Alignments for a candidate for serA in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Sinorhizobium meliloti 1021

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate SMc00641 SMc00641 D-3-phosphoglycerate dehydrogenase

Query= CharProtDB::CH_004924
         (525 letters)



>FitnessBrowser__Smeli:SMc00641
          Length = 531

 Score =  411 bits (1056), Expect = e-119
 Identities = 217/514 (42%), Positives = 332/514 (64%), Gaps = 9/514 (1%)

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

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

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

Query: 177 KKIGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEA 236
           +++GV     +E+L  AD I++H PLT +T+ +LN E IAK K GVR+INCARGG++DE 
Sbjct: 182 EEMGVVKVELDELLAQADFISLHVPLTDKTRNILNAEAIAKAKPGVRIINCARGGLVDEK 241

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

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

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

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

Query: 477 NIATMQVGRKEKGGEAIMMLSFDRHLEDKIVKEL 510
           NIA  Q+GR+++GG+AI +L  D  + + ++ +L
Sbjct: 481 NIANFQLGREKQGGDAIALLYVDGPVSEIVLDKL 514


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: 631
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: 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 SMc00641 SMc00641 (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.21162.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.7e-206  671.9   9.0   4.2e-206  671.7   9.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc00641  SMc00641 D-3-phosphoglycerate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00641  SMc00641 D-3-phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.7   9.0  4.2e-206  4.2e-206       1     521 [.       4     524 ..       4     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 671.7 bits;  conditional E-value: 4.2e-206
                           TIGR01327   1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 
                                         +vlv+d+lse+++++++++++evd + +l  +ke+l e+i +yd+l +RSatkvte+l++aa++Lkv+gRaG+Gv
  lcl|FitnessBrowser__Smeli:SMc00641   4 RVLVSDELSETAVQIFRDHGVEVDFQPKLgkDKEKLAEIIGNYDGLAIRSATKVTEKLIAAATNLKVVGRAGIGV 78 
                                         79***********************998733678899************************************** PP

                           TIGR01327  74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGlGr 148
                                         DN+di+aa+++Gi+v+N+P gn+i++aE+a+al++a+aR++p+ad s++++kWe++kf+G+E++gk lGviG+G+
  lcl|FitnessBrowser__Smeli:SMc00641  79 DNVDIPAASRRGIIVMNTPFGNSITTAEHAIALMFAVARQLPAADGSTQAGKWEKSKFMGVEITGKVLGVIGAGN 153
                                         *************************************************************************** PP

                           TIGR01327 149 iGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakmKkgv 223
                                         iGs+v  ra +l+m+v+ayDP++s+e+ae++gv +++ ldella+aD+i++HvPlt++t++++++e++ak+K+gv
  lcl|FitnessBrowser__Smeli:SMc00641 154 IGSIVCARAIGLKMHVIAYDPFLSKERAEEMGVVKVE-LDELLAQADFISLHVPLTDKTRNILNAEAIAKAKPGV 227
                                         **********************************666.************************************* PP

                           TIGR01327 224 iivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvavevaeevl 298
                                         +i+NcaRGG++dEkAL+eal++g+v++a++Dvfe EP+t+++l+ l+nvv tpHlgAst+Eaqenva++vae+++
  lcl|FitnessBrowser__Smeli:SMc00641 228 RIINCARGGLVDEKALAEALKAGHVAGAGFDVFEVEPATESPLFGLPNVVCTPHLGASTTEAQENVALQVAEQMS 302
                                         *************************************************************************** PP

                           TIGR01327 299 ealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeeselltsallkgll 373
                                         e+l   +v++a+N+p+++aee+  lkp+++la+ lG++++q++++a+k++e+ + G  a++++++ltsa+l+gl+
  lcl|FitnessBrowser__Smeli:SMc00641 303 EYLVKGAVTNAINMPSITAEEAPILKPFIRLADVLGAFVGQVTESAIKEIEILYDGSTAAMNTKALTSAALAGLI 377
                                         *************************************************************************** PP

                           TIGR01327 374 kevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriveidgfevdle 448
                                         +++++ +vn+v+A++++ke+g+ ++e k++++  ++ +++++v+++++++svagtv+++ +pr ++i+g+++d  
  lcl|FitnessBrowser__Smeli:SMc00641 378 RPQVA-DVNMVSAPVMVKEKGVILSEVKRDKTGVFDGYIKLTVKTANQTRSVAGTVFSDGKPRFIQIKGINLDAD 451
                                         ****9.8******************************************************************** PP

                           TIGR01327 449 pegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleeikevpeiksvk 521
                                           +++++i+n+D+pG+ig +gs+lg+ag+Nia++qlgr+++gg+a++ll +D +vse vl+++++ ++i+++k
  lcl|FitnessBrowser__Smeli:SMc00641 452 VGNHMVYITNTDVPGMIGFIGSTLGDAGVNIANFQLGREKQGGDAIALLYVDGPVSEIVLDKLRANEAIRQAK 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: 10.86
//
[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