Alignments for a candidate for serA in Sulfurihydrogenibium subterraneum DSM 15120

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Sulfurihydrogenibium subterraneum DSM 15120

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_028949751.1 Q385_RS0100260 phosphoglycerate dehydrogenase

Query= curated2:O27051
         (525 letters)



>NCBI__GCF_000619805.1:WP_028949751.1
          Length = 529

 Score =  422 bits (1085), Expect = e-122
 Identities = 222/520 (42%), Positives = 340/520 (65%), Gaps = 8/520 (1%)

Query: 5   KVLIADSINEKGISEL--EEVAEVVVNTTITPEELLDAIKDFDAIVVRSRTKVTREVIEA 62
           KVL+ D I+ KG+  L  +E+ ++     I   ELL+ +KD+DAI+ RSRT VT+E++E 
Sbjct: 3   KVLVTDDISPKGLEILNNDEMIDLDYQPEIKFNELLEIVKDYDAIITRSRTPVTKELLER 62

Query: 63  APRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIADR 122
           A +LK++ RAGVGVDNVD++ A+ RGI+VIN P + +I  AE ++  + A+ RK+ +A +
Sbjct: 63  AEKLKVVGRAGVGVDNVDLEEASRRGILVINTPGANTIGAAEITMAHLYAVLRKLHLAHK 122

Query: 123 SVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEEM 182
           S+ EG W++ RFMG EL+GK +GIIG+G +GSQV +R KA G  ++ YDPYI +E  E +
Sbjct: 123 SMMEGYWDRKRFMGEELDGKVVGIIGLGNVGSQVAIRCKAAGSKVIAYDPYIPREKGERL 182

Query: 183 GVTVTD-LETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDAL 241
           GV + D L  L++ SDI+T+H PLT ETR++I + EF LMK   + +NCARGGI+DEDAL
Sbjct: 183 GVELIDNLHDLIKMSDIITLHCPLTEETRNMIGKKEFDLMKKGVYFINCARGGIVDEDAL 242

Query: 242 YRALKDGEIAGAALDVFEEEPPEG--SPLLELENVVLTPHIGASTSEAQRDAAIIVANEI 299
           Y A+K+G+IAG  LDVF +EPP+     L E  N+ L+PHIGA+T E+Q + AI +A  +
Sbjct: 243 YEAVKEGKIAGLGLDVFSKEPPDDRIRRLFEFPNISLSPHIGANTYESQDNVAIKIAQYV 302

Query: 300 KTVFQGGAPRNVLNMPVMDSETYKSLKPYIELAEKMGAIIAQALPGNIEKLDVTYCGELA 359
               +G      +N P   +E ++++K Y+ELAEK+G+ + Q   G+  +++V   G + 
Sbjct: 303 IAALKGQFVEVAVNAPFTITEGFENIKAYLELAEKLGSFLTQYAGGHFTEINVEVRGTIR 362

Query: 360 EMQFDILTRTMLQAILNPILTEPVNLINAPSIAKKRGIMVTEARRSESDGYRSIIIATAE 419
           +   + +    L+  L+P+L  PVN+INAP IAK+RGI V ++ R     ++  I  TA+
Sbjct: 363 D-HIEPIVAFFLKGYLSPVLDTPVNIINAPFIAKERGINVVKSTREAGLNFKEFIKITAK 421

Query: 420 SDRGGFSVEAT--HIKEPTIIGINGYRVDVKPEGTMIIARYRDLPGTIGAIGTKLGQHGI 477
           SD     V  T  + K P I+ ++ Y +D++P G +++   +D+PG IG +GT L +H I
Sbjct: 422 SDGKEVVVGGTAFYDKLPRIMLVDNYWIDIEPYGVILMFENKDVPGVIGKLGTILARHNI 481

Query: 478 NIATMQVGRKEIGGEAVMVLKVDQSVPAEVIEEVKKLDNV 517
           NIA  ++GR E G  A+  L++D  +   V+EE+ +L  +
Sbjct: 482 NIAGFRLGRLEKGKIALGALQLDDKLNEAVLEEIHQLPEI 521


Lambda     K      H
   0.316    0.135    0.366 

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: 704
Number of extensions: 37
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: 525
Length of database: 529
Length adjustment: 35
Effective length of query: 490
Effective length of database: 494
Effective search space:   242060
Effective search space used:   242060
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_028949751.1 Q385_RS0100260 (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.18354.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-210  684.6   0.8   5.5e-210  684.5   0.8    1.0  1  lcl|NCBI__GCF_000619805.1:WP_028949751.1  Q385_RS0100260 phosphoglycerate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000619805.1:WP_028949751.1  Q385_RS0100260 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  684.5   0.8  5.5e-210  5.5e-210       1     523 [.       3     527 ..       3     529 .] 0.98

  Alignments for each domain:
  == domain 1  score: 684.5 bits;  conditional E-value: 5.5e-210
                                 TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 
                                               kvlv+d++s++g+e l +++ +++d++ +++ +elle++kdyda+i+RS+t+vt+elle+aekLkv+gR
  lcl|NCBI__GCF_000619805.1:WP_028949751.1   3 KVLVTDDISPKGLEiLNNDEMIDLDYQPEIKFNELLEIVKDYDAIITRSRTPVTKELLERAEKLKVVGR 71 
                                               7*************66677889*********************************************** PP

                                 TIGR01327  69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137
                                               aGvGvDN+d+e+a+++Gilv+N+P +nti+aaE ++a+l a+ Rk++ a+ks+ e+ W+rk+f+G+El 
  lcl|NCBI__GCF_000619805.1:WP_028949751.1  72 AGVGVDNVDLEEASRRGILVINTPGANTIGAAEITMAHLYAVLRKLHLAHKSMMEGYWDRKRFMGEELD 140
                                               ********************************************************************* PP

                                 TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206
                                               gk +G+iGlG++Gs+va r+ka g kv+ayDPyi++ek e+lgvel+++l++l++ +D+it+H Plt+e
  lcl|NCBI__GCF_000619805.1:WP_028949751.1 141 GKVVGIIGLGNVGSQVAIRCKAAGSKVIAYDPYIPREKGERLGVELIDNLHDLIKMSDIITLHCPLTEE 209
                                               ********************************************************************* PP

                                 TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt..dnklleldnvv 273
                                               t+++igk+e++ mKkgv+ +NcaRGGi+dE+AL+ea++egk+++++lDvf+kEPp     +l+e++n++
  lcl|NCBI__GCF_000619805.1:WP_028949751.1 210 TRNMIGKKEFDLMKKGVYFINCARGGIVDEDALYEAVKEGKIAGLGLDVFSKEPPDdrIRRLFEFPNIS 278
                                               *******************************************************944479******** PP

                                 TIGR01327 274 vtpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllk 342
                                               ++pH+gA+t+E+q+nva+++a+ v+ alkg++ve avN+p + +e +e++k+yl+laeklG++ +q+++
  lcl|NCBI__GCF_000619805.1:WP_028949751.1 279 LSPHIGANTYESQDNVAIKIAQYVIAALKGQFVEVAVNAPFTITEGFENIKAYLELAEKLGSFLTQYAG 347
                                               ********************************************************************* PP

                                 TIGR01327 343 eavkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknl 411
                                               ++ ++++v+++G++ ++  e++++++lkg+l++vl++ vn++nA+++akergi+v  s++e+  ++k+ 
  lcl|NCBI__GCF_000619805.1:WP_028949751.1 348 GHFTEINVEVRGTIRDHI-EPIVAFFLKGYLSPVLDTPVNIINAPFIAKERGINVVKSTREAGLNFKEF 415
                                               **************9877.9999********************************************** PP

                                 TIGR01327 412 levkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNia 480
                                               +++++++d +ev v+gt + +k pri+ +d++ +d+ep g++l+++nkD+pGvigk+g++l++++iNia
  lcl|NCBI__GCF_000619805.1:WP_028949751.1 416 IKITAKSDGKEVVVGGTAFYDKLPRIMLVDNYWIDIEPYGVILMFENKDVPGVIGKLGTILARHNINIA 484
                                               ********************************************************************* PP

                                 TIGR01327 481 smqlgrkekggealmllslDeevseevleeikevpeiksvklv 523
                                               +++lgr ekg+ al  l+lD++++e vleei+++pei ++k v
  lcl|NCBI__GCF_000619805.1:WP_028949751.1 485 GFRLGRLEKGKIALGALQLDDKLNEAVLEEIHQLPEIIKAKQV 527
                                               ***************************************9988 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 11.08
//
[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