Alignments for a candidate for serA in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Magnetospirillum magneticum AMB-1

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_011385558.1 AMB_RS16130 phosphoglycerate dehydrogenase

Query= CharProtDB::CH_004924
         (525 letters)



>NCBI__GCF_000009985.1:WP_011385558.1
          Length = 526

 Score =  424 bits (1090), Expect = e-123
 Identities = 224/524 (42%), Positives = 333/524 (63%), Gaps = 3/524 (0%)

Query: 1   MFRVLVSDKMSNDGLQPLIESDFIEIVQKNVADAEDE--LHTFDALLVRSATKVTEDLFN 58
           M +VL+SDK+S   +Q   +      V+  +A  E +  +  +D L +RS TKVT ++  
Sbjct: 1   MPKVLISDKLSPAAVQIFKDRGIETDVKTGLAPDELKAIIGQYDGLAIRSNTKVTTEILA 60

Query: 59  KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118
             T+LK+VGRAG+GVDN+D+  AT  G++V+N P GN+I+TAEH  AM+ +L R IP+AN
Sbjct: 61  AATNLKVVGRAGIGVDNVDVPAATARGIVVMNTPFGNSITTAEHAIAMMFALAREIPEAN 120

Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKK 178
            S  + +W +  ++G EL GK LGIVG G IG+ +A R     M V  +DPFL+ ERAK+
Sbjct: 121 ASTHAGKWEKNRFMGVELTGKVLGIVGCGNIGAIVADRAQGLRMRVIAYDPFLSVERAKE 180

Query: 179 IGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAAL 238
           + V     +E+   AD IT+HTPLT  T+ +++ + +AK KKGVR+INCARGG++ E  L
Sbjct: 181 LNVEKVELDELFPRADFITLHTPLTDATRNIIDAKAMAKMKKGVRIINCARGGLVVEEDL 240

Query: 239 LEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQ 298
           L ALE+G VAGAALDVF+ EP  +N L  +P V+ TPHLGAST EAQ NVA QV+E++  
Sbjct: 241 LAALESGQVAGAALDVFKTEPAKENALFGNPKVVCTPHLGASTSEAQENVALQVAEQMAD 300

Query: 299 FAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKL 358
           +     V +A+N+P+++ ++  K++PY  +A +IGS   Q  +  ++DV I+Y G +A L
Sbjct: 301 YLLTGAVTNALNIPSVSAEDAPKLRPYMTLANQIGSFAGQLTETGIKDVKIEYLGHVASL 360

Query: 359 ETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGD 418
            T  +T  +L G LKP ++  VN VNA  VAKER I  SE  S SE  Y   + + VT D
Sbjct: 361 NTKPLTAMVLEGLLKP-MNEAVNMVNAPVVAKERNIKVSEVKSESEGDYHTLVRLTVTTD 419

Query: 419 RSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINI 478
           +   +V  T       R+VEI G +I+     +++Y+ +QD  G IG +G +LG N +NI
Sbjct: 420 KRERSVAGTLFGGNKARVVEIKGISIEAELGQNMLYVTNQDKPGFIGALGSLLGANGVNI 479

Query: 479 ATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLI 522
           AT  +GR E GG+AI++   D+ + + +++++  +P +V  K +
Sbjct: 480 ATFHLGRSEAGGDAILLTQVDQPVSNDLLEKVRALPQVVQAKFL 523


Lambda     K      H
   0.317    0.134    0.374 

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: 584
Number of extensions: 23
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: 525
Length of database: 526
Length adjustment: 35
Effective length of query: 490
Effective length of database: 491
Effective search space:   240590
Effective search space used:   240590
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_011385558.1 AMB_RS16130 (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.24183.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-213  695.7   8.1   2.4e-213  695.6   8.1    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011385558.1  AMB_RS16130 phosphoglycerate deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011385558.1  AMB_RS16130 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  695.6   8.1  2.4e-213  2.4e-213       1     523 [.       3     523 ..       3     525 .. 0.99

  Alignments for each domain:
  == domain 1  score: 695.6 bits;  conditional E-value: 2.4e-213
                                 TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 
                                               kvl++dkls+++++++k++++e dvktgl+ +el ++i +yd+l +RS+tkvt e+l+aa++Lkv+gRa
  lcl|NCBI__GCF_000009985.1:WP_011385558.1   3 KVLISDKLSPAAVQIFKDRGIETDVKTGLAPDELKAIIGQYDGLAIRSNTKVTTEILAAATNLKVVGRA 71 
                                               7******************************************************************** PP

                                 TIGR01327  70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138
                                               G+GvDN+d++aat++Gi+v+N+P gn+i++aE+a+a+++alaR+ip+a++s++++kWe+++f+G+El+g
  lcl|NCBI__GCF_000009985.1:WP_011385558.1  72 GIGVDNVDVPAATARGIVVMNTPFGNSITTAEHAIAMMFALAREIPEANASTHAGKWEKNRFMGVELTG 140
                                               ********************************************************************* PP

                                 TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207
                                               k lG++G G+iG +va+ra++l+m+v+ayDP++s e+a++l ve+++ ldel+ +aD+it+H+Plt+ t
  lcl|NCBI__GCF_000009985.1:WP_011385558.1 141 KVLGIVGCGNIGAIVADRAQGLRMRVIAYDPFLSVERAKELNVEKVE-LDELFPRADFITLHTPLTDAT 208
                                               ********************************************666.********************* PP

                                 TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtp 276
                                               +++i+++++akmKkgv+i+NcaRGG++ E+ L+ ale+g+v++aalDvf++EP+++n l+  ++vv tp
  lcl|NCBI__GCF_000009985.1:WP_011385558.1 209 RNIIDAKAMAKMKKGVRIINCARGGLVVEEDLLAALESGQVAGAALDVFKTEPAKENALFGNPKVVCTP 277
                                               ********************************************************************* PP

                                 TIGR01327 277 HlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeav 345
                                               HlgAst+Eaqenva++vae++ ++l + +v++a+N+p+++ae++ kl+py++la+++G++a+ql+++ +
  lcl|NCBI__GCF_000009985.1:WP_011385558.1 278 HLGASTSEAQENVALQVAEQMADYLLTGAVTNALNIPSVSAEDAPKLRPYMTLANQIGSFAGQLTETGI 346
                                               ********************************************************************* PP

                                 TIGR01327 346 kkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllev 414
                                               k+v++++ G++a+ ++++lt+++l+gllk++  e+vn+vnA++vaker+i+v+e k+e++ dy++l+++
  lcl|NCBI__GCF_000009985.1:WP_011385558.1 347 KDVKIEYLGHVASLNTKPLTAMVLEGLLKPMN-EAVNMVNAPVVAKERNIKVSEVKSESEGDYHTLVRL 414
                                               *****************************985.59********************************** PP

                                 TIGR01327 415 kveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmq 483
                                               +v++dk e+svagt++++++ r+vei+g++++ e  + +l+++n+DkpG+ig +gsllg +g+Nia+++
  lcl|NCBI__GCF_000009985.1:WP_011385558.1 415 TVTTDKRERSVAGTLFGGNKARVVEIKGISIEAELGQNMLYVTNQDKPGFIGALGSLLGANGVNIATFH 483
                                               ********************************************************************* PP

                                 TIGR01327 484 lgrkekggealmllslDeevseevleeikevpeiksvklv 523
                                               lgr+e+gg+a++l ++D++vs+++le+++++p++ ++k +
  lcl|NCBI__GCF_000009985.1:WP_011385558.1 484 LGRSEAGGDAILLTQVDQPVSNDLLEKVRALPQVVQAKFL 523
                                               ***********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (526 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.21
//
[ok]

This GapMind analysis is from Apr 09 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