Alignments for a candidate for serA in Arcobacter nitrofigilis DSM 7299

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Arcobacter nitrofigilis DSM 7299

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95; 2-oxoglutarate reductase; EC 1.1.1.399 (uncharacterized)
to candidate WP_013134297.1 ARNIT_RS02445 phosphoglycerate dehydrogenase

Query= curated2:P35136
         (525 letters)



>NCBI__GCF_000092245.1:WP_013134297.1
          Length = 527

 Score =  345 bits (885), Expect = 2e-99
 Identities = 192/526 (36%), Positives = 309/526 (58%), Gaps = 9/526 (1%)

Query: 4   VLVSDKMSNDGLQPLIESDFIEIVQKNVADAE---DELHTFDALLVRSATKVTEDLFNKM 60
           ++V D +  +GL  L  ++ I  V     D     D +   D  + RS+T V E   N  
Sbjct: 6   IVVCDHIHENGLNILKAAEDINYVFAADIDKTALLDVIKDADVAITRSSTDVDEKFLNAA 65

Query: 61  TSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQANIS 120
            +LK + RAGVG DN+D++  +K G+I +N P  NTI+  E T   + S MR  P A+  
Sbjct: 66  VNLKAIIRAGVGYDNVDMEGCSKRGIIAMNVPTANTIAAVELTMTHMLSCMRKFPYAHNQ 125

Query: 121 VKS-REWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRARAFGMTVHVFDPFLTEERAKKI 179
           +K+ R W R  + G+EL+GK LG++G G IG  +A RA++F M V  +DP++   +A  +
Sbjct: 126 LKNERVWKREDWYGNELFGKKLGVIGFGNIGHRVALRAKSFEMDVVTYDPYIPSTKATDL 185

Query: 180 GVNSRT-FEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAAL 238
           G+   T F+++L S DIIT+HTP  +ET  ++ ++ IAK K GV LINCARGG+ +E AL
Sbjct: 186 GIKYTTNFDDIL-SCDIITIHTPKNQETIDMIGEDEIAKMKDGVILINCARGGLYNEEAL 244

Query: 239 LEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQ 298
              L++G +A A +DVF+ EP ++N L+D P +  T HLGA+T+E+Q  +A Q +   ++
Sbjct: 245 FNNLKSGKIAMAGIDVFKKEPAINNPLLDLPNITVTAHLGANTRESQKEIAVQAARNAIE 304

Query: 299 FAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKL 358
            A+G+   +A+NLP       + +KPY ++  KI  L +Q  K  ++ + +  +G I + 
Sbjct: 305 SARGISYPNALNLPIDESKIPSFVKPYIELTQKIAFLSAQTDKTAIRSITVSAQGEIKEY 364

Query: 359 ETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGD 418
             S +T A + G LK      VN VNA   A+E+GI        + SGY N ++VK+T +
Sbjct: 365 LDSLLTFATV-GALKVAGGDEVNYVNAKFWAEEKGIKVDTCEIINGSGYSNKVTVKITTE 423

Query: 419 RSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINI 478
           +   T++ T      +RIVE+NGF  D  P G+++++++ D  GVIG VG+ LGDN+INI
Sbjct: 424 KGVNTISGTVFDEDVQRIVEVNGFVFDIAPKGNMIFLRNSDIPGVIGTVGKTLGDNNINI 483

Query: 479 ATMQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLIDL 524
           A  ++ R +    A++++  D  +   ++K+L N+   +SV  +++
Sbjct: 484 ADFRLSRGKDSALAVILV--DTFVSHDVLKQLENLEAAISVSYVEI 527


Lambda     K      H
   0.317    0.134    0.373 

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: 644
Number of extensions: 35
Number of successful extensions: 4
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: 527
Length adjustment: 35
Effective length of query: 490
Effective length of database: 492
Effective search space:   241080
Effective search space used:   241080
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_013134297.1 ARNIT_RS02445 (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.677064.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-184  600.8   8.7   1.4e-184  600.6   8.7    1.0  1  NCBI__GCF_000092245.1:WP_013134297.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000092245.1:WP_013134297.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.6   8.7  1.4e-184  1.4e-184       2     525 .]       6     527 .]       5     527 .] 0.98

  Alignments for each domain:
  == domain 1  score: 600.6 bits;  conditional E-value: 1.4e-184
                             TIGR01327   2 vlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 
                                           ++v+d+++e+g++ l + ++++   + +++k +ll++ikd+d+ i+RS+t v+e++l+aa +Lk i RaGvG 
  NCBI__GCF_000092245.1:WP_013134297.1   6 IVVCDHIHENGLNiLKAAEDINYVFAADIDKTALLDVIKDADVAITRSSTDVDEKFLNAAVNLKAIIRAGVGY 78 
                                           79***********666678899999************************************************ PP

                             TIGR01327  74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekk.WerkkflGtElygktlGviG 145
                                           DN+d+e ++k+Gi+ +N P++nti+a+El+++++l+ +Rk+p a++++k+++ W+r++++G El+gk+lGviG
  NCBI__GCF_000092245.1:WP_013134297.1  79 DNVDMEGCSKRGIIAMNVPTANTIAAVELTMTHMLSCMRKFPYAHNQLKNERvWKREDWYGNELFGKKLGVIG 151
                                           **************************************************999******************** PP

                             TIGR01327 146 lGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelak 218
                                           +G+iG++va rak+++m+v++yDPyi++ ka++lg+++++++d++l ++D+it+H+P+++et+++ig++e+ak
  NCBI__GCF_000092245.1:WP_013134297.1 152 FGNIGHRVALRAKSFEMDVVTYDPYIPSTKATDLGIKYTTNFDDIL-SCDIITIHTPKNQETIDMIGEDEIAK 223
                                           **********************************************.9************************* PP

                             TIGR01327 219 mKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvav 291
                                           mK+gvi++NcaRGG+++E+AL + l++gk+++a++Dvf+kEP+ +n+ll+l+n++vt+HlgA+t+E+q+++av
  NCBI__GCF_000092245.1:WP_013134297.1 224 MKDGVILINCARGGLYNEEALFNNLKSGKIAMAGIDVFKKEPAINNPLLDLPNITVTAHLGANTRESQKEIAV 296
                                           ************************************************************************* PP

                             TIGR01327 292 evaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesell 364
                                           + a + +e+++g + ++a+Nlp  + +  + +kpy++l++k+  l+ q+ k+a+++++v+ +Ge+ e+  +ll
  NCBI__GCF_000092245.1:WP_013134297.1 297 QAARNAIESARGISYPNALNLPIDESKIPSFVKPYIELTQKIAFLSAQTDKTAIRSITVSAQGEIKEYLDSLL 369
                                           **********************988777788*************************************95555 PP

                             TIGR01327 365 tsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepri 437
                                            +++  g lk +  +evn+vnAk+ a+e+gi+v  ++  + + y+n ++vk++++kg  +++gtv++e+ +ri
  NCBI__GCF_000092245.1:WP_013134297.1 370 -TFATVGALKVAGGDEVNYVNAKFWAEEKGIKVDTCEIINGSGYSNKVTVKITTEKGVNTISGTVFDEDVQRI 441
                                           .78889******************************************************************* PP

                             TIGR01327 438 veidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevlee 510
                                           ve++gf +d++p+g +++++n+D+pGvig vg++lg+++iNia+++l+r +    al+++ +D  vs++vl++
  NCBI__GCF_000092245.1:WP_013134297.1 442 VEVNGFVFDIAPKGNMIFLRNSDIPGVIGTVGKTLGDNNINIADFRLSRGKDS--ALAVILVDTFVSHDVLKQ 512
                                           *************************************************9876..999*************** PP

                             TIGR01327 511 ikevpeiksvklvel 525
                                           +++++++ sv++ve+
  NCBI__GCF_000092245.1:WP_013134297.1 513 LENLEAAISVSYVEI 527
                                           ***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (527 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: 18.53
//
[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:

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