Alignments for a candidate for serA in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Sinorhizobium fredii NGR234

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate YP_002827271.1 NGR_c27700 D-3-phosphoglycerate dehydrogenase

Query= CharProtDB::CH_004924
         (525 letters)



>NCBI__GCF_000018545.1:YP_002827271.1
          Length = 531

 Score =  413 bits (1062), Expect = e-120
 Identities = 217/524 (41%), Positives = 338/524 (64%), Gaps = 9/524 (1%)

Query: 3   RVLVSDKMSNDGLQPL----IESDFIEIVQKNVADAEDELHTFDALLVRSATKVTEDLFN 58
           RVLVSD++S   +Q      +E DF   + K+     + +  +D L +RSATKVTE L  
Sbjct: 4   RVLVSDELSETAVQIFRDRGVEVDFQPKLGKDKEKLAEIIGNYDGLAIRSATKVTEKLIA 63

Query: 59  KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118
           + T+LK+VGRAG+GVDN+DI  A++ G+IV+N P GN+I+TAEH  A++ ++ R +P A+
Sbjct: 64  EATNLKVVGRAGIGVDNVDIPAASRRGIIVMNTPFGNSITTAEHAIALMFAVARQLPAAD 123

Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHV--FDPFLTEERA 176
            S ++ +W ++ ++G E+ GK LG++G G IGS +  R  A G+ +HV  +DPFL++ERA
Sbjct: 124 NSTQAGKWEKSKFMGVEITGKVLGVIGAGNIGSIVCAR--AIGLKMHVLAYDPFLSKERA 181

Query: 177 KKIGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEA 236
           +++GV     +E+L  AD IT+H PLT +T+ +L+ E +AKTK GVR++NCARGG++DE 
Sbjct: 182 EEMGVVKVELDELLAQADFITLHVPLTDKTRNILSAEALAKTKPGVRIVNCARGGLVDEK 241

Query: 237 ALLEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEV 296
           AL +AL++GHVAGA  DVFEVEP  ++ L   P V+ TPHLGAST EAQ NVA QV+E++
Sbjct: 242 ALADALKSGHVAGAGFDVFEVEPATESPLFGLPNVVCTPHLGASTTEAQENVALQVAEQM 301

Query: 297 LQFAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIA 356
             +     V +AIN+P++T +E   +KP  ++A  +G+ V Q  +  ++++ I Y+G+ A
Sbjct: 302 ADYLVKGAVSNAINMPSITAEEAPILKPVIRLADVLGAFVGQVTESAIKEIEILYDGSTA 361

Query: 357 KLETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVT 416
            + T  +T A+L+G ++P+V + VN V+A  + KE+GI  SE        +D  I + V 
Sbjct: 362 TMNTKALTSAVLAGLIRPQV-ADVNMVSAPIMIKEKGIILSEVKRDKTGVFDGYIKLTVK 420

Query: 417 GDRSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDI 476
               T +V  T       R ++I G N+D     H+VY+ + D  G+IG +G  LGD ++
Sbjct: 421 TANQTRSVAGTVFSDGKPRFIQIKGINLDADVGNHMVYLTNTDVPGMIGFIGTTLGDANV 480

Query: 477 NIATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVK 520
           NIA  Q+GR+++GG+AI +L  D  + + ++ +L   P +   K
Sbjct: 481 NIANFQLGREKQGGDAIALLYVDGPVSEAVLDKLRANPAVRQAK 524


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: 625
Number of extensions: 24
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: 531
Length adjustment: 35
Effective length of query: 490
Effective length of database: 496
Effective search space:   243040
Effective search space used:   243040
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 YP_002827271.1 NGR_c27700 (D-3-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.32259.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-206  673.6   8.0   1.2e-206  673.4   8.0    1.0  1  lcl|NCBI__GCF_000018545.1:YP_002827271.1  NGR_c27700 D-3-phosphoglycerate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002827271.1  NGR_c27700 D-3-phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  673.4   8.0  1.2e-206  1.2e-206       1     521 [.       4     524 ..       4     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 673.4 bits;  conditional E-value: 1.2e-206
                                 TIGR01327   1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvig 67 
                                               +vlv+d+lse+++++++++++evd + +l  +ke+l e+i +yd+l +RSatkvte+l+++a++Lkv+g
  lcl|NCBI__GCF_000018545.1:YP_002827271.1   4 RVLVSDELSETAVQIFRDRGVEVDFQPKLgkDKEKLAEIIGNYDGLAIRSATKVTEKLIAEATNLKVVG 72 
                                               79***********************998733678899******************************** PP

                                 TIGR01327  68 RaGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEl 136
                                               RaG+GvDN+di+aa+++Gi+v+N+P gn+i++aE+a+al++a+aR++p+ad+s++++kWe++kf+G+E+
  lcl|NCBI__GCF_000018545.1:YP_002827271.1  73 RAGIGVDNVDIPAASRRGIIVMNTPFGNSITTAEHAIALMFAVARQLPAADNSTQAGKWEKSKFMGVEI 141
                                               ********************************************************************* PP

                                 TIGR01327 137 ygktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltk 205
                                               +gk lGviG+G+iGs+v  ra +l+m+vlayDP++s+e+ae++gv +++ ldella+aD+it+HvPlt+
  lcl|NCBI__GCF_000018545.1:YP_002827271.1 142 TGKVLGVIGAGNIGSIVCARAIGLKMHVLAYDPFLSKERAEEMGVVKVE-LDELLAQADFITLHVPLTD 209
                                               **********************************************666.******************* PP

                                 TIGR01327 206 etkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvv 274
                                               +t++++++e+lak+K+gv+ivNcaRGG++dEkAL++al++g+v++a++Dvfe EP+t+++l+ l+nvv 
  lcl|NCBI__GCF_000018545.1:YP_002827271.1 210 KTRNILSAEALAKTKPGVRIVNCARGGLVDEKALADALKSGHVAGAGFDVFEVEPATESPLFGLPNVVC 278
                                               ********************************************************************* PP

                                 TIGR01327 275 tpHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllke 343
                                               tpHlgAst+Eaqenva++vae++ ++l   +v++a+N+p+++aee+  lkp ++la+ lG++++q++++
  lcl|NCBI__GCF_000018545.1:YP_002827271.1 279 TPHLGASTTEAQENVALQVAEQMADYLVKGAVSNAINMPSITAEEAPILKPVIRLADVLGAFVGQVTES 347
                                               ********************************************************************* PP

                                 TIGR01327 344 avkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknll 412
                                               a+k++e+ + G  a++++++ltsa+l+gl++++++ +vn+v+A+++ ke+gi ++e k++++  ++ ++
  lcl|NCBI__GCF_000018545.1:YP_002827271.1 348 AIKEIEILYDGSTATMNTKALTSAVLAGLIRPQVA-DVNMVSAPIMIKEKGIILSEVKRDKTGVFDGYI 415
                                               **********************************9.8******************************** PP

                                 TIGR01327 413 evkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNias 481
                                               +++v+++++++svagtv+++ +pr ++i+g+++d    +++++++n+D+pG+ig +g++lg+a++Nia+
  lcl|NCBI__GCF_000018545.1:YP_002827271.1 416 KLTVKTANQTRSVAGTVFSDGKPRFIQIKGINLDADVGNHMVYLTNTDVPGMIGFIGTTLGDANVNIAN 484
                                               ********************************************************************* PP

                                 TIGR01327 482 mqlgrkekggealmllslDeevseevleeikevpeiksvk 521
                                               +qlgr+++gg+a++ll +D +vse vl+++++ p+++++k
  lcl|NCBI__GCF_000018545.1:YP_002827271.1 485 FQLGREKQGGDAIALLYVDGPVSEAVLDKLRANPAVRQAK 524
                                               ********************************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (531 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: 11.59
//
[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