Alignments for a candidate for serA in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Methanococcus maripaludis C5

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_011869563.1 MMARC5_RS09360 phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>NCBI__GCF_000016125.1:WP_011869563.1
          Length = 523

 Score =  966 bits (2497), Expect = 0.0
 Identities = 497/523 (95%), Positives = 510/523 (97%)

Query: 1   MSKILITDPLHESAVEILKQAGEVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEA 60
           MSK+LITDPLHESAVEILKQAGEVEVATGL VEE+KLKIKD DALV+RSGTT TREIIEA
Sbjct: 1   MSKVLITDPLHESAVEILKQAGEVEVATGLNVEEIKLKIKDADALVVRSGTTVTREIIEA 60

Query: 61  SENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATA 120
           SENLKVIARAGVG+DNVDLDAATEKGIVVVNAPDASSISVAELLFGMML+AARNIPQATA
Sbjct: 61  SENLKVIARAGVGIDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLSAARNIPQATA 120

Query: 121 SIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180
           SIK G+WDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL
Sbjct: 121 SIKKGEWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180

Query: 181 GIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALY 240
           GIKLLTVDELC  SDFITLHVPLTPKTKHMIGK+QIALMKSNMVIMNCARGGLIDE ALY
Sbjct: 181 GIKLLTVDELCAASDFITLHVPLTPKTKHMIGKDQIALMKSNMVIMNCARGGLIDEDALY 240

Query: 241 DALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI 300
           +ALNSGKIKAA LDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI
Sbjct: 241 EALNSGKIKAAGLDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI 300

Query: 301 LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAKEK 360
           LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLA EK
Sbjct: 301 LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLANEK 360

Query: 361 TEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSESDYGNSIKISAKGEND 420
           TEI+KRSFLKGILAPILLAGVNLVNAPVIAKSRNIK+AEGTMSESDYGN IKI AKGEND
Sbjct: 361 TEIIKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKLAEGTMSESDYGNLIKIVAKGEND 420

Query: 421 EISIIGSIEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGM 480
           EISIIGSIEHNE+VFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGM
Sbjct: 421 EISIIGSIEHNEIVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGM 480

Query: 481 QVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSINI 523
           QVGRREPGGHSIMFLD+DHMISDEV+ EI KMENVRAAKSINI
Sbjct: 481 QVGRREPGGHSIMFLDVDHMISDEVMAEITKMENVRAAKSINI 523


Lambda     K      H
   0.316    0.134    0.364 

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: 1058
Number of extensions: 30
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: 523
Length of database: 523
Length adjustment: 35
Effective length of query: 488
Effective length of database: 488
Effective search space:   238144
Effective search space used:   238144
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_011869563.1 MMARC5_RS09360 (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.3235.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-211  689.6  14.4   1.7e-211  689.5  14.4    1.0  1  lcl|NCBI__GCF_000016125.1:WP_011869563.1  MMARC5_RS09360 phosphoglycerate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016125.1:WP_011869563.1  MMARC5_RS09360 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  689.5  14.4  1.7e-211  1.7e-211       1     524 [.       3     522 ..       3     523 .] 0.99

  Alignments for each domain:
  == domain 1  score: 689.5 bits;  conditional E-value: 1.7e-211
                                 TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 
                                               kvl++d+l+e+++e+lk+ + ev+v+tgl+ ee+  kikd+dal+vRS t+vt+e++ea e+Lkvi+Ra
  lcl|NCBI__GCF_000016125.1:WP_011869563.1   3 KVLITDPLHESAVEILKQAG-EVEVATGLNVEEIKLKIKDADALVVRSGTTVTREIIEASENLKVIARA 70 
                                               7****************998.************************************************ PP

                                 TIGR01327  70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138
                                               GvG+DN+d++aat+kGi+vvNaP++++is+aEl + ++l++aR+ipqa++s+k+++W+rk+f+G+E+yg
  lcl|NCBI__GCF_000016125.1:WP_011869563.1  71 GVGIDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLSAARNIPQATASIKKGEWDRKSFKGMEIYG 139
                                               ********************************************************************* PP

                                 TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207
                                               ktlG++GlGriG++vakra+a+gm+++ayDPyi+e+ a++lg++l  ++del+a +D+it+HvPlt++t
  lcl|NCBI__GCF_000016125.1:WP_011869563.1 140 KTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASELGIKL-LTVDELCAASDFITLHVPLTPKT 207
                                               ********************************************5.55********************* PP

                                 TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtp 276
                                               k++igk+++a mK++++i+NcaRGG+idE+AL+eal++gk++aa+lDvfe+EPp++++ll+l+n++ tp
  lcl|NCBI__GCF_000016125.1:WP_011869563.1 208 KHMIGKDQIALMKSNMVIMNCARGGLIDEDALYEALNSGKIKAAGLDVFEQEPPKESPLLTLNNLIGTP 276
                                               ********************************************************************* PP

                                 TIGR01327 277 HlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeav 345
                                               H+gAsteEaq  ++++vae+ +++lkge++e++vNlp++ +e+++klkpy+ laek+G++a+q+l++++
  lcl|NCBI__GCF_000016125.1:WP_011869563.1 277 HQGASTEEAQLSAGTIVAEQTVKILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSI 345
                                               ********************************************************************* PP

                                 TIGR01327 346 kkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllev 414
                                               + +e+t+ G la+e++e++++++lkg+l ++l + vnlvnA+++ak r+i++ e + +e +dy nl+++
  lcl|NCBI__GCF_000016125.1:WP_011869563.1 346 ELLEITYMGGLANEKTEIIKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKLAEGTMSE-SDYGNLIKI 413
                                               *****************************************************988776.9******** PP

                                 TIGR01327 415 kveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmq 483
                                                ++++++e+s+ g++ + +e    ei+g+++d++peg++ iik+ D+pG++gkvg llge+giNia+mq
  lcl|NCBI__GCF_000016125.1:WP_011869563.1 414 VAKGENDEISIIGSIEH-NEIVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGMQ 481
                                               *************9877.5999*********************************************** PP

                                 TIGR01327 484 lgrkekggealmllslDeevseevleeikevpeiksvklve 524
                                               +gr+e gg+++m l +D+ +s+ev++ei+++++++ +k ++
  lcl|NCBI__GCF_000016125.1:WP_011869563.1 482 VGRREPGGHSIMFLDVDHMISDEVMAEITKMENVRAAKSIN 522
                                               ***********************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (523 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: 10.34
//
[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