Alignments for a candidate for serA in Sulfurimonas denitrificans DSM 1251

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Sulfurimonas denitrificans DSM 1251

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_011372505.1 SUDEN_RS04600 phosphoglycerate dehydrogenase

Query= curated2:O29445
         (527 letters)



>NCBI__GCF_000012965.1:WP_011372505.1
          Length = 529

 Score =  334 bits (857), Expect = 4e-96
 Identities = 190/530 (35%), Positives = 311/530 (58%), Gaps = 11/530 (2%)

Query: 3   VLVAEPISEEAIDYMRKN-GLEVEVKTGMSREELIREVPKYEAIVVRSQTKVDAEVIQAA 61
           ++V + I E  ++ ++ +  +   +     +E+L+  +   +  + RS T VDA+ I  A
Sbjct: 6   IVVCDHIHEAGLEMLQNDKNINFIMAADEDKEKLLTIIESADVAITRSSTDVDAKFIAHA 65

Query: 62  KNLKIIGRAGVGVDNIDINAATQRGIVVVNAPGGNTISTAEHAIALMLAAARKIPQADRS 121
           KN+K I RAGVGVDN+DI   ++ GI+V+N P  NTI+  E  +A ML+  R  P +   
Sbjct: 66  KNMKAIVRAGVGVDNVDIAGCSKEGIIVMNVPTANTIAAVELTMAHMLSCMRMFPYSHNH 125

Query: 122 VKEGK-WERKKFMGIELRGKTAGVIGLGRVGFEVAKRCKALEMNVLAYDPFVSKERAEQI 180
           +K  + W+R+K+ G EL+GK  GVIG G +G  VAKR +A EM+++AYDP+++  +   +
Sbjct: 126 LKLDRVWKREKWYGYELKGKKLGVIGFGNIGSRVAKRAQAFEMDIIAYDPYINPSKVTDL 185

Query: 181 G-VKLVDFDTLLASSDVITVHVPRTKETIGLIGKGQFEKMKDGVIVVNAARGGIVDEAAL 239
             V   +F+ +L S D+IT+H P+ KET+ +I   +  KMKDGV+++N ARGG+ +E AL
Sbjct: 186 DMVYTKNFEDIL-SCDIITIHTPKNKETVNMIDVAEIAKMKDGVVLINCARGGLYNEEAL 244

Query: 240 YEAIKAGKVAAAALDVYEKEPPSPDNPLLKLDNVVTTPHIAASTREAQLNVGMIIAEDIV 299
           Y  + +GK+  A +DV+ KE P+ ++PLL LDNV  +PH+ A+T E+Q N+G+  AE+ +
Sbjct: 245 YAGLTSGKIRFAGIDVFMKE-PATNHPLLDLDNVTVSPHLGANTYESQYNIGVQAAENAI 303

Query: 300 NMAKGLPVRNAVNLPSIEPSDFEFMMPFLTLAEKMGKIASVRLGGAIRKVKVTCSGKLAT 359
             AKG+   +A+NLP  E     F+ PFL + + +G + +      I  +KV+  G++A 
Sbjct: 304 AAAKGISYAHAMNLPIDESKIPPFVKPFLEMGQTIGFLETQLNQSQIVTIKVSGQGEIA- 362

Query: 360 KNTEFVTRALLKGLFEPILSNEINLVSAKPVAVERGITIEESKVESVEHYESLLEV-WVE 418
           K  + +   +  G    I  N IN V+A  VA E+GI IE   +     Y++L+ +    
Sbjct: 363 KYVDSLATFVAVGAMSQISDNTINYVNADFVAKEKGIKIETEALLDSTVYKNLITIKLTT 422

Query: 419 SNGKEMYLAGTCF-GNEYRILKIDVYNVNFVPKGHYIISLHEDKPGVIGRVGTLFGRNNI 477
           + G    ++ T F  N +RI+ ID +++    KG  II  ++D PGVIG +G+   ++N+
Sbjct: 423 AEGGTTTISATIFDDNVFRIVSIDGFDIEVALKGDMIILKNQDVPGVIGNIGSTLAKHNV 482

Query: 478 NIAGMIVGRSGDKPGGIQLMLLLVDDPPTPEVLEEMTKLDGIIDATYVEL 527
           NIA   + R+  K     L ++LVD+  + + LEE+ ++D      Y  L
Sbjct: 483 NIADFSLARNDKKQA---LAVILVDNVISDDTLEELLRIDACSSVQYARL 529


Lambda     K      H
   0.317    0.136    0.376 

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: 636
Number of extensions: 36
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: 527
Length of database: 529
Length adjustment: 35
Effective length of query: 492
Effective length of database: 494
Effective search space:   243048
Effective search space used:   243048
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_011372505.1 SUDEN_RS04600 (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.31653.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-181  590.5  13.2   1.9e-181  590.3  13.2    1.0  1  lcl|NCBI__GCF_000012965.1:WP_011372505.1  SUDEN_RS04600 phosphoglycerate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000012965.1:WP_011372505.1  SUDEN_RS04600 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.3  13.2  1.9e-181  1.9e-181       2     524 ..       6     528 ..       5     529 .] 0.98

  Alignments for each domain:
  == domain 1  score: 590.3 bits;  conditional E-value: 1.9e-181
                                 TIGR01327   2 vlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 
                                               ++v+d+++e+g+e l+++k++++ ++ + +ke+ll++i+++d+ i+RS+t v+++++++a+++k i+Ra
  lcl|NCBI__GCF_000012965.1:WP_011372505.1   6 IVVCDHIHEAGLEmLQNDKNINFIMAADEDKEKLLTIIESADVAITRSSTDVDAKFIAHAKNMKAIVRA 74 
                                               79***********8889999************************************************* PP

                                 TIGR01327  70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekk.WerkkflGtEly 137
                                               GvGvDN+di  ++k Gi+v+N P++nti+a+El++a++l+ +R +p +++++k  + W+r+k++G El+
  lcl|NCBI__GCF_000012965.1:WP_011372505.1  75 GVGVDNVDIAGCSKEGIIVMNVPTANTIAAVELTMAHMLSCMRMFPYSHNHLKLDRvWKREKWYGYELK 143
                                               *****************************************************8888************ PP

                                 TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206
                                               gk+lGviG+G+iGs+vakra+a++m+++ayDPyi ++k+++l + ++k+++++l ++D+it+H+P++ke
  lcl|NCBI__GCF_000012965.1:WP_011372505.1 144 GKKLGVIGFGNIGSRVAKRAQAFEMDIIAYDPYINPSKVTDLDMVYTKNFEDIL-SCDIITIHTPKNKE 211
                                               ******************************************************.9************* PP

                                 TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvt 275
                                               t ++i+  e+akmK+gv+++NcaRGG+++E+AL+  l++gk+r a++Dvf kEP+t+++ll+ldnv+v+
  lcl|NCBI__GCF_000012965.1:WP_011372505.1 212 TVNMIDVAEIAKMKDGVVLINCARGGLYNEEALYAGLTSGKIRFAGIDVFMKEPATNHPLLDLDNVTVS 280
                                               ********************************************************************* PP

                                 TIGR01327 276 pHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkea 344
                                               pHlgA+t+E+q n++v+ ae+ + a+kg +  +a+Nlp  + +    +kp+l++++++G l +ql +++
  lcl|NCBI__GCF_000012965.1:WP_011372505.1 281 PHLGANTYESQYNIGVQAAENAIAAAKGISYAHAMNLPIDESKIPPFVKPFLEMGQTIGFLETQLNQSQ 349
                                               **************************************988888889********************** PP

                                 TIGR01327 345 vkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknlle 413
                                               + +++v+ +Ge+a++  + l +++  g ++++ ++++n+vnA +vake+gi++e +   +s+ yknl++
  lcl|NCBI__GCF_000012965.1:WP_011372505.1 350 IVTIKVSGQGEIAKYV-DSLATFVAVGAMSQISDNTINYVNADFVAKEKGIKIETEALLDSTVYKNLIT 417
                                               **************98.9999************************************************ PP

                                 TIGR01327 414 vkveadkg.evsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNias 481
                                               +k+++++g ++++++t+++++  riv idgf+++++ +g ++i+kn+D+pGvig++gs+l+++++Nia+
  lcl|NCBI__GCF_000012965.1:WP_011372505.1 418 IKLTTAEGgTTTISATIFDDNVFRIVSIDGFDIEVALKGDMIILKNQDVPGVIGNIGSTLAKHNVNIAD 486
                                               ***9887769*********************************************************** PP

                                 TIGR01327 482 mqlgrkekggealmllslDeevseevleeikevpeiksvklve 524
                                               ++l+r+ k+ +al+++ +D+ +s++ lee+  ++++ sv++ +
  lcl|NCBI__GCF_000012965.1:WP_011372505.1 487 FSLARNDKK-QALAVILVDNVISDDTLEELLRIDACSSVQYAR 528
                                               ******998.9****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (529 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.52
//
[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