Alignments for a candidate for serA in Desulfacinum infernum DSM 9756

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Desulfacinum infernum DSM 9756

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_073040765.1 BUB04_RS14555 phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>NCBI__GCF_900129305.1:WP_073040765.1
          Length = 526

 Score =  406 bits (1043), Expect = e-117
 Identities = 219/524 (41%), Positives = 333/524 (63%), Gaps = 6/524 (1%)

Query: 3   KILITDPLHESAVEILKQAGEVEVATGLTV--EELKLKIKDVDALVIRSGTTATREIIEA 60
           KILI D +H   +++L+   ++EV        EE++    D DALV+RS T  T ++I A
Sbjct: 2   KILICDGMHPKGLDLLRAEDDLEVLAPDQPGPEEVRELAADCDALVVRSRTKVTEDLISA 61

Query: 61  SENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATA 120
           +  LKVI RAG GVDN+D+ AA+ +GI+V+N P A++++ AE    +MLA AR++PQAT 
Sbjct: 62  APRLKVIGRAGTGVDNIDIAAASARGILVMNTPGANAMAAAEHTMALMLALARHVPQATQ 121

Query: 121 SIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180
           S++ G+W++K F G E+Y +TLGI+GLG+IG  VA RA    M ++ YDP+I  + A+ +
Sbjct: 122 SLRDGRWEKKRFMGTELYQQTLGIIGLGKIGAIVADRALGMKMNVLVYDPHITPETAAIM 181

Query: 181 GIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALY 240
           G + + ++EL   SDFITLH PLTP T+++I ++ IALMK  + I+NCARGGL+DE ALY
Sbjct: 182 GTEWVPLEELFQRSDFITLHTPLTPDTRNIINRDSIALMKKGVRIINCARGGLVDEEALY 241

Query: 241 DALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI 300
           +AL SG +  AALDVF +EPP+ +PLL L N+I TPH GAS+ +AQ +    +A Q V  
Sbjct: 242 EALVSGHVAGAALDVFAKEPPEGNPLLRLENVIFTPHLGASSFQAQENVARAIASQIVDY 301

Query: 301 LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMG-GLAKE 359
           LK     N VN P +     +++KPY+ LAE++G +  Q L + IE +EI Y G  L + 
Sbjct: 302 LKRGIIRNAVNFPSISPRDYERIKPYLTLAERLGHLQGQ-LCSPIERVEIEYSGPELTEL 360

Query: 360 KTEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSES-DYGNSIKISAKGE 418
             + L +S  KG+L PIL   VNLVNAP++ K R I++   T SE+  Y   I+++ +G+
Sbjct: 361 PLDPLTQSIAKGLLDPILAEKVNLVNAPMLLKERKIQLVATTTSEARGYTGLIRVTVEGK 420

Query: 419 NDEISIIGSI-EHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINI 477
             + S  G++   NE+    +N YR++ + EG   I++++D+PG++G +G  LG H +NI
Sbjct: 421 GRKRSATGAVFPGNEIRLVRMNTYRLEAELEGINLIVQNVDKPGVIGFIGTTLGTHQVNI 480

Query: 478 AGMQVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSI 521
           A M + R      +I  + +D     E LD +R   ++ + + +
Sbjct: 481 ANMHLSRTPEKDRAIAIIRLDGEAPPEALDALRSNPDILSVEQV 524


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: 634
Number of extensions: 27
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_073040765.1 BUB04_RS14555 (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.8735.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.8e-199  647.5   0.0   9.8e-199  647.3   0.0    1.0  1  lcl|NCBI__GCF_900129305.1:WP_073040765.1  BUB04_RS14555 phosphoglycerate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_073040765.1  BUB04_RS14555 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  647.3   0.0  9.8e-199  9.8e-199       1     523 [.       2     524 ..       2     526 .] 0.98

  Alignments for each domain:
  == domain 1  score: 647.3 bits;  conditional E-value: 9.8e-199
                                 TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 
                                               k+l++d ++++g++ l +e++lev   ++   ee+ e   d dal+vRS+tkvte+l++aa++LkvigR
  lcl|NCBI__GCF_900129305.1:WP_073040765.1   2 KILICDGMHPKGLDlLRAEDDLEVLAPDQPGPEEVRELAADCDALVVRSRTKVTEDLISAAPRLKVIGR 70 
                                               79************7778899************************************************ PP

                                 TIGR01327  69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137
                                               aG GvDNidi aa+++Gilv+N+P +n ++aaE+++al+lalaR++pqa++s+++++We+k+f+GtEly
  lcl|NCBI__GCF_900129305.1:WP_073040765.1  71 AGTGVDNIDIAAASARGILVMNTPGANAMAAAEHTMALMLALARHVPQATQSLRDGRWEKKRFMGTELY 139
                                               ********************************************************************* PP

                                 TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206
                                               ++tlG+iGlG+iG +va+ra +++m+vl+yDP+i++e a+ +g e    l+el++++D+it+H+Plt++
  lcl|NCBI__GCF_900129305.1:WP_073040765.1 140 QQTLGIIGLGKIGAIVADRALGMKMNVLVYDPHITPETAAIMGTE-WVPLEELFQRSDFITLHTPLTPD 207
                                               *********************************************.555******************** PP

                                 TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvt 275
                                               t+++i+++++a mKkgv+i+NcaRGG++dE+AL+eal +g+v++aalDvf+kEPp+ n+ll+l+nv+ t
  lcl|NCBI__GCF_900129305.1:WP_073040765.1 208 TRNIINRDSIALMKKGVRIINCARGGLVDEEALYEALVSGHVAGAALDVFAKEPPEGNPLLRLENVIFT 276
                                               ********************************************************************* PP

                                 TIGR01327 276 pHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkea 344
                                               pHlgAs   aqenva  +a++++++lk  + ++avN p+++  + e++kpyl+lae+lG+l +ql +  
  lcl|NCBI__GCF_900129305.1:WP_073040765.1 277 PHLGASSFQAQENVARAIASQIVDYLKRGIIRNAVNFPSISPRDYERIKPYLTLAERLGHLQGQLCS-P 344
                                               ****************************************************************986.6 PP

                                 TIGR01327 345 vkkvevtleG.elaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknll 412
                                               +++ve++++G el+e   ++lt+++ kgll+++l+e+vnlvnA+++ ker+i++  ++++e++ y+ l+
  lcl|NCBI__GCF_900129305.1:WP_073040765.1 345 IERVEIEYSGpELTELPLDPLTQSIAKGLLDPILAEKVNLVNAPMLLKERKIQLVATTTSEARGYTGLI 413
                                               778*******89********************************************************* PP

                                 TIGR01327 413 evkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNias 481
                                               +v+ve++  ++s +g+v+ ++e r+v++++++++ e egi+li++n DkpGvig +g++lg++++Nia+
  lcl|NCBI__GCF_900129305.1:WP_073040765.1 414 RVTVEGKGRKRSATGAVFPGNEIRLVRMNTYRLEAELEGINLIVQNVDKPGVIGFIGTTLGTHQVNIAN 482
                                               ********************************************************************* PP

                                 TIGR01327 482 mqlgrkekggealmllslDeevseevleeikevpeiksvklv 523
                                               m+l+r+ +++ a+++++lD e+++e l+++++ p+i sv+ v
  lcl|NCBI__GCF_900129305.1:WP_073040765.1 483 MHLSRTPEKDRAIAIIRLDGEAPPEALDALRSNPDILSVEQV 524
                                               ***************************************988 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.86
//
[ok]

This GapMind analysis is from Apr 10 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