Alignments for a candidate for serA in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Mycolicibacterium vanbaalenii PYR-1

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_011779357.1 MVAN_RS10670 phosphoglycerate dehydrogenase

Query= BRENDA::P9WNX3
         (528 letters)



>NCBI__GCF_000015305.1:WP_011779357.1
          Length = 528

 Score =  846 bits (2185), Expect = 0.0
 Identities = 446/528 (84%), Positives = 482/528 (91%)

Query: 1   MSLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVL 60
           MSLPVVLIADKLA STV ALGDQVEVRWVDGPDR+KLLAAV +ADALLVRSATTVDAEVL
Sbjct: 1   MSLPVVLIADKLAQSTVEALGDQVEVRWVDGPDREKLLAAVADADALLVRSATTVDAEVL 60

Query: 61  AAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAA 120
           AAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAA+RQIPAA
Sbjct: 61  AAAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAAARQIPAA 120

Query: 121 DASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAA 180
           DA+LREH+WKRSSFSGTEIFGKTVGVVGLGRIGQLVAQR+AAFGA++ AYDPYVS ARAA
Sbjct: 121 DATLREHSWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRLAAFGAHITAYDPYVSHARAA 180

Query: 181 QLGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAA 240
           QLGIELL+LD+LL RADFISVHLPKT ETAGLI KEALAKTKPGVIIVNAARGGL+DEAA
Sbjct: 181 QLGIELLTLDELLGRADFISVHLPKTKETAGLIGKEALAKTKPGVIIVNAARGGLIDEAA 240

Query: 241 LADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVR 300
           LADAI  GHVR AGLDVF+TEPCTDSPLFEL QVVVTPHLGAST EAQDRAGTDVA SV+
Sbjct: 241 LADAINSGHVRGAGLDVFSTEPCTDSPLFELPQVVVTPHLGASTVEAQDRAGTDVAASVK 300

Query: 301 LALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEE 360
           LALAGEFVPDAVNVGGG V EEVAPWLDLVRKLG+L GVLS E PVSL VQV+GELA+EE
Sbjct: 301 LALAGEFVPDAVNVGGGAVGEEVAPWLDLVRKLGLLVGVLSSEPPVSLQVQVQGELASEE 360

Query: 361 VEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGAD 420
           VEVL+LSALRGLFSAVIE  VTFVNAPALA+ERGV A I  A+ES NHRSVVDVRAV AD
Sbjct: 361 VEVLKLSALRGLFSAVIEHPVTFVNAPALASERGVEASITTATESANHRSVVDVRAVAAD 420

Query: 421 GSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVN 480
           GS V V+GTL GPQL +KIVQINGR+ +LRA+G+NLII+Y D+PGALGKIGTLLG A VN
Sbjct: 421 GSTVNVAGTLTGPQLVEKIVQINGRNLELRAEGVNLIINYDDQPGALGKIGTLLGGAAVN 480

Query: 481 IQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVDLS 528
           I AAQLS+DA+G GAT++LRLD++VP +V  AI   V+A  LEVVDL+
Sbjct: 481 ILAAQLSQDADGIGATVMLRLDREVPGEVLAAIGRDVNAVTLEVVDLT 528


Lambda     K      H
   0.317    0.133    0.370 

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: 857
Number of extensions: 23
Number of successful extensions: 1
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: 528
Length of database: 528
Length adjustment: 35
Effective length of query: 493
Effective length of database: 493
Effective search space:   243049
Effective search space used:   243049
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_011779357.1 MVAN_RS10670 (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.9855.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.7e-200  651.4   6.7   6.5e-200  651.2   6.7    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011779357.1  MVAN_RS10670 phosphoglycerate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011779357.1  MVAN_RS10670 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  651.2   6.7  6.5e-200  6.5e-200       2     524 ..       6     526 ..       5     527 .. 0.97

  Alignments for each domain:
  == domain 1  score: 651.2 bits;  conditional E-value: 6.5e-200
                                 TIGR01327   2 vlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaG 70 
                                               vl+adkl+++++e+l ++ +ev++ +g ++e+ll+++ d+dal+vRSat+v++e+l+aa+kLk+++RaG
  lcl|NCBI__GCF_000015305.1:WP_011779357.1   6 VLIADKLAQSTVEALGDQ-VEVRWVDGPDREKLLAAVADADALLVRSATTVDAEVLAAAPKLKIVARAG 73 
                                               9**************977.8************************************************* PP

                                 TIGR01327  71 vGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygk 139
                                               vG+DN+d++aat++G+lvvNaP++n++saaE+alallla+aR+ip+ad+ ++e+ W+r++f+GtE++gk
  lcl|NCBI__GCF_000015305.1:WP_011779357.1  74 VGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAAARQIPAADATLREHSWKRSSFSGTEIFGK 142
                                               ********************************************************************* PP

                                 TIGR01327 140 tlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketk 208
                                               t+Gv+GlGriG+ va+r +a+g+++ ayDPy+s+++a++lg+el  +ldell +aD+i+vH+P+tket+
  lcl|NCBI__GCF_000015305.1:WP_011779357.1 143 TVGVVGLGRIGQLVAQRLAAFGAHITAYDPYVSHARAAQLGIEL-LTLDELLGRADFISVHLPKTKETA 210
                                               *******************************************5.55********************** PP

                                 TIGR01327 209 gligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpH 277
                                               gligke+lak+K+gviivN+aRGG+idE+AL++a+++g+vr+a+lDvf++EP+td++l+el++vvvtpH
  lcl|NCBI__GCF_000015305.1:WP_011779357.1 211 GLIGKEALAKTKPGVIIVNAARGGLIDEAALADAINSGHVRGAGLDVFSTEPCTDSPLFELPQVVVTPH 279
                                               ********************************************************************* PP

                                 TIGR01327 278 lgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavk 346
                                               lgAst Eaq++++++va +v+ al+ge+v++avN++     + e+++p+ldl++klG l+++l++e + 
  lcl|NCBI__GCF_000015305.1:WP_011779357.1 280 LGASTVEAQDRAGTDVAASVKLALAGEFVPDAVNVGG--GAVGEEVAPWLDLVRKLGLLVGVLSSEPPV 346
                                               ************************************9..677889************************ PP

                                 TIGR01327 347 kvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevk 415
                                               +++v+++Gela+ee+e+l+ ++l+gl+++v+e+ v++vnA+a+a erg++ +++++ es +++++++v+
  lcl|NCBI__GCF_000015305.1:WP_011779357.1 347 SLQVQVQGELASEEVEVLKLSALRGLFSAVIEHPVTFVNAPALASERGVEASITTATESANHRSVVDVR 415
                                               ********************************************************************9 PP

                                 TIGR01327 416 veadkg.evsvagtvlee.kepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482
                                               + a++g +v+vagt+ +    ++iv+i+g +++l++eg++lii++ D+pG++gk+g+llg a +Ni ++
  lcl|NCBI__GCF_000015305.1:WP_011779357.1 416 AVAADGsTVNVAGTLTGPqLVEKIVQINGRNLELRAEGVNLIINYDDQPGALGKIGTLLGGAAVNILAA 484
                                               887776599*******984689*********************************************** PP

                                 TIGR01327 483 qlgrkekggealmllslDeevseevleeikevpeiksvklve 524
                                               ql++++ g  a+++l+lD+ev+ evl++i    ++ ++++v+
  lcl|NCBI__GCF_000015305.1:WP_011779357.1 485 QLSQDADGIGATVMLRLDREVPGEVLAAIGRDVNAVTLEVVD 526
                                               *****************************8877777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (528 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: 8.09
//
[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