Alignments for a candidate for serA in Methylobacterium nodulans ORS 2060

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Methylobacterium nodulans ORS 2060

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_015933125.1 MNOD_RS32135 phosphoglycerate dehydrogenase

Query= BRENDA::Q9Z564
         (529 letters)



>NCBI__GCF_000022085.1:WP_015933125.1
          Length = 531

 Score =  358 bits (920), Expect = e-103
 Identities = 212/532 (39%), Positives = 316/532 (59%), Gaps = 9/532 (1%)

Query: 1   MSSKPVVLIAEELSPATVDAL---GPDFEIRHCNGADRAELLPAIADVDAILVRSATKVD 57
           M++   VLI++ LSPA V      G   ++R   G D+  L  AI D D + +RS TKV 
Sbjct: 1   MTTPKRVLISDALSPAAVAIFRERGLVADLRPELGKDKEALAAAIGDYDGLAIRSTTKVT 60

Query: 58  AEAVAAAKKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARN 117
           A  +  A++L+VV RAG+G+DNVDV AAT  GV+V+N P  N VT AE A  +++A AR 
Sbjct: 61  AALLDKAERLRVVGRAGIGVDNVDVPAATARGVIVMNTPHGNAVTTAEHAIAMMLALARE 120

Query: 118 IPQANAALKNGEWKRSKYTGVELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYVQP 177
           IPQA+A+ + G W+++++ G+EL  KTLGV+G G IG++VA R     M+V+AYDP++ P
Sbjct: 121 IPQADASTQQGRWEKNRFLGIELTAKTLGVIGCGNIGSIVADRGIGLRMRVIAYDPFLTP 180

Query: 178 ARAAQMGVKVLSLDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGIV 237
            RA ++GV+ + LDELL  +D IT+H+P T +T  ++  EAL + KP VRIVN ARGG+V
Sbjct: 181 ERAIEIGVEKVELDELLRRADVITLHVPLTEKTRNILSAEALARTKPGVRIVNCARGGLV 240

Query: 238 DEEALYSALKEGRVAGAGLDVYAKEPCTDSPLFEFDQVVATPHLGASTDEAQEKAGIAVA 297
           DE AL +AL  G VAGA  DV++ EP T++ LF    V+ TPHLGAST EAQE   + VA
Sbjct: 241 DEAALRAALDRGHVAGAAFDVFSVEPATENVLFGHPHVICTPHLGASTREAQENVALQVA 300

Query: 298 KSVRLALAGELVPDAVNVQGGVIAED---VKPGLPLAERLGRIFTALAGEVAVRLDVEVY 354
           + +   L    + +AVN    + AE+   ++P + LAE+LG     L       + +   
Sbjct: 301 EQMADHLLHGAIRNAVNFP-SISAEEAPRLRPFVTLAEQLGSFLGQLTEAPIRGIRIAFE 359

Query: 355 GEITQHDVKVLELSALKGVFEDVVDETVSYVNAPLFAQERGVEVRLTTSSESPEHRNVVI 414
           GEI   ++K L  SA+ G  +  + E V+ V+A   A++RG+ V  TT + S  +   V+
Sbjct: 360 GEIASMNLKALTASAVAGALKPFL-EGVNMVSATEVARQRGIVVETTTRTGSAHNYASVL 418

Query: 415 VRGTLSDGEEVSVSGTLAGPKHLQKIVAIGEYDVDLALADHMVVLRYEDRPGVVGTVGRI 474
                ++      +GT+     + + V I    ++ A A HM+ +R  D+PG +G  G +
Sbjct: 419 HVTVEAEDMPRDAAGTVF-HDGVPRTVEIRSIPLEAAFAPHMLYVRNADQPGFIGRFGTL 477

Query: 475 IGEAGLNIAGMQVARATVGGEALAVLTVDDTVPSGVLAEVAAEIGATSARSV 526
           +GEAG+N+A   + R   GG+A+  + VD  V   +L ++ A      AR+V
Sbjct: 478 LGEAGVNVATFHLGRDRPGGDAICFVAVDQPVSPALLRQIEAIPQVKRARAV 529


Lambda     K      H
   0.315    0.133    0.362 

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: 678
Number of extensions: 33
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: 529
Length of database: 531
Length adjustment: 35
Effective length of query: 494
Effective length of database: 496
Effective search space:   245024
Effective search space used:   245024
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_015933125.1 MNOD_RS32135 (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.3387036.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.5e-201  655.0   0.1   5.1e-201  654.9   0.1    1.0  1  NCBI__GCF_000022085.1:WP_015933125.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022085.1:WP_015933125.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  654.9   0.1  5.1e-201  5.1e-201       1     524 [.       6     530 ..       6     531 .] 0.98

  Alignments for each domain:
  == domain 1  score: 654.9 bits;  conditional E-value: 5.1e-201
                             TIGR01327   1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvigRaGv 71 
                                           +vl++d ls++++++++e++l  d + +l  +ke+l ++i dyd+l +RS+tkvt+ ll++ae+L+v+gRaG+
  NCBI__GCF_000022085.1:WP_015933125.1   6 RVLISDALSPAAVAIFRERGLVADLRPELgkDKEALAAAIGDYDGLAIRSTTKVTAALLDKAERLRVVGRAGI 78 
                                           79******************999888776226678999*********************************** PP

                             TIGR01327  72 GvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGvi 144
                                           GvDN+d++aat++G++v+N+P+gn +++aE+a+a++lalaR+ipqad+s+++++We+++flG+El++ktlGvi
  NCBI__GCF_000022085.1:WP_015933125.1  79 GVDNVDVPAATARGVIVMNTPHGNAVTTAEHAIAMMLALAREIPQADASTQQGRWEKNRFLGIELTAKTLGVI 151
                                           ************************************************************************* PP

                             TIGR01327 145 GlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeela 217
                                           G G+iGs+va+r  +l+m+v+ayDP++++e+a ++gve+++ ldell++aDvit+HvPlt++t++++++e+la
  NCBI__GCF_000022085.1:WP_015933125.1 152 GCGNIGSIVADRGIGLRMRVIAYDPFLTPERAIEIGVEKVE-LDELLRRADVITLHVPLTEKTRNILSAEALA 223
                                           **************************************666.******************************* PP

                             TIGR01327 218 kmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenva 290
                                           ++K+gv+ivNcaRGG++dE+AL  al+ g+v++aa+Dvf+ EP+t+n l+ +++v+ tpHlgAst+Eaqenva
  NCBI__GCF_000022085.1:WP_015933125.1 224 RTKPGVRIVNCARGGLVDEAALRAALDRGHVAGAAFDVFSVEPATENVLFGHPHVICTPHLGASTREAQENVA 296
                                           ************************************************************************* PP

                             TIGR01327 291 vevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesel 363
                                           ++vae++ + l   + ++avN p+++aee+ +l+p+++lae+lG++ +ql+++ ++ +++++eGe+a+++ ++
  NCBI__GCF_000022085.1:WP_015933125.1 297 LQVAEQMADHLLHGAIRNAVNFPSISAEEAPRLRPFVTLAEQLGSFLGQLTEAPIRGIRIAFEGEIASMNLKA 369
                                           ************************************************************************* PP

                             TIGR01327 364 ltsallkgllkevleeevnlvnAkavakergitveesk.eeesedyknllevkveadkgevsvagtvleekep 435
                                           lt+++++g lk+ le  vn+v+A+ va++rgi ve ++ + ++++y ++l+v+vea++  +  agtv+++  p
  NCBI__GCF_000022085.1:WP_015933125.1 370 LTASAVAGALKPFLE-GVNMVSATEVARQRGIVVETTTrTGSAHNYASVLHVTVEAEDMPRDAAGTVFHDGVP 441
                                           **************8.9*****************98751668899**************************** PP

                             TIGR01327 436 riveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevl 508
                                           r vei+++ ++ ++  ++l+++n D+pG+ig+ g+llgeag+N+a+++lgr++ gg+a++ + +D++vs+ +l
  NCBI__GCF_000022085.1:WP_015933125.1 442 RTVEIRSIPLEAAFAPHMLYVRNADQPGFIGRFGTLLGEAGVNVATFHLGRDRPGGDAICFVAVDQPVSPALL 514
                                           ************************************************************************* PP

                             TIGR01327 509 eeikevpeiksvklve 524
                                           ++i+++p++k++++v+
  NCBI__GCF_000022085.1:WP_015933125.1 515 RQIEAIPQVKRARAVR 530
                                           ***********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (531 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: 00:00:00.01
# Mc/sec: 19.20
//
[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