Alignments for a candidate for serA in Desulfuromonas acetexigens DSM 1397

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Desulfuromonas acetexigens DSM 1397

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_092057260.1 BQ4888_RS10930 phosphoglycerate dehydrogenase

Query= CharProtDB::CH_004924
         (525 letters)



>NCBI__GCF_900111775.1:WP_092057260.1
          Length = 530

 Score =  400 bits (1027), Expect = e-116
 Identities = 211/528 (39%), Positives = 324/528 (61%), Gaps = 7/528 (1%)

Query: 3   RVLVSDKMSNDGLQPLIESDFIEI-VQKN--VADAEDELHTFDALLVRSATKVTEDLFNK 59
           +VL++D++S +GLQPL++   +++ V+ N  VA+    +  +DAL+ RS T+V   L   
Sbjct: 2   KVLITDEISPEGLQPLLDDPRVQLDVRLNLPVAELHQIIGGYDALITRSGTRVDAALLEH 61

Query: 60  MTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQANI 119
             +L+IV RAGVG+DN+D+  A+K G+IV+NAP GN  S AEHT A++ SL R++  AN 
Sbjct: 62  SGNLRIVARAGVGIDNVDVPAASKKGIIVVNAPFGNVNSAAEHTMAILLSLCRNVTVANA 121

Query: 120 SVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKKI 179
           S+KS EW R  + G EL GKT+GI+GLG++G  +A R  AF   V   DP+++E+RA+  
Sbjct: 122 SLKSGEWKRAPFTGYELKGKTVGIIGLGKVGGRVALRCRAFEANVLACDPYISEKRAEDH 181

Query: 180 GVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAALL 239
           GV   + ++++  ADIITVHTPL +ET G++  E  A  K GV ++NCARGGII+EAA+L
Sbjct: 182 GVKLVSLDDIVRYADIITVHTPLNEETTGMIRSEHFAAMKDGVIVVNCARGGIIEEAAIL 241

Query: 240 EALENGHVAGAALDVFEVEPP---VDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEV 296
           EALE+G   GAA DV+  EPP   V  KL+ HP ++ TPHLGA+T EAQ NVA  VS E+
Sbjct: 242 EALESGKAVGAAFDVWSEEPPATEVLRKLIAHPRMVVTPHLGANTFEAQKNVAVDVSREI 301

Query: 297 LQFAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIA 356
           + +  G P+ +A+N+P    D    +KP+  +  KIG  V+Q        V   Y G IA
Sbjct: 302 INYLDGRPIENAVNIPRFDPDLMEHMKPFMGLVSKIGEFVAQLAPPNPNKVVFTYNGKIA 361

Query: 357 KLETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVT 416
           + + + +T   L+  L  + D  VN VNA  VA+  GI+  E  ++    + + ++V + 
Sbjct: 362 RFDCAPLTVCGLASLLNRQTDQEVNMVNARLVAETMGITVEEVRNTESESFSSLVTVCIE 421

Query: 417 GDRSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDI 476
               + ++  T       ++V++  F  DF P  H++ I + D  G+IG++G ILG+  +
Sbjct: 422 TPEGSRSIAGTLFEGI-PKVVKMRDFQTDFTPEPHMLVISYDDKPGLIGKIGTILGEAKV 480

Query: 477 NIATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLIDL 524
           NI  M +GR+ K GEA+++LS D   +D  ++++    D   +K + +
Sbjct: 481 NIGNMTLGRRAKAGEAMVVLSIDSPADDATLEKVAKAVDARFLKAVHM 528


Lambda     K      H
   0.317    0.134    0.374 

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: 644
Number of extensions: 26
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: 530
Length adjustment: 35
Effective length of query: 490
Effective length of database: 495
Effective search space:   242550
Effective search space used:   242550
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_092057260.1 BQ4888_RS10930 (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.2645264.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-192  626.0   0.3   3.3e-192  625.8   0.3    1.0  1  NCBI__GCF_900111775.1:WP_092057260.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900111775.1:WP_092057260.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  625.8   0.3  3.3e-192  3.3e-192       1     524 [.       2     527 ..       2     528 .. 0.99

  Alignments for each domain:
  == domain 1  score: 625.8 bits;  conditional E-value: 3.3e-192
                             TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvG 72 
                                           kvl++d++s+eg++ ll++ ++++dv+ +l  +el ++i  ydali+RS t+v++ lle+  +L++++RaGvG
  NCBI__GCF_900111775.1:WP_092057260.1   2 KVLITDEISPEGLQpLLDDPRVQLDVRLNLPVAELHQIIGGYDALITRSGTRVDAALLEHSGNLRIVARAGVG 74 
                                           7************************************************************************ PP

                             TIGR01327  73 vDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviG 145
                                           +DN+d++aa+kkGi+vvNaP gn  saaE+++a+ll+l R+++ a++s+k+++W+r  f+G El+gkt+G+iG
  NCBI__GCF_900111775.1:WP_092057260.1  75 IDNVDVPAASKKGIIVVNAPFGNVNSAAEHTMAILLSLCRNVTVANASLKSGEWKRAPFTGYELKGKTVGIIG 147
                                           ************************************************************************* PP

                             TIGR01327 146 lGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelak 218
                                           lG++G +va r++a++++vla DPyise++ae+ gv+ l +ld++++ aD+itvH+Pl++et g+i  e++a 
  NCBI__GCF_900111775.1:WP_092057260.1 148 LGKVGGRVALRCRAFEANVLACDPYISEKRAEDHGVK-LVSLDDIVRYADIITVHTPLNEETTGMIRSEHFAA 219
                                           *************************************.556******************************** PP

                             TIGR01327 219 mKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt...dnklleldnvvvtpHlgAsteEaqen 288
                                           mK+gvi+vNcaRGGii+E+A++eale+gk  +aa+Dv+++EPp      kl++++++vvtpHlgA+t Eaq+n
  NCBI__GCF_900111775.1:WP_092057260.1 220 MKDGVIVVNCARGGIIEEAAILEALESGKAVGAAFDVWSEEPPAtevLRKLIAHPRMVVTPHLGANTFEAQKN 292
                                           ******************************************99666689999******************** PP

                             TIGR01327 289 vavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeees 361
                                           vav+v+ e++++l g + e+avN+p  d + +e++kp++ l+ k+G+++ ql+  +++kv  t++G++a+++ 
  NCBI__GCF_900111775.1:WP_092057260.1 293 VAVDVSREIINYLDGRPIENAVNIPRFDPDLMEHMKPFMGLVSKIGEFVAQLAPPNPNKVVFTYNGKIARFDC 365
                                           ************************************************************************* PP

                             TIGR01327 362 elltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleeke 434
                                            +lt   l+ ll+ ++++evn+vnA+ va+  gitvee ++ ese++++l++v +e+ +g++s+agt++e  +
  NCBI__GCF_900111775.1:WP_092057260.1 366 APLTVCGLASLLNRQTDQEVNMVNARLVAETMGITVEEVRNTESESFSSLVTVCIETPEGSRSIAGTLFE-GI 437
                                           **********************************************************************.5* PP

                             TIGR01327 435 priveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseev 507
                                           p++v++++f+ d++pe ++l+i++ DkpG+igk+g++lgea +Ni +m+lgr++k gea+++ls+D+++++  
  NCBI__GCF_900111775.1:WP_092057260.1 438 PKVVKMRDFQTDFTPEPHMLVISYDDKPGLIGKIGTILGEAKVNIGNMTLGRRAKAGEAMVVLSIDSPADDAT 510
                                           ************************************************************************* PP

                             TIGR01327 508 leeikevpeiksvklve 524
                                           le++++  +++ +k+v+
  NCBI__GCF_900111775.1:WP_092057260.1 511 LEKVAKAVDARFLKAVH 527
                                           ******99999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (530 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 22.20
//
[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