Alignments for a candidate for serA in Synechococcus elongatus PCC 7942

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Synechococcus elongatus PCC 7942

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate Synpcc7942_1501 Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>FitnessBrowser__SynE:Synpcc7942_1501
          Length = 546

 Score =  432 bits (1111), Expect = e-125
 Identities = 237/528 (44%), Positives = 347/528 (65%), Gaps = 8/528 (1%)

Query: 1   MSKILITDPLHESAVEILKQAGEVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEA 60
           M K+L++DP+ +  ++IL Q  +V+V TGL+  EL   I + DAL++RSGT  T E+IEA
Sbjct: 18  MPKVLVSDPIDQVGLDILSQVAQVDVKTGLSPSELAQIIGEYDALMLRSGTRVTAEVIEA 77

Query: 61  SENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATA 120
            + L++I RAGVGVDNVD+ AAT +GIVVVN+P+ ++I+ AE    MML+ +R+IP A A
Sbjct: 78  GQKLRIIGRAGVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHTLAMMLSLSRHIPDANA 137

Query: 121 SIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180
           S KSG WDRKSF G E+Y KTLG+VGLG+IG  VA  A+A GM ++AYDP+I  + A ++
Sbjct: 138 STKSGGWDRKSFVGTEVYKKTLGVVGLGKIGSHVATVAKAMGMKLLAYDPFISAERAEQI 197

Query: 181 GIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALY 240
           G +L+ +D L   +D+ITLH+P TP+T ++I  E +A MK    I+NCARGG+I+E AL 
Sbjct: 198 GARLVELDILFQEADYITLHIPKTPETANLINAETLAKMKPTTRIINCARGGVINEQALA 257

Query: 241 DALNSGKIKAAALDVFEQEP-PKESPLLTL-NNLIGTPHQGASTEEAQLSAGTIVAEQTV 298
           DA+ +GKI  AALDV++QEP   +SPL  L  NLI TPH GAST EAQ++    VAEQ  
Sbjct: 258 DAIAAGKIGGAALDVYDQEPLQADSPLRALGKNLILTPHLGASTTEAQVNVAVDVAEQIR 317

Query: 299 KILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAK 358
            +L G  A + VN+P +  + ++KL+PY+ LAE +G++  Q     +E L +   G LA 
Sbjct: 318 DVLLGLPARSAVNIPGLYPDILEKLRPYLQLAETLGNLLSQVAGGRLEQLTVRLQGELAA 377

Query: 359 EKTEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSES---DY-GNSIKIS 414
           ++++ +  + LKG+L   L   VN VNA + AK R I+I E T  ES   DY G S+++ 
Sbjct: 378 QQSQPIVVAALKGLLTQALRERVNYVNAMIEAKERGIRIIE-TRDESVRDDYAGGSLQLV 436

Query: 415 AKGENDEISIIGS-IEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEH 473
           A G N E  ++G+ +   E+    ++ + +++ P   +   +H D PG++GK+G LLG  
Sbjct: 437 ATGSNGEHRVMGALLGDGEIRITNVDEFPVNVPPSRYMLFTRHRDMPGIIGKIGSLLGSF 496

Query: 474 GINIAGMQVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSI 521
            +NIA MQVGRR   G ++M L +D  + + +L EI K+  +  A ++
Sbjct: 497 NVNIASMQVGRRIVRGDAVMVLSLDDPLPEGILAEITKVAGISDAYTV 544


Lambda     K      H
   0.316    0.134    0.364 

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: 694
Number of extensions: 28
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: 523
Length of database: 546
Length adjustment: 35
Effective length of query: 488
Effective length of database: 511
Effective search space:   249368
Effective search space used:   249368
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.12666.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: 0.01u 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.96
//
[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