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.849540.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  NCBI__GCF_000016125.1:WP_011869563.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016125.1:WP_011869563.1  
   #    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 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 
                                           kvl++d+l+e+++e+lk+ + ev+v+tgl+ ee+  kikd+dal+vRS t+vt+e++ea e+Lkvi+RaGvG+
  NCBI__GCF_000016125.1:WP_011869563.1   3 KVLITDPLHESAVEILKQAG-EVEVATGLNVEEIKLKIKDADALVVRSGTTVTREIIEASENLKVIARAGVGI 74 
                                           7****************998.**************************************************** PP

                             TIGR01327  74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGl 146
                                           DN+d++aat+kGi+vvNaP++++is+aEl + ++l++aR+ipqa++s+k+++W+rk+f+G+E+ygktlG++Gl
  NCBI__GCF_000016125.1:WP_011869563.1  75 DNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLSAARNIPQATASIKKGEWDRKSFKGMEIYGKTLGIVGL 147
                                           ************************************************************************* PP

                             TIGR01327 147 GriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakm 219
                                           GriG++vakra+a+gm+++ayDPyi+e+ a++lg++l  ++del+a +D+it+HvPlt++tk++igk+++a m
  NCBI__GCF_000016125.1:WP_011869563.1 148 GRIGQQVAKRAQAFGMTIVAYDPYIPEDVASELGIKL-LTVDELCAASDFITLHVPLTPKTKHMIGKDQIALM 219
                                           ************************************5.55********************************* PP

                             TIGR01327 220 KkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvave 292
                                           K++++i+NcaRGG+idE+AL+eal++gk++aa+lDvfe+EPp++++ll+l+n++ tpH+gAsteEaq  ++++
  NCBI__GCF_000016125.1:WP_011869563.1 220 KSNMVIMNCARGGLIDEDALYEALNSGKIKAAGLDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTI 292
                                           ************************************************************************* PP

                             TIGR01327 293 vaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesellt 365
                                           vae+ +++lkge++e++vNlp++ +e+++klkpy+ laek+G++a+q+l+++++ +e+t+ G la+e++e+++
  NCBI__GCF_000016125.1:WP_011869563.1 293 VAEQTVKILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLANEKTEIIK 365
                                           ************************************************************************* PP

                             TIGR01327 366 sallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriv 438
                                           +++lkg+l ++l + vnlvnA+++ak r+i++ e + +e +dy nl+++ ++++++e+s+ g++ + +e    
  NCBI__GCF_000016125.1:WP_011869563.1 366 RSFLKGILAPILLAGVNLVNAPVIAKSRNIKLAEGTMSE-SDYGNLIKIVAKGENDEISIIGSIEH-NEIVFR 436
                                           *********************************988776.9*********************9877.5999** PP

                             TIGR01327 439 eidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleei 511
                                           ei+g+++d++peg++ iik+ D+pG++gkvg llge+giNia+mq+gr+e gg+++m l +D+ +s+ev++ei
  NCBI__GCF_000016125.1:WP_011869563.1 437 EINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGMQVGRREPGGHSIMFLDVDHMISDEVMAEI 509
                                           ************************************************************************* PP

                             TIGR01327 512 kevpeiksvklve 524
                                           +++++++ +k ++
  NCBI__GCF_000016125.1:WP_011869563.1 510 TKMENVRAAKSIN 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: 00:00:00.01
# Mc/sec: 15.88
//
[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:

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:

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:

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:

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