GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Methanosarcina mazei Go1

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_015412066.1 MM_RS09090 phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>NCBI__GCF_000007065.1:WP_015412066.1
          Length = 523

 Score =  483 bits (1242), Expect = e-141
 Identities = 246/522 (47%), Positives = 359/522 (68%), Gaps = 1/522 (0%)

Query: 3   KILITDPLHESAVEILKQAGEVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEASE 62
           K+L++D L    +EILK+  +++V TGL  +EL  KIK  DALVIRSGT  T+ IIEA++
Sbjct: 2   KVLVSDSLSNEGLEILKEHFDIDVCTGLCEDELVEKIKGYDALVIRSGTQVTQRIIEAAD 61

Query: 63  NLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATASI 122
           NLK+I RAGVGVDNVD+DAAT+KGI+V NAP+ + IS AE    MM++ +RNIPQA AS+
Sbjct: 62  NLKIIGRAGVGVDNVDVDAATKKGIIVANAPEGNMISAAEHTIAMMMSMSRNIPQANASL 121

Query: 123 KSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASELGI 182
           K+ +W R  F G+E+ GKTLG++GLGRIG +VAKRA    M ++ YDP+I E  A ELG+
Sbjct: 122 KAREWKRNKFMGVEVKGKTLGVIGLGRIGSEVAKRAAGLEMNLMGYDPFISEKRAMELGV 181

Query: 183 KLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALYDA 242
           KL TV+E+   +D+IT+H PL  +T++++  EQ ALMK  + ++NCARGG+I+E AL  A
Sbjct: 182 KLATVNEIAKEADYITVHTPLIKETRNILDDEQFALMKKGVRVLNCARGGIINEEALARA 241

Query: 243 LNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKILK 302
           L SGK+  AA+DVF +EPP  SPLL  +N+I TPH GAST+EAQ++    +A++ V +L 
Sbjct: 242 LESGKVGGAAIDVFVEEPPFSSPLLNFDNVIVTPHLGASTQEAQVNVAIDIAKEVVSVLT 301

Query: 303 GESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAKEKTE 362
           G SA+N +N+P V  E M  L PY+ L+E MG +A Q +D++ E +EI Y G ++ + T 
Sbjct: 302 GGSAKNAINIPSVKPEAMAVLAPYIRLSELMGKIAGQLVDSNYEKVEIAYNGEISGKDTR 361

Query: 363 ILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEG-TMSESDYGNSIKISAKGENDE 421
            L  S LKG+L   + +GVN VNAP++AKSR I + E  + S  +Y +++ I        
Sbjct: 362 PLTVSALKGLLEMAVGSGVNYVNAPILAKSRKIAVVESKSESAEEYSSTVSIRLSSGEST 421

Query: 422 ISIIGSIEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGMQ 481
             + G++  +E     I+  ++DI P G +   KHI++P ++G   ++LG++ INI+GMQ
Sbjct: 422 KMVAGTVVGDEPKIVSIDDDKVDIFPAGRMIFAKHINKPNVIGPCCMVLGKNNINISGMQ 481

Query: 482 VGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSINI 523
           VGR E GG ++M L++D  +SD +LDE+R++  +  AK + +
Sbjct: 482 VGRSEVGGVTMMVLNVDTDVSDAILDEVRQVPGILNAKLVTL 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: 740
Number of extensions: 26
Number of successful extensions: 2
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_015412066.1 MM_RS09090 (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.1102567.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.9e-212  690.5  14.0   8.9e-212  690.4  14.0    1.0  1  NCBI__GCF_000007065.1:WP_015412066.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007065.1:WP_015412066.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  690.4  14.0  8.9e-212  8.9e-212       1     525 []       2     523 .]       2     523 .] 0.99

  Alignments for each domain:
  == domain 1  score: 690.4 bits;  conditional E-value: 8.9e-212
                             TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 
                                           kvlv+d+ls+eg+e+lke+ +++dv tgl ++el+ekik ydal++RS t+vt+ ++eaa++Lk+igRaGvGv
  NCBI__GCF_000007065.1:WP_015412066.1   2 KVLVSDSLSNEGLEILKEH-FDIDVCTGLCEDELVEKIKGYDALVIRSGTQVTQRIIEAADNLKIIGRAGVGV 73 
                                           7***************966.8**************************************************** PP

                             TIGR01327  74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGl 146
                                           DN+d++aatkkGi+v NaPegn isaaE+++a++++++R+ipqa++s+k+++W+r+kf+G+E++gktlGviGl
  NCBI__GCF_000007065.1:WP_015412066.1  74 DNVDVDAATKKGIIVANAPEGNMISAAEHTIAMMMSMSRNIPQANASLKAREWKRNKFMGVEVKGKTLGVIGL 146
                                           ************************************************************************* PP

                             TIGR01327 147 GriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakm 219
                                           GriGsevakra++l+m++++yDP+ise++a +lgv+ l++++e+++eaD itvH+Pl ket+++++ e++a m
  NCBI__GCF_000007065.1:WP_015412066.1 147 GRIGSEVAKRAAGLEMNLMGYDPFISEKRAMELGVK-LATVNEIAKEADYITVHTPLIKETRNILDDEQFALM 218
                                           ************************************.888********************************* PP

                             TIGR01327 220 KkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvave 292
                                           Kkgv+++NcaRGGii+E+AL+ ale+gkv +aa+Dvf +EPp +++ll++dnv+vtpHlgAst+Eaq nva++
  NCBI__GCF_000007065.1:WP_015412066.1 219 KKGVRVLNCARGGIINEEALARALESGKVGGAAIDVFVEEPPFSSPLLNFDNVIVTPHLGASTQEAQVNVAID 291
                                           ************************************************************************* PP

                             TIGR01327 293 vaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesellt 365
                                           +a+ev+++l+g ++++a+N+p+++ e+++ l+py++l+e +Gk+a+ql++++ +kve++++Ge++ +++ +lt
  NCBI__GCF_000007065.1:WP_015412066.1 292 IAKEVVSVLTGGSAKNAINIPSVKPEAMAVLAPYIRLSELMGKIAGQLVDSNYEKVEIAYNGEISGKDTRPLT 364
                                           ************************************************************************* PP

                             TIGR01327 366 sallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriv 438
                                            ++lkgll+ ++ + vn+vnA+++ak r+i v esk+e++e+y++++++++++ ++++ vagtv++ +ep+iv
  NCBI__GCF_000007065.1:WP_015412066.1 365 VSALKGLLEMAVGSGVNYVNAPILAKSRKIAVVESKSESAEEYSSTVSIRLSSGESTKMVAGTVVG-DEPKIV 436
                                           ******************************************************************.5***** PP

                             TIGR01327 439 eidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleei 511
                                            id+ +vd+ p g ++++k+ +kp vig  +++lg+++iNi +mq+gr+e gg ++m+l++D +vs+ +l+e+
  NCBI__GCF_000007065.1:WP_015412066.1 437 SIDDDKVDIFPAGRMIFAKHINKPNVIGPCCMVLGKNNINISGMQVGRSEVGGVTMMVLNVDTDVSDAILDEV 509
                                           ************************************************************************* PP

                             TIGR01327 512 kevpeiksvklvel 525
                                           ++vp i ++klv+l
  NCBI__GCF_000007065.1:WP_015412066.1 510 RQVPGILNAKLVTL 523
                                           **********9986 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 27.25
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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