Alignments for a candidate for serA in Malonomonas rubra DSM 5091

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Malonomonas rubra DSM 5091

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_072909457.1 BUB13_RS14310 phosphoglycerate dehydrogenase

Query= curated2:O27051
         (525 letters)



>NCBI__GCF_900142125.1:WP_072909457.1
          Length = 530

 Score =  411 bits (1057), Expect = e-119
 Identities = 209/521 (40%), Positives = 330/521 (63%), Gaps = 6/521 (1%)

Query: 4   MKVLIADSINEKGISELEEVAEVVVNTTI--TPEELLDAIKDFDAIVVRSRTKVTREVIE 61
           MKVL+ D I++ G+  + +   + V+  +    EEL   I D+ AI+ RS T+V   ++E
Sbjct: 1   MKVLVTDEISKNGLLPILDDPRITVDFKVGLPKEELHQVIGDYQAIITRSMTQVDEALLE 60

Query: 62  AAPRLKIIARAGVGVDNVDVKAATDRGIMVINAPESTSITVAEHSIGLMLALARKIAIAD 121
            A  LK+IARAGVG+DNVDV AA+ RGI+V+NAP     + AEH++ ++L+  R + +A+
Sbjct: 61  HATNLKMIARAGVGIDNVDVDAASSRGIIVVNAPYGNVNSAAEHTMAILLSYCRNVTLAN 120

Query: 122 RSVKEGKWEKNRFMGIELNGKTLGIIGMGRIGSQVVVRTKAFGMDIMVYDPYISKEAAEE 181
            S+K G+W++  F G EL  KT+G+IG+G++G +V +R +AF  +++ YDPYIS++ AE+
Sbjct: 121 ASLKSGQWQRAPFTGHELKEKTIGVIGLGKVGGRVALRCRAFEANVITYDPYISEKRAED 180

Query: 182 MGVTVTDLETLLRESDIVTIHVPLTPETRHLISEDEFKLMKDTAFIVNCARGGIIDEDAL 241
            GV +  LE ++R SDI+T+H PL  ETR LI+ + F+ M+D  FIVNCARGGII+E+A+
Sbjct: 181 FGVKLVSLEDVIRFSDIITVHTPLNDETRDLITAEHFEGMQDGVFIVNCARGGIINEEAM 240

Query: 242 YRALKDGEIAGAALDVFEEEPPEGSPLLEL---ENVVLTPHIGASTSEAQRDAAIIVANE 298
             AL+ G+  GAA DV+ +EPP+   L +L     +++TPH+GA+T EAQ++ A+ V+ E
Sbjct: 241 LAALESGKCGGAAFDVWSQEPPKSDTLKKLIAHPKMLVTPHLGANTYEAQKNVAVDVSKE 300

Query: 299 IKTVFQGGAPRNVLNMPVMDSETYKSLKPYIELAEKMGAIIAQALPGNIEKLDVTYCGEL 358
           I     G    N +N+P  D +  + +KPY++L   +G  I+Q  P N  K+  TY G+L
Sbjct: 301 IVNYVDGRPISNAVNVPRFDPDLMEQMKPYMKLVSIIGDFISQLAPPNPNKITFTYNGKL 360

Query: 359 AEMQFDILTRTMLQAILNPILTEPVNLINAPSIAKKRGIMVTEARRSESDGYRSIIIATA 418
           A      L+   L A+LN +  + +N++NA  +A++ G+ V E R +E+D + ++I  T 
Sbjct: 361 ARFDCAPLSVCGLAALLNHVTDQEINMVNAGMVAREMGVAVEEVRSTETDSFSNLITLTL 420

Query: 419 ESDRGGFSVEATHIKE-PTIIGINGYRVDVKPEGTMIIARYRDLPGTIGAIGTKLGQHGI 477
           E  +G  ++  T  +  P I+ +  + +D KPE  M++  Y D+PG +G IGT LG   +
Sbjct: 421 EGPQGKRTIAGTLFEGIPKIVKMRNFDIDFKPEEHMLVMTYADVPGALGKIGTILGNAEV 480

Query: 478 NIATMQVGRKEIGGEAVMVLKVDQSVPAEVIEEVKKLDNVD 518
           NI +M +GR E  G+A++V  +D  V  E IE++K     D
Sbjct: 481 NIGSMSLGRTEKAGKAIVVFSIDSPVEEETIEQLKAAIGAD 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: 652
Number of extensions: 25
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: 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_072909457.1 BUB13_RS14310 (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.5287.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-194  632.8   0.6   2.7e-194  632.7   0.6    1.0  1  lcl|NCBI__GCF_900142125.1:WP_072909457.1  BUB13_RS14310 phosphoglycerate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900142125.1:WP_072909457.1  BUB13_RS14310 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  632.7   0.6  2.7e-194  2.7e-194       1     521 [.       2     524 ..       2     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 632.7 bits;  conditional E-value: 2.7e-194
                                 TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 
                                               kvlv+d++s++g+  +l++ ++ vd k gl keel ++i dy+a+i+RS+t+v+e lle+a++Lk+i+R
  lcl|NCBI__GCF_900142125.1:WP_072909457.1   2 KVLVTDEISKNGLLpILDDPRITVDFKVGLPKEELHQVIGDYQAIITRSMTQVDEALLEHATNLKMIAR 70 
                                               7***********999****************************************************** PP

                                 TIGR01327  69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137
                                               aGvG+DN+d++aa+ +Gi+vvNaP gn  saaE+++a+ll+  R+++ a++s+k+++W+r  f+G El+
  lcl|NCBI__GCF_900142125.1:WP_072909457.1  71 AGVGIDNVDVDAASSRGIIVVNAPYGNVNSAAEHTMAILLSYCRNVTLANASLKSGQWQRAPFTGHELK 139
                                               ********************************************************************* PP

                                 TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206
                                               +kt+GviGlG++G +va r++a++++v++yDPyise++ae++gv+ l +l+++++ +D+itvH+Pl++e
  lcl|NCBI__GCF_900142125.1:WP_072909457.1 140 EKTIGVIGLGKVGGRVALRCRAFEANVITYDPYISEKRAEDFGVK-LVSLEDVIRFSDIITVHTPLNDE 207
                                               *********************************************.556******************** PP

                                 TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt...dnklleldnv 272
                                               t++li +e+++ m++gv ivNcaRGGii+E+A++ ale+gk  +aa+Dv+++EPp+    +kl++++++
  lcl|NCBI__GCF_900142125.1:WP_072909457.1 208 TRDLITAEHFEGMQDGVFIVNCARGGIINEEAMLAALESGKCGGAAFDVWSQEPPKsdtLKKLIAHPKM 276
                                               *******************************************************97777899****** PP

                                 TIGR01327 273 vvtpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqll 341
                                                vtpHlgA+t+Eaq+nvav+v++e+++++ g + ++avN+p  d + +e++kpy++l+  +G ++sql+
  lcl|NCBI__GCF_900142125.1:WP_072909457.1 277 LVTPHLGANTYEAQKNVAVDVSKEIVNYVDGRPISNAVNVPRFDPDLMEQMKPYMKLVSIIGDFISQLA 345
                                               ********************************************************************* PP

                                 TIGR01327 342 keavkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedykn 410
                                                 +++k++ t++G+la+++  +l+   l+ ll++v+++e+n+vnA +va+e g+ vee ++ e+++++n
  lcl|NCBI__GCF_900142125.1:WP_072909457.1 346 PPNPNKITFTYNGKLARFDCAPLSVCGLAALLNHVTDQEINMVNAGMVAREMGVAVEEVRSTETDSFSN 414
                                               ********************************************************************* PP

                                 TIGR01327 411 llevkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNi 479
                                               l+++++e+ +g++++agt++e  +p+iv++++f++d++pe+++l++++ D+pG++gk+g++lg+a++Ni
  lcl|NCBI__GCF_900142125.1:WP_072909457.1 415 LITLTLEGPQGKRTIAGTLFE-GIPKIVKMRNFDIDFKPEEHMLVMTYADVPGALGKIGTILGNAEVNI 482
                                               *********************.5********************************************** PP

                                 TIGR01327 480 asmqlgrkekggealmllslDeevseevleeikevpeiksvk 521
                                                sm+lgr+ek g+a+++ s+D++v+ee +e++k+   +  ++
  lcl|NCBI__GCF_900142125.1:WP_072909457.1 483 GSMSLGRTEKAGKAIVVFSIDSPVEEETIEQLKAAIGADFIR 524
                                               *********************************987766665 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.19
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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