GapMind for Amino acid biosynthesis

 

Alignments 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::A0A2R6X868
         (630 letters)



>FitnessBrowser__Caulo:CCNA_03322
          Length = 526

 Score =  381 bits (979), Expect = e-110
 Identities = 221/536 (41%), Positives = 321/536 (59%), Gaps = 20/536 (3%)

Query: 90  PTVLVAEKLGEAGLELLKKIANV-DCSYNLSQEELCAKISLCDALIVRSGTKVTREVFEA 148
           P VL+A+KL  A +E+ K      D    LS++EL A I   D + +RSG K+ ++V  A
Sbjct: 4   PRVLIADKLSPAAVEIFKNRGLAFDIKTGLSKDELIAVIGDYDGIAIRSGAKLDKDVIAA 63

Query: 149 SNGRLKVVGRAGVGIDNVDLQAATEVGCLVVNAPTANTIAAAEHGIALLTALARNVAQAS 208
           +N +L+V+ RAG+G+DNVD+ AAT  G +V+N P  N+I  AEH IA++ ALAR +  A 
Sbjct: 64  AN-KLRVIARAGIGVDNVDIPAATAKGIVVMNTPFGNSITTAEHAIAMMFALARQIPAAD 122

Query: 209 ASMKAGEWKRNKYVGVSLVDKTLAVMGFGKVGSEVARRAKGLGMQVIAHDPYAPADRARA 268
            S + G+W++N+++GV L  KTL ++G G +G  VA RA GL M+V+A+DP+   +RA  
Sbjct: 123 VSTQGGKWEKNRFMGVELYAKTLGLIGAGNIGGIVADRALGLKMKVVAYDPFLSPERAVE 182

Query: 269 IGVELVSFDEALQRADFISLHMPLTPSTDKCFNDESFAKCKKGVRIVNVARGGVIDEEAL 328
           +GVE V  DE L RAD I+LH PLT  T    + E+ AK KKGV IVN ARGG++DE AL
Sbjct: 183 MGVEKVELDELLARADVITLHTPLTDKTRNILSAENLAKTKKGVMIVNCARGGLVDEAAL 242

Query: 329 VRALDSGIVAQAALDVFTVEPPAKDDKLIQHENVVVTPHLGASTMEAQEGVAVEIAEAVV 388
            + LD G V  AA DVFTVE PAK++ L   + VV TPHLGAST EAQE VA+++AE V 
Sbjct: 243 RKLLDEGHVGGAAFDVFTVE-PAKENPLFGSDKVVATPHLGASTNEAQENVALQVAEQVS 301

Query: 389 GALQGELAATAVNAPMVPAEVLAELSPYVTLAERLGRLAVQLVSGGAGVKDVKVTYTSSR 448
             L       A+N+P + AE   +L P+V LAE++G  A Q+V    GVK + + Y    
Sbjct: 302 DYLLTGAVTNALNSPSITAEEAPKLKPFVALAEKIGAFAGQMVD--FGVKAIDIAYEGEV 359

Query: 449 ADDDLDTRLLRAMITKGLIEPVSSAFINLVNADFIAKQRGLRISEERRPSDGAVEVPLES 508
           +  +L+ + + +    G+++P+  A IN+V+A  IAK+RG+ +SE R+     V    +S
Sbjct: 360 S--NLNVKPMTSAALAGVLKPM-LAEINMVSAPAIAKERGITVSESRQ----EVSPTYDS 412

Query: 509 IEVRISKVDSRFNTAMSSGDITLVGTVKGGVPHLSKVGGFSVDVSLEGSIILCRQVDQPG 568
           +         R       G     GTV  G P + +V G  +D +   +++    +D+PG
Sbjct: 413 L--------MRVTITTEKGKRAFAGTVIAGAPRIVEVKGMELDAAFSPAMLYVNNLDKPG 464

Query: 569 MIGKVGNFLGEQNVNISFMSVGRDSPRKQAVMAIGVDDVPSKEVLTKIGQISAIEE 624
            IG +G  LGE  VNI+  ++GR S  + A+  +GVD  P   +L KI  +  ++E
Sbjct: 465 FIGALGMLLGEAGVNIATFNLGRVSADEDAIALVGVDQAPDAGLLAKIQALPHVKE 520


Lambda     K      H
   0.316    0.131    0.356 

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: 620
Number of extensions: 25
Number of successful extensions: 5
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: 630
Length of database: 526
Length adjustment: 36
Effective length of query: 594
Effective length of database: 490
Effective search space:   291060
Effective search space used:   291060
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: 53 (25.0 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.2110150.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 23.08
//
[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