:
  == domain 1  score: 729.0 bits;  conditional E-value: 1.8e-223
                             TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 
                                           +vl+adkls++++e++k+++l++d+ktglsk+el+++i dyd++ +RS +k+++++++aa+kL+vi+RaG+Gv
  lcl|FitnessBrowser__Caulo:CCNA_03322   5 RVLIADKLSPAAVEIFKNRGLAFDIKTGLSKDELIAVIGDYDGIAIRSGAKLDKDVIAAANKLRVIARAGIGV 77 
                                           79*********************************************************************** PP

                             TIGR01327  74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGl 146
                                           DN+di+aat+kGi+v+N+P gn+i++aE+a+a+++alaR+ip+ad s++ +kWe+++f+G+Ely+ktlG+iG+
  lcl|FitnessBrowser__Caulo:CCNA_03322  78 DNVDIPAATAKGIVVMNTPFGNSITTAEHAIAMMFALARQIPAADVSTQGGKWEKNRFMGVELYAKTLGLIGA 150
                                           ************************************************************************* PP

                             TIGR01327 147 GriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakm 219
                                           G+iG +va+ra +l+mkv+ayDP++s+e+a ++gve+++ ldella+aDvit+H+Plt++t++++++e+lak+
  lcl|FitnessBrowser__Caulo:CCNA_03322 151 GNIGGIVADRALGLKMKVVAYDPFLSPERAVEMGVEKVE-LDELLARADVITLHTPLTDKTRNILSAENLAKT 222
                                           ************************************666.********************************* PP

                             TIGR01327 220 KkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvave 292
                                           Kkgv+ivNcaRGG++dE+AL ++l+eg+v +aa+Dvf+ EP+++n+l+ +d+vv+tpHlgAst+Eaqenva++
  lcl|FitnessBrowser__Caulo:CCNA_03322 223 KKGVMIVNCARGGLVDEAALRKLLDEGHVGGAAFDVFTVEPAKENPLFGSDKVVATPHLGASTNEAQENVALQ 295
                                           ************************************************************************* PP

                             TIGR01327 293 vaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesellt 365
                                           vae+v+++l + +v++a+N p+++aee+ klkp+++laek+G++a+q+++  vk++++++eGe+++ +++++t
  lcl|FitnessBrowser__Caulo:CCNA_03322 296 VAEQVSDYLLTGAVTNALNSPSITAEEAPKLKPFVALAEKIGAFAGQMVDFGVKAIDIAYEGEVSNLNVKPMT 368
                                           ************************************************************************* PP

                             TIGR01327 366 sallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriv 438
                                           sa+l+g+lk++l+ e+n+v+A+a+akergitv+es++e s++y++l++v+++++kg++++agtv+++ +priv
  lcl|FitnessBrowser__Caulo:CCNA_03322 369 SAALAGVLKPMLA-EINMVSAPAIAKERGITVSESRQEVSPTYDSLMRVTITTEKGKRAFAGTVIAG-APRIV 439
                                           ************9.9***************************************************5.***** PP

                             TIGR01327 439 eidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleei 511
                                           e++g+e+d +++ ++l+++n DkpG+ig +g+llgeag+Nia+++lgr +++++a++l+ +D+++++++l++i
  lcl|FitnessBrowser__Caulo:CCNA_03322 440 EVKGMELDAAFSPAMLYVNNLDKPGFIGALGMLLGEAGVNIATFNLGRVSADEDAIALVGVDQAPDAGLLAKI 512
                                           ************************************************************************* PP

                             TIGR01327 512 kevpeiksvklv 523
                                           +++p++k+++++
  lcl|FitnessBrowser__Caulo:CCNA_03322 513 QALPHVKEARAL 524
                                           *******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (526 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.31
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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