GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Sulfurihydrogenibium subterraneum DSM 15120

Align D-3-phosphoglycerate dehydrogenase (characterized, see rationale)
to candidate WP_028949751.1 Q385_RS0100260 phosphoglycerate dehydrogenase

Query= uniprot:Q5JGC4
         (304 letters)



>NCBI__GCF_000619805.1:WP_028949751.1
          Length = 529

 Score =  265 bits (676), Expect = 2e-75
 Identities = 141/309 (45%), Positives = 205/309 (66%), Gaps = 9/309 (2%)

Query: 2   KVLVAAPLHEKAIEVLKNAGFEVVYEEYPDE---DRLVELVKDVDAIIVRSKPKVTRKVI 58
           KVLV   +  K +E+L N   E++  +Y  E   + L+E+VKD DAII RS+  VT++++
Sbjct: 3   KVLVTDDISPKGLEILNND--EMIDLDYQPEIKFNELLEIVKDYDAIITRSRTPVTKELL 60

Query: 59  EAAPKLKVIGRAGVGLDNIDLKAAEERGIKVVNSPGASSRSVAELAIGLIFAVARKIAFA 118
           E A KLKV+GRAGVG+DN+DL+ A  RGI V+N+PGA++   AE+ +  ++AV RK+  A
Sbjct: 61  ERAEKLKVVGRAGVGVDNVDLEEASRRGILVINTPGANTIGAAEITMAHLYAVLRKLHLA 120

Query: 119 DRKMREGVWAKKQCMGIELEGKTIGVVGFGRIGYQVAKIANALGMKVLFYDPYPNEERAK 178
            + M EG W +K+ MG EL+GK +G++G G +G QVA    A G KV+ YDPY   E+ +
Sbjct: 121 HKSMMEGYWDRKRFMGEELDGKVVGIIGLGNVGSQVAIRCKAAGSKVIAYDPYIPREKGE 180

Query: 179 EVGGKFAD-LETLLKESDVVTLHVPLVDATYHLINEERLKLMKPTAILINAARGAVVDTD 237
            +G +  D L  L+K SD++TLH PL + T ++I ++   LMK     IN ARG +VD D
Sbjct: 181 RLGVELIDNLHDLIKMSDIITLHCPLTEETRNMIGKKEFDLMKKGVYFINCARGGIVDED 240

Query: 238 ALVKALQEGWIAGAGLDVFEEEPLPAD--HPLTKLDNVVLTPHIGASTVEAQMRAGVEVA 295
           AL +A++EG IAG GLDVF +EP P D    L +  N+ L+PHIGA+T E+Q    +++A
Sbjct: 241 ALYEAVKEGKIAGLGLDVFSKEP-PDDRIRRLFEFPNISLSPHIGANTYESQDNVAIKIA 299

Query: 296 EKIVEALKG 304
           + ++ ALKG
Sbjct: 300 QYVIAALKG 308


Lambda     K      H
   0.317    0.136    0.378 

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: 454
Number of extensions: 30
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: 304
Length of database: 529
Length adjustment: 31
Effective length of query: 273
Effective length of database: 498
Effective search space:   135954
Effective search space used:   135954
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: 50 (23.9 bits)

Align candidate WP_028949751.1 Q385_RS0100260 (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.1445162.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-210  684.6   0.8   5.5e-210  684.5   0.8    1.0  1  NCBI__GCF_000619805.1:WP_028949751.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000619805.1:WP_028949751.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  684.5   0.8  5.5e-210  5.5e-210       1     523 [.       3     527 ..       3     529 .] 0.98

  Alignments for each domain:
  == domain 1  score: 684.5 bits;  conditional E-value: 5.5e-210
                             TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvG 72 
                                           kvlv+d++s++g+e l +++ +++d++ +++ +elle++kdyda+i+RS+t+vt+elle+aekLkv+gRaGvG
  NCBI__GCF_000619805.1:WP_028949751.1   3 KVLVTDDISPKGLEiLNNDEMIDLDYQPEIKFNELLEIVKDYDAIITRSRTPVTKELLERAEKLKVVGRAGVG 75 
                                           7*************66677889*************************************************** PP

                             TIGR01327  73 vDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviG 145
                                           vDN+d+e+a+++Gilv+N+P +nti+aaE ++a+l a+ Rk++ a+ks+ e+ W+rk+f+G+El gk +G+iG
  NCBI__GCF_000619805.1:WP_028949751.1  76 VDNVDLEEASRRGILVINTPGANTIGAAEITMAHLYAVLRKLHLAHKSMMEGYWDRKRFMGEELDGKVVGIIG 148
                                           ************************************************************************* PP

                             TIGR01327 146 lGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelak 218
                                           lG++Gs+va r+ka g kv+ayDPyi++ek e+lgvel+++l++l++ +D+it+H Plt+et+++igk+e++ 
  NCBI__GCF_000619805.1:WP_028949751.1 149 LGNVGSQVAIRCKAAGSKVIAYDPYIPREKGERLGVELIDNLHDLIKMSDIITLHCPLTEETRNMIGKKEFDL 221
                                           ************************************************************************* PP

                             TIGR01327 219 mKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt..dnklleldnvvvtpHlgAsteEaqenv 289
                                           mKkgv+ +NcaRGGi+dE+AL+ea++egk+++++lDvf+kEPp     +l+e++n++++pH+gA+t+E+q+nv
  NCBI__GCF_000619805.1:WP_028949751.1 222 MKKGVYFINCARGGIVDEDALYEAVKEGKIAGLGLDVFSKEPPDdrIRRLFEFPNISLSPHIGANTYESQDNV 294
                                           *******************************************944479************************ PP

                             TIGR01327 290 avevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeese 362
                                           a+++a+ v+ alkg++ve avN+p + +e +e++k+yl+laeklG++ +q+++++ ++++v+++G++ ++  e
  NCBI__GCF_000619805.1:WP_028949751.1 295 AIKIAQYVIAALKGQFVEVAVNAPFTITEGFENIKAYLELAEKLGSFLTQYAGGHFTEINVEVRGTIRDHI-E 366
                                           *******************************************************************9877.9 PP

                             TIGR01327 363 lltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekep 435
                                           ++++++lkg+l++vl++ vn++nA+++akergi+v  s++e+  ++k+ +++++++d +ev v+gt + +k p
  NCBI__GCF_000619805.1:WP_028949751.1 367 PIVAFFLKGYLSPVLDTPVNIINAPFIAKERGINVVKSTREAGLNFKEFIKITAKSDGKEVVVGGTAFYDKLP 439
                                           999********************************************************************** PP

                             TIGR01327 436 riveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevl 508
                                           ri+ +d++ +d+ep g++l+++nkD+pGvigk+g++l++++iNia+++lgr ekg+ al  l+lD++++e vl
  NCBI__GCF_000619805.1:WP_028949751.1 440 RIMLVDNYWIDIEPYGVILMFENKDVPGVIGKLGTILARHNINIAGFRLGRLEKGKIALGALQLDDKLNEAVL 512
                                           ************************************************************************* PP

                             TIGR01327 509 eeikevpeiksvklv 523
                                           eei+++pei ++k v
  NCBI__GCF_000619805.1:WP_028949751.1 513 EEIHQLPEIIKAKQV 527
                                           ***********9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (529 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 22.03
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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