Alignments for a candidate for serA in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_012411500.1 NPUN_RS26385 phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>NCBI__GCF_000020025.1:WP_012411500.1
          Length = 526

 Score =  427 bits (1099), Expect = e-124
 Identities = 235/526 (44%), Positives = 336/526 (63%), Gaps = 3/526 (0%)

Query: 1   MSKILITDPLHESAVEILKQAGEVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEA 60
           MSK+L++D + ++ ++IL Q   V+V  GL   +L   I + DAL+IRS T  T+EIIEA
Sbjct: 1   MSKVLVSDSIDQAGIDILSQVATVDVKIGLKPAQLLEIIGEYDALMIRSSTRVTQEIIEA 60

Query: 61  SENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATA 120
              LK+I RAGVGVDNVD+ AAT +GIVVVN+P+ ++I+ AE    M+LA +R+IP A A
Sbjct: 61  GTQLKIIGRAGVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHALAMILALSRHIPDANA 120

Query: 121 SIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180
           S+K G WDR SF G E+Y KTLG+VGLG+IG  VA  A+  GM ++AYDP+I  + A ++
Sbjct: 121 SVKRGAWDRNSFVGAEVYKKTLGVVGLGKIGSHVAAVAKTMGMKLLAYDPFISTERAEQI 180

Query: 181 GIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALY 240
           G +L+ +D L   +D+ITLH+P TP+T H+I    +A MK    I+NCARGG+IDE AL 
Sbjct: 181 GCQLVELDLLFQQADYITLHIPKTPETTHLINATTLAKMKPTARIINCARGGIIDEVALA 240

Query: 241 DALNSGKIKAAALDVFEQEPPKESPLLTL-NNLIGTPHQGASTEEAQLSAGTIVAEQTVK 299
            AL +GKI  AALDVFE EP  ES L +L   +I TPH GAST EAQ++    VAEQ   
Sbjct: 241 AALKAGKIGGAALDVFESEPLGESELRSLGKEVILTPHLGASTAEAQVNVAIDVAEQIRD 300

Query: 300 ILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAKE 359
           +L G  A + VN+P +  + +++LKPYM LAE +G++  Q     +E+L I   G LA  
Sbjct: 301 VLLGLPARSAVNIPGLGPDVLEELKPYMQLAETLGNLVGQLAGGRVEVLNIRLQGELATN 360

Query: 360 KTEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAE-GTMSESDYGNSIKISAKGE 418
           K++ L  + LKG+L   L   VN VNA + AK R I++ E    S  DY  ++ + A G 
Sbjct: 361 KSQPLVVAALKGLLYQALRERVNYVNASIEAKERGIRVIETRDASIRDYAGTLHLEATGT 420

Query: 419 NDEISIIGS-IEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINI 477
               S+ G+ +   E+   +++G+ +++ P   +    H D PG++GK+G LLG   +NI
Sbjct: 421 LGTHSVTGALLGEREIHLTDVDGFPINVPPSKYMLFTLHRDMPGIIGKLGSLLGSFNVNI 480

Query: 478 AGMQVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSINI 523
           A MQVGR+   G ++M L ID  + + +LDEI K+  +R A ++ +
Sbjct: 481 ASMQVGRKIVRGDAVMALSIDDPLPEGILDEIIKVPGIRDAYTVTL 526


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: 727
Number of extensions: 36
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: 526
Length adjustment: 35
Effective length of query: 488
Effective length of database: 491
Effective search space:   239608
Effective search space used:   239608
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 WP_012411500.1 NPUN_RS26385 (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.3522692.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.1e-218  710.5   4.0     8e-218  710.3   4.0    1.0  1  NCBI__GCF_000020025.1:WP_012411500.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020025.1:WP_012411500.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  710.3   4.0    8e-218    8e-218       1     525 []       3     526 .]       3     526 .] 0.99

  Alignments for each domain:
  == domain 1  score: 710.3 bits;  conditional E-value: 8e-218
                             TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 
                                           kvlv+d+++++gi++l++ +  vdvk gl+ ++lle+i +ydal++RS+t+vt+e++ea ++Lk+igRaGvGv
  NCBI__GCF_000020025.1:WP_012411500.1   3 KVLVSDSIDQAGIDILSQVA-TVDVKIGLKPAQLLEIIGEYDALMIRSSTRVTQEIIEAGTQLKIIGRAGVGV 74 
                                           7****************997.9*************************************************** PP

                             TIGR01327  74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGl 146
                                           DN+d++aat++Gi+vvN+Pegnti+aaE+ala++lal+R+ip+a++svk++ W+r++f+G E+y+ktlGv+Gl
  NCBI__GCF_000020025.1:WP_012411500.1  75 DNVDVPAATRRGIVVVNSPEGNTIAAAEHALAMILALSRHIPDANASVKRGAWDRNSFVGAEVYKKTLGVVGL 147
                                           ************************************************************************* PP

                             TIGR01327 147 GriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakm 219
                                           G+iGs+va  ak++gmk+layDP+is+e+ae++g++l+ +ld l+++aD it+H+P+t+et +li++ +lakm
  NCBI__GCF_000020025.1:WP_012411500.1 148 GKIGSHVAAVAKTMGMKLLAYDPFISTERAEQIGCQLV-ELDLLFQQADYITLHIPKTPETTHLINATTLAKM 219
                                           ************************************55.5********************************* PP

                             TIGR01327 220 KkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldn.vvvtpHlgAsteEaqenvav 291
                                           K++++i+NcaRGGiidE AL+ al++gk+ +aalDvfe+EP  +++l +l + v++tpHlgAst+Eaq nva+
  NCBI__GCF_000020025.1:WP_012411500.1 220 KPTARIINCARGGIIDEVALAAALKAGKIGGAALDVFESEPLGESELRSLGKeVILTPHLGASTAEAQVNVAI 292
                                           ************************************************98766******************** PP

                             TIGR01327 292 evaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesell 364
                                           +vae+++++l g +++savN+p l  ++le+lkpy++lae+lG+l++ql++++v+ +++ l+Gela+++s++l
  NCBI__GCF_000020025.1:WP_012411500.1 293 DVAEQIRDVLLGLPARSAVNIPGLGPDVLEELKPYMQLAETLGNLVGQLAGGRVEVLNIRLQGELATNKSQPL 365
                                           ************************************************************************* PP

                             TIGR01327 365 tsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepri 437
                                           + a+lkgll ++l+e+vn+vnA + akergi+v e+++++ +dy  +l+++++++ g++sv+g++l+e e ++
  NCBI__GCF_000020025.1:WP_012411500.1 366 VVAALKGLLYQALRERVNYVNASIEAKERGIRVIETRDASIRDYAGTLHLEATGTLGTHSVTGALLGEREIHL 438
                                           ************************************************************************* PP

                             TIGR01327 438 veidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevlee 510
                                           +++dgf +++ p++++l++ ++D+pG+igk+gsllg++++Niasmq+grk  +g+a+m ls+D++++e++l+e
  NCBI__GCF_000020025.1:WP_012411500.1 439 TDVDGFPINVPPSKYMLFTLHRDMPGIIGKLGSLLGSFNVNIASMQVGRKIVRGDAVMALSIDDPLPEGILDE 511
                                           ************************************************************************* PP

                             TIGR01327 511 ikevpeiksvklvel 525
                                           i +vp i+++++v+l
  NCBI__GCF_000020025.1:WP_012411500.1 512 IIKVPGIRDAYTVTL 526
                                           ***********9986 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: 24.52
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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