Alignments for a candidate for serA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Dinoroseobacter shibae DFL-12

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate 3609936 Dshi_3318 D-3-phosphoglycerate dehydrogenase (RefSeq)

Query= CharProtDB::CH_004924
         (525 letters)



>FitnessBrowser__Dino:3609936
          Length = 531

 Score =  413 bits (1062), Expect = e-120
 Identities = 218/513 (42%), Positives = 320/513 (62%), Gaps = 9/513 (1%)

Query: 3   RVLVSDKMSNDGLQPL----IESDFIEIVQKNVADAEDELHTFDALLVRSATKVTEDLFN 58
           +VLVSDK+S   +Q      IE DF   + K+     + +  +D L +RSATKVTE L  
Sbjct: 4   KVLVSDKLSETAVQIFRDRGIEVDFEPSLGKDKDKLAEVIGKYDGLAIRSATKVTEKLLA 63

Query: 59  KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118
              +LK+VGRAG+G DN+D   A+K GVIV+N P GN I+TAEH  AM+ ++ R IP+A+
Sbjct: 64  HADNLKVVGRAGIGTDNVDKVAASKKGVIVMNTPFGNMITTAEHAIAMMFAVARQIPEAS 123

Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKK 178
            S  + +W ++ ++G EL  KTLG++G G IG  + +R     M V  +DPFL+EERA K
Sbjct: 124 ASTHAGKWEKSKFMGVELTAKTLGVIGAGNIGGIVCERALGLKMKVIAYDPFLSEERADK 183

Query: 179 IGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAAL 238
           +GV     + +L  AD IT+H PLT +T+ +L++E + KTKKGVR+INCARGG++DE AL
Sbjct: 184 LGVEKVDLDTLLARADFITLHVPLTDQTRNILSREALEKTKKGVRIINCARGGLVDEQAL 243

Query: 239 LEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQ 298
            + L++GHVAGAA DVF  EP  +N L   P V+ TPHLGAST EAQ NVA QV+E++  
Sbjct: 244 ADLLKSGHVAGAAFDVFAEEPATENPLFGLPNVVCTPHLGASTTEAQENVALQVAEQMSN 303

Query: 299 FAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKL 358
           +     V +A+N+P++T +E   + P+ ++AG +G+ V Q   EP+  + I Y GT+AK+
Sbjct: 304 YLLSGAVENALNMPSVTAEEAKTMGPWVKLAGHLGTFVGQLTDEPIDSIEILYNGTVAKM 363

Query: 359 ETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGD 418
               +  A+++G ++   +  VN V+A  +AKERGI  S         +D  + + V  D
Sbjct: 364 NLEALNCAVIAGIMQ-ATNPDVNMVSAPVIAKERGIGLSTTTQDKSGVFDGYVKLTVKTD 422

Query: 419 RSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINI 478
           + T ++  T       R ++I G NID     H++Y  ++DT G+IG +G ILG+N +NI
Sbjct: 423 QRTRSIAGTVFSDGKPRFIQIKGINIDAEIGEHMLYTTNKDTPGMIGTLGGILGENQVNI 482

Query: 479 ATMQVGRKEKGGEAIMMLSFD----RHLEDKIV 507
           A   +GR E  G+AI ML  D    R ++DK++
Sbjct: 483 ANFTLGRNETNGDAIAMLYLDAPLPRDVQDKLI 515


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: 639
Number of extensions: 26
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
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 3609936 Dshi_3318 (D-3-phosphoglycerate dehydrogenase (RefSeq))
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.24824.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.5e-203  663.2   3.8   1.7e-203  663.1   3.8    1.0  1  lcl|FitnessBrowser__Dino:3609936  Dshi_3318 D-3-phosphoglycerate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609936  Dshi_3318 D-3-phosphoglycerate dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  663.1   3.8  1.7e-203  1.7e-203       1     520 [.       4     523 ..       4     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 663.1 bits;  conditional E-value: 1.7e-203
                         TIGR01327   1 kvlvadklseegiellkekelevdvktgl..skeellekikdydalivRSatkvteelleaaekLkvigRaGvGvDN 75 
                                       kvlv+dklse+++++++++++evd +  l  +k++l e+i +yd+l +RSatkvte+ll++a++Lkv+gRaG+G DN
  lcl|FitnessBrowser__Dino:3609936   4 KVLVSDKLSETAVQIFRDRGIEVDFEPSLgkDKDKLAEVIGKYDGLAIRSATKVTEKLLAHADNLKVVGRAGIGTDN 80 
                                       7***********************9987622677899**************************************** PP

                         TIGR01327  76 idieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGlGriGse 152
                                       +d  aa+kkG++v+N+P gn i++aE+a+a+++a+aR+ip+a +s++++kWe++kf+G+El++ktlGviG+G+iG +
  lcl|FitnessBrowser__Dino:3609936  81 VDKVAASKKGVIVMNTPFGNMITTAEHAIAMMFAVARQIPEASASTHAGKWEKSKFMGVELTAKTLGVIGAGNIGGI 157
                                       ***************************************************************************** PP

                         TIGR01327 153 vakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakmKkgviivNca 229
                                       v +ra +l+mkv+ayDP++see+a+klgve + dld+lla+aD+it+HvPlt++t++++++e+l+k+Kkgv+i+Nca
  lcl|FitnessBrowser__Dino:3609936 158 VCERALGLKMKVIAYDPFLSEERADKLGVE-KVDLDTLLARADFITLHVPLTDQTRNILSREALEKTKKGVRIINCA 233
                                       ******************************.556******************************************* PP

                         TIGR01327 230 RGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvavevaeevlealkgevv 306
                                       RGG++dE+AL+++l++g+v++aa+Dvf++EP+t+n+l+ l+nvv tpHlgAst+Eaqenva++vae+++++l   +v
  lcl|FitnessBrowser__Dino:3609936 234 RGGLVDEQALADLLKSGHVAGAAFDVFAEEPATENPLFGLPNVVCTPHLGASTTEAQENVALQVAEQMSNYLLSGAV 310
                                       ***************************************************************************** PP

                         TIGR01327 307 esavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeeselltsallkgllkevleeevnl 383
                                       e+a+N+p+++aee++++ p+++la +lG++++ql++e ++++e+ ++G++a+++ e+l+ a+++g++++ ++ +vn+
  lcl|FitnessBrowser__Dino:3609936 311 ENALNMPSVTAEEAKTMGPWVKLAGHLGTFVGQLTDEPIDSIEILYNGTVAKMNLEALNCAVIAGIMQA-TNPDVNM 386
                                       ******************************************************************975.678**** PP

                         TIGR01327 384 vnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepriveidgfevdlepegilliiknkD 460
                                       v+A+++akergi ++ +++++s  ++ +++++v++d+ ++s+agtv+++ +pr ++i+g+++d e  +++l+++nkD
  lcl|FitnessBrowser__Dino:3609936 387 VSAPVIAKERGIGLSTTTQDKSGVFDGYVKLTVKTDQRTRSIAGTVFSDGKPRFIQIKGINIDAEIGEHMLYTTNKD 463
                                       ***************************************************************************** PP

                         TIGR01327 461 kpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevleeikevpeiksv 520
                                       +pG+ig +g +lge+++Nia+++lgr+e++g+a+++l lD +++ +v +++ +    ++v
  lcl|FitnessBrowser__Dino:3609936 464 TPGMIGTLGGILGENQVNIANFTLGRNETNGDAIAMLYLDAPLPRDVQDKLIATGLFQQV 523
                                       ************************************************999877666665 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.39
//
[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