Alignments for a candidate for serA in Nitratiruptor tergarcus DSM 16512

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Nitratiruptor tergarcus DSM 16512

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_084276582.1 B8779_RS05635 phosphoglycerate dehydrogenase

Query= CharProtDB::CH_004924
         (525 letters)



>NCBI__GCF_900176045.1:WP_084276582.1
          Length = 529

 Score =  364 bits (935), Expect = e-105
 Identities = 209/525 (39%), Positives = 316/525 (60%), Gaps = 13/525 (2%)

Query: 3   RVLVSDKMSNDGLQPLIESDFIEIVQKNVADAE------DELHTFDALLVRSATKVTEDL 56
           +++V D +     + L +   IE V  N AD        +++   D ++ RS+T V ++L
Sbjct: 5   KIVVCDHLHKKAEEILAKEQDIEYV--NAADVPKGGPLYEKIKDADVIITRSSTPVDKEL 62

Query: 57  FNKMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQ 116
                +LK + RAGVGVDN+D++E ++ G+IV+N P  NTI+  E TFA + S MR  P 
Sbjct: 63  LEHAKNLKAIVRAGVGVDNVDMEECSRRGIIVMNVPTANTIAAVELTFAHMLSCMRAFPY 122

Query: 117 ANISVK-SREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEER 175
           A+  +K  R W R A++G+EL GK LGI+G G IGS + +R  AF M V  +DP+++ E+
Sbjct: 123 AHNQLKLERIWKREAWIGNELKGKKLGIIGFGNIGSRVGKRALAFEMEVITYDPYISPEK 182

Query: 176 AKKIGVNSRT-FEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIID 234
           A  +GV   T F ++L + DIIT+HTP TKET  ++++E IAK K GV LINCARGG+ +
Sbjct: 183 ATNLGVKYTTDFNDIL-ACDIITIHTPKTKETINMIDREEIAKMKDGVILINCARGGLYN 241

Query: 235 EAALLEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSE 294
           E AL E L++G +  A +DVF  EP  DNKL++   V  TPHLGA+T+E+Q  +A   + 
Sbjct: 242 EDALYEGLKSGKIKFAGIDVFAKEPATDNKLLELDNVTVTPHLGANTEESQEKIAIGAAT 301

Query: 295 EVLQFAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGT 354
           + L+ A+G+   +A+NLP    +    +KPY ++  K+G L +Q  K   + + +  EG 
Sbjct: 302 QALEAARGISYPNALNLPIKEDEMPPFVKPYLELTQKMGFLAAQVNKGAYKSIKVIAEGE 361

Query: 355 IAKLETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVK 414
           I +   S IT A++ G LK  +  T+N VNA  VAKERGI    K +   SGY N ++VK
Sbjct: 362 IGEYIKSLITFAVV-GVLKESLGETINYVNAEFVAKERGIEILSKKNPETSGYKNKVTVK 420

Query: 415 VTGDRSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDN 474
           +T DR    ++ T      +RIV+IN F +D  P G ++  ++ D  GVIG VG IL  +
Sbjct: 421 LTTDRDIIEISGTIFEENVQRIVDINHFALDVEPKGKMILFKNTDVPGVIGEVGMILAKH 480

Query: 475 DINIATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSV 519
           +INIA  ++GR +  G A+ ++  D  +   ++KEL ++   +SV
Sbjct: 481 NINIADFRLGR-DNHGLALAVIIVDDDVSKDVLKELADLKACLSV 524


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: 670
Number of extensions: 38
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: 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_084276582.1 B8779_RS05635 (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.6493.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.7e-200  652.5   8.6     3e-200  652.3   8.6    1.0  1  lcl|NCBI__GCF_900176045.1:WP_084276582.1  B8779_RS05635 phosphoglycerate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176045.1:WP_084276582.1  B8779_RS05635 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  652.3   8.6    3e-200    3e-200       1     522 [.       5     526 ..       5     529 .] 0.97

  Alignments for each domain:
  == domain 1  score: 652.3 bits;  conditional E-value: 3e-200
                                 TIGR01327   1 kvlvadklseegie.llkekelevdvktglske.ellekikdydalivRSatkvteelleaaekLkvig 67 
                                               k++v+d+l++++ e l ke+++e  ++ ++ k   l ekikd+d++i+RS+t+v++elle+a++Lk i+
  lcl|NCBI__GCF_900176045.1:WP_084276582.1   5 KIVVCDHLHKKAEEiLAKEQDIEYVNAADVPKGgPLYEKIKDADVIITRSSTPVDKELLEHAKNLKAIV 73 
                                               699***********77788899977777777752688******************************** PP

                                 TIGR01327  68 RaGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekk.WerkkflGtE 135
                                               RaGvGvDN+d+e+++++Gi+v+N P++nti+a+El++a++l+ +R +p a++++k ++ W+r++++G E
  lcl|NCBI__GCF_900176045.1:WP_084276582.1  74 RAGVGVDNVDMEECSRRGIIVMNVPTANTIAAVELTFAHMLSCMRAFPYAHNQLKLERiWKREAWIGNE 142
                                               *******************************************************8888********** PP

                                 TIGR01327 136 lygktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPlt 204
                                               l+gk+lG+iG+G+iGs+v+kra a++m+v++yDPyis+eka++lgv++++d++++l  +D+it+H+P+t
  lcl|NCBI__GCF_900176045.1:WP_084276582.1 143 LKGKKLGIIGFGNIGSRVGKRALAFEMEVITYDPYISPEKATNLGVKYTTDFNDIL-ACDIITIHTPKT 210
                                               ********************************************************.8*********** PP

                                 TIGR01327 205 ketkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvv 273
                                               ket+++i++ee+akmK+gvi++NcaRGG+++E+AL+e l++gk++ a++Dvf+kEP+tdnklleldnv+
  lcl|NCBI__GCF_900176045.1:WP_084276582.1 211 KETINMIDREEIAKMKDGVILINCARGGLYNEDALYEGLKSGKIKFAGIDVFAKEPATDNKLLELDNVT 279
                                               ********************************************************************* PP

                                 TIGR01327 274 vtpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllk 342
                                               vtpHlgA+teE+qe++a+  a + lea++g + ++a+Nlp  + e    +kpyl+l++k+G la q+ k
  lcl|NCBI__GCF_900176045.1:WP_084276582.1 280 VTPHLGANTEESQEKIAIGAATQALEAARGISYPNALNLPIKEDEMPPFVKPYLELTQKMGFLAAQVNK 348
                                               *****************************************99999999******************** PP

                                 TIGR01327 343 eavkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknl 411
                                               +a k+++v  eGe+ e+  +l+ ++++ g+lke+l e++n+vnA++vakergi++  +k+ e++ ykn 
  lcl|NCBI__GCF_900176045.1:WP_084276582.1 349 GAYKSIKVIAEGEIGEYIKSLI-TFAVVGVLKESLGETINYVNAEFVAKERGIEILSKKNPETSGYKNK 416
                                               *****************96666.78889***************************************** PP

                                 TIGR01327 412 levkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNia 480
                                               ++vk+++d++ ++++gt++ee+ +riv+i++f +d+ep+g+++++kn+D+pGvig+vg++l++++iNia
  lcl|NCBI__GCF_900176045.1:WP_084276582.1 417 VTVKLTTDRDIIEISGTIFEENVQRIVDINHFALDVEPKGKMILFKNTDVPGVIGEVGMILAKHNINIA 485
                                               ********************************************************************* PP

                                 TIGR01327 481 smqlgrkekggealmllslDeevseevleeikevpeiksvkl 522
                                               +++lgr+++g  al+++ +D++vs++vl+e+++++++ sv++
  lcl|NCBI__GCF_900176045.1:WP_084276582.1 486 DFRLGRDNHG-LALAVIIVDDDVSKDVLKELADLKACLSVSY 526
                                               ******9987.9*************************99986 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.24
//
[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