GapMind for Amino acid biosynthesis

 

Aligments for a candidate for serA in Synechococcus elongatus PCC 7942

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Synpcc7942_1501 Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase

Query= BRENDA::Q9Z564
         (529 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_1501 Synpcc7942_1501
           D-3-phosphoglycerate dehydrogenase
          Length = 546

 Score =  394 bits (1013), Expect = e-114
 Identities = 217/531 (40%), Positives = 333/531 (62%), Gaps = 10/531 (1%)

Query: 5   PVVLIAEELSPATVDALGPDFEIRHCNGADRAELLPAIADVDAILVRSATKVDAEAVAAA 64
           P VL+++ +    +D L    ++    G   +EL   I + DA+++RS T+V AE + A 
Sbjct: 19  PKVLVSDPIDQVGLDILSQVAQVDVKTGLSPSELAQIIGEYDALMLRSGTRVTAEVIEAG 78

Query: 65  KKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNIPQANAA 124
           +KL+++ RAGVG+DNVDV AAT+ G++VVN+P  N + AAE    ++++ +R+IP ANA+
Sbjct: 79  QKLRIIGRAGVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHTLAMMLSLSRHIPDANAS 138

Query: 125 LKNGEWKRSKYTGVELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYVQPARAAQMG 184
            K+G W R  + G E+ +KTLGVVGLG+IG+ VA    A GMK++AYDP++   RA Q+G
Sbjct: 139 TKSGGWDRKSFVGTEVYKKTLGVVGLGKIGSHVATVAKAMGMKLLAYDPFISAERAEQIG 198

Query: 185 VKVLSLDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGIVDEEALYS 244
            +++ LD L + +D+IT+H+PKTPET  LI  E L K+KP+ RI+N ARGG+++E+AL  
Sbjct: 199 ARLVELDILFQEADYITLHIPKTPETANLINAETLAKMKPTTRIINCARGGVINEQALAD 258

Query: 245 ALKEGRVAGAGLDVYAKEPC-TDSPLFEFDQ-VVATPHLGASTDEAQEKAGIAVAKSVRL 302
           A+  G++ GA LDVY +EP   DSPL    + ++ TPHLGAST EAQ    + VA+ +R 
Sbjct: 259 AIAAGKIGGAALDVYDQEPLQADSPLRALGKNLILTPHLGASTTEAQVNVAVDVAEQIRD 318

Query: 303 ALAGELVPDAVNVQG--GVIAEDVKPGLPLAERLGRIFTALAGEVAVRLDVEVYGEITQH 360
            L G     AVN+ G    I E ++P L LAE LG + + +AG    +L V + GE+   
Sbjct: 319 VLLGLPARSAVNIPGLYPDILEKLRPYLQLAETLGNLLSQVAGGRLEQLTVRLQGELAAQ 378

Query: 361 DVKVLELSALKGVFEDVVDETVSYVNAPLFAQERGVEVRLTTSSESPEH---RNVVIVRG 417
             + + ++ALKG+    + E V+YVNA + A+ERG+ + + T  ES         + +  
Sbjct: 379 QSQPIVVAALKGLLTQALRERVNYVNAMIEAKERGIRI-IETRDESVRDDYAGGSLQLVA 437

Query: 418 TLSDGEEVSVSGTLAGPKHLQKIVAIGEYDVDLALADHMVVLRYEDRPGVVGTVGRIIGE 477
           T S+GE   V G L G   + +I  + E+ V++  + +M+  R+ D PG++G +G ++G 
Sbjct: 438 TGSNGEH-RVMGALLGDGEI-RITNVDEFPVNVPPSRYMLFTRHRDMPGIIGKIGSLLGS 495

Query: 478 AGLNIAGMQVARATVGGEALAVLTVDDTVPSGVLAEVAAEIGATSARSVNL 528
             +NIA MQV R  V G+A+ VL++DD +P G+LAE+    G + A +V L
Sbjct: 496 FNVNIASMQVGRRIVRGDAVMVLSLDDPLPEGILAEITKVAGISDAYTVVL 546


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: 754
Number of extensions: 24
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: 529
Length of database: 546
Length adjustment: 35
Effective length of query: 494
Effective length of database: 511
Effective search space:   252434
Effective search space used:   252434
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 Synpcc7942_1501 Synpcc7942_1501 (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.14046.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.1e-216  703.7   2.8   9.1e-216  703.6   2.8    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1501  Synpcc7942_1501 D-3-phosphoglyce


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1501  Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  703.6   2.8  9.1e-216  9.1e-216       1     525 []      20     546 .]      20     546 .] 0.98

  Alignments for each domain:
  == domain 1  score: 703.6 bits;  conditional E-value: 9.1e-216
                                 TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 
                                               kvlv+d++++ g+++l++ + +vdvktgls  el ++i +ydal++RS t+vt+e++ea +kL++igRa
  lcl|FitnessBrowser__SynE:Synpcc7942_1501  20 KVLVSDPIDQVGLDILSQVA-QVDVKTGLSPSELAQIIGEYDALMLRSGTRVTAEVIEAGQKLRIIGRA 87 
                                               7****************996.************************************************ PP

                                 TIGR01327  70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138
                                               GvGvDN+d++aat++Gi+vvN+Pegnti+aaE++la++l+l+R+ip+a++s+k++ W+rk+f+GtE+y+
  lcl|FitnessBrowser__SynE:Synpcc7942_1501  88 GVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHTLAMMLSLSRHIPDANASTKSGGWDRKSFVGTEVYK 156
                                               ********************************************************************* PP

                                 TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207
                                               ktlGv+GlG+iGs+va+ aka+gmk+layDP+is e+ae++g +l  +ld l++eaD it+H+P+t+et
  lcl|FitnessBrowser__SynE:Synpcc7942_1501 157 KTLGVVGLGKIGSHVATVAKAMGMKLLAYDPFISAERAEQIGARL-VELDILFQEADYITLHIPKTPET 224
                                               ********************************************5.55********************* PP

                                 TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt.dnklleldn.vvv 274
                                               ++li++e+lakmK++ +i+NcaRGG+i+E+AL++a+ +gk+ +aalDv+ +EP + d++l +l + +++
  lcl|FitnessBrowser__SynE:Synpcc7942_1501 225 ANLINAETLAKMKPTTRIINCARGGVINEQALADAIAAGKIGGAALDVYDQEPLQaDSPLRALGKnLIL 293
                                               *****************************************************9989***987544*** PP

                                 TIGR01327 275 tpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllke 343
                                               tpHlgAst+Eaq nvav+vae+++++l g +++savN+p l  + lekl+pyl+lae+lG+l sq++++
  lcl|FitnessBrowser__SynE:Synpcc7942_1501 294 TPHLGASTTEAQVNVAVDVAEQIRDVLLGLPARSAVNIPGLYPDILEKLRPYLQLAETLGNLLSQVAGG 362
                                               ********************************************************************* PP

                                 TIGR01327 344 avkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeese.dyk.n 410
                                               + ++++v l+Gela+++s++++ a+lkgll ++l+e+vn+vnA++ akergi++ e+++e+++ dy   
  lcl|FitnessBrowser__SynE:Synpcc7942_1501 363 RLEQLTVRLQGELAAQQSQPIVVAALKGLLTQALRERVNYVNAMIEAKERGIRIIETRDESVRdDYAgG 431
                                               ******************************************************999998875268636 PP

                                 TIGR01327 411 llevkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNi 479
                                               +l++ +++++ge+ v g++l++ e ri+++d+f v++ p+ ++l+++++D+pG+igk+gsllg++++Ni
  lcl|FitnessBrowser__SynE:Synpcc7942_1501 432 SLQLVATGSNGEHRVMGALLGDGEIRITNVDEFPVNVPPSRYMLFTRHRDMPGIIGKIGSLLGSFNVNI 500
                                               9******************************************************************** PP

                                 TIGR01327 480 asmqlgrkekggealmllslDeevseevleeikevpeiksvklvel 525
                                               asmq+gr+  +g+a+m+lslD++++e++l+ei++v+ i ++++v l
  lcl|FitnessBrowser__SynE:Synpcc7942_1501 501 ASMQVGRRIVRGDAVMVLSLDDPLPEGILAEITKVAGISDAYTVVL 546
                                               *****************************************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (546 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.48
//
[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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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