Alignments for a candidate for serA in Methanosarcina acetivorans C2A

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Methanosarcina acetivorans C2A

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_011020641.1 MA_RS03105 phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>NCBI__GCF_000007345.1:WP_011020641.1
          Length = 523

 Score =  484 bits (1247), Expect = e-141
 Identities = 253/522 (48%), Positives = 358/522 (68%), Gaps = 1/522 (0%)

Query: 3   KILITDPLHESAVEILKQAGEVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEASE 62
           K+L++D L    +EILK+   V+V TGL+ +EL  KI + DALVIRSGT  T+ +IEA++
Sbjct: 2   KVLVSDSLSNEGLEILKEHFTVDVNTGLSEDELVEKIGEYDALVIRSGTQVTQRVIEAAD 61

Query: 63  NLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATASI 122
           NLK++ RAGVGVDNVD+DAAT+KGI+V NAP+ + IS AE   GMM+A +RNIPQA AS+
Sbjct: 62  NLKIVGRAGVGVDNVDVDAATKKGIIVANAPEGNMISAAEHTIGMMMAMSRNIPQANASL 121

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

Query: 183 KLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALYDA 242
           KL TV+E+   +D+IT+H PL  +T++++  EQ  LMKS + I+NCARGG+I+EAAL  A
Sbjct: 182 KLATVNEISKEADYITVHTPLIKETRNILDDEQFDLMKSGVRILNCARGGIINEAALVRA 241

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

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

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

Query: 422 ISIIGSIEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIAGMQ 481
             + G++  +E     I+  R+DI P G +   KHI++P ++G   ++LG++ INI+GMQ
Sbjct: 422 KLVAGTVVGDEPKIVSIDEDRVDIFPAGRMIFAKHINKPNVIGPCCMVLGKNNINISGMQ 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: 747
Number of extensions: 23
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: 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_011020641.1 MA_RS03105 (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.1260.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.4e-211  687.6  13.2   7.1e-211  687.4  13.2    1.0  1  lcl|NCBI__GCF_000007345.1:WP_011020641.1  MA_RS03105 phosphoglycerate dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000007345.1:WP_011020641.1  MA_RS03105 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  687.4  13.2  7.1e-211  7.1e-211       1     525 []       2     523 .]       2     523 .] 0.99

  Alignments for each domain:
  == domain 1  score: 687.4 bits;  conditional E-value: 7.1e-211
                                 TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 
                                               kvlv+d+ls+eg+e+lke+ + vdv+tgls++el+eki +ydal++RS t+vt+ ++eaa++Lk++gRa
  lcl|NCBI__GCF_000007345.1:WP_011020641.1   2 KVLVSDSLSNEGLEILKEH-FTVDVNTGLSEDELVEKIGEYDALVIRSGTQVTQRVIEAADNLKIVGRA 69 
                                               7***************976.8************************************************ PP

                                 TIGR01327  70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138
                                               GvGvDN+d++aatkkGi+v NaPegn isaaE+++ +++a++R+ipqa++s+k ++W+r+kf+G+E++g
  lcl|NCBI__GCF_000007345.1:WP_011020641.1  70 GVGVDNVDVDAATKKGIIVANAPEGNMISAAEHTIGMMMAMSRNIPQANASLKGREWKRNKFMGVEVKG 138
                                               ********************************************************************* PP

                                 TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207
                                               ktlG+iGlGriGsevakra +l+m++++yDP+ise++a +lgv+ l++++e+ +eaD itvH+Pl ket
  lcl|NCBI__GCF_000007345.1:WP_011020641.1 139 KTLGIIGLGRIGSEVAKRASGLEMNLMGYDPFISEKRAMELGVK-LATVNEISKEADYITVHTPLIKET 206
                                               ********************************************.888********************* PP

                                 TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtp 276
                                               +++++ e+++ mK+gv+i+NcaRGGii+E+ALv ale+gkv +aalDvf +EPp  ++ll++dnv+vtp
  lcl|NCBI__GCF_000007345.1:WP_011020641.1 207 RNILDDEQFDLMKSGVRILNCARGGIINEAALVRALESGKVGGAALDVFVEEPPFGSPLLNFDNVIVTP 275
                                               ********************************************************************* PP

                                 TIGR01327 277 HlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeav 345
                                               HlgAst+Eaq nva+++a+ev+++l+g  +++a+N+p+++ e+++ l+py++lae +Gk+a+ql++++ 
  lcl|NCBI__GCF_000007345.1:WP_011020641.1 276 HLGASTQEAQVNVAIDIAKEVVSVLTGGLAKNAINIPSVKPEAMAVLAPYIRLAELMGKIAGQLVDSNY 344
                                               ********************************************************************* PP

                                 TIGR01327 346 kkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllev 414
                                               +kve+ ++Ge++ +++ +lt ++lkgll+ +l + vn+vnA+a+ak r+i v esk+e++e+y++++++
  lcl|NCBI__GCF_000007345.1:WP_011020641.1 345 EKVEIGYNGEISGKDTRPLTVSALKGLLEMALGAGVNYVNAPALAKSRQIAVVESKSESAEEYSSTVSI 413
                                               ********************************************************************* PP

                                 TIGR01327 415 kveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmq 483
                                               k+++ +  + vagtv++ +ep+iv id+ +vd+ p g ++++k+ +kp vig  +++lg+++iNi +mq
  lcl|NCBI__GCF_000007345.1:WP_011020641.1 414 KLSSGETAKLVAGTVVG-DEPKIVSIDEDRVDIFPAGRMIFAKHINKPNVIGPCCMVLGKNNINISGMQ 481
                                               *****************.5************************************************** PP

                                 TIGR01327 484 lgrkekggealmllslDeevseevleeikevpeiksvklvel 525
                                               +gr+e gg ++m+l++D +vs+ +l+e+++vp i ++klv+l
  lcl|NCBI__GCF_000007345.1:WP_011020641.1 482 VGRSEVGGVTMMVLNVDTDVSDAILDEVRQVPGILNAKLVTL 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.63
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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