Alignments for a candidate for serA in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Denitrovibrio acetiphilus DSM 12809

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_013010554.1 DACET_RS06335 phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>NCBI__GCF_000025725.1:WP_013010554.1
          Length = 544

 Score =  395 bits (1016), Expect = e-114
 Identities = 224/542 (41%), Positives = 325/542 (59%), Gaps = 27/542 (4%)

Query: 3   KILITDPLHESAVEILKQAGEVEV--ATGLTVEELKLKIKDVDALVIRSGTTATREIIEA 60
           K+LITD + +  V ILK   ++EV    G+   +LK  I + DA++ RSGTT T E+IE 
Sbjct: 5   KVLITDHISQDGVNILKSDKDIEVDIQAGIKNPDLKKIIGNYDAIITRSGTTVTAELIEN 64

Query: 61  SENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATA 120
              LK+I RAGVG+DNVD++AA+ KGI+V+NAP  ++++  EL  GMML+  R +P A  
Sbjct: 65  PGKLKIIGRAGVGLDNVDIEAASMKGIIVMNAPTGNTLAACELTMGMMLSVVRKLPLANQ 124

Query: 121 SIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASEL 180
             KSG+WDRK F G+++Y KTL +VGLGRIG  VAKR +AF M +VAYDPYI +  A  L
Sbjct: 125 VTKSGEWDRKRFMGIQLYQKTLAVVGLGRIGGNVAKRCKAFDMKVVAYDPYIKKSRAESL 184

Query: 181 GIKLL-TVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAAL 239
           G++L  +++E  + +D IT H PLT +TK++I K++IA MK  +VI+NCARGG+++E  L
Sbjct: 185 GVELCNSLEEAISQADIITFHTPLTDETKNLITKDEIAKMKDGVVIINCARGGIVNELDL 244

Query: 240 YDALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVK 299
            DA  SGK+ AA LDVF  EPP   P   + N+  TPH GA+T E Q     I+AEQ V 
Sbjct: 245 VDACKSGKVTAAGLDVFMSEPPVNHPFFDVENIYVTPHIGANTAEGQYGVAVIIAEQVVN 304

Query: 300 ILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAKE 359
            L G S +N VN+P + T+  + ++ Y  L E +G MA Q      E +EI  +G   K 
Sbjct: 305 ALHGRSYKNAVNIPFMKTQLPEDMQKYFELLENIGHMAAQLTKGRPERIEIQMVG--HKF 362

Query: 360 KTEILKRSF-------------LKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSESD 406
           + +  +R+F             LKG +   +   V+ +NAP +AK RNI I E   +  D
Sbjct: 363 EEDFGERTFDTPFNFQPFTVAGLKGFMEVAVAENVSFINAPYVAKERNIDIIETKSAHYD 422

Query: 407 -YGNSIKISAKGENDEISIIGSI---EHNEVVFREINGYRMDIKPEGTICIIKHIDRPGM 462
            Y + + +  K + +E    G++   +   +V    + Y  D+  EGT     ++DRPG+
Sbjct: 423 KYNDLVMVKVKTDVEEKIYAGTVFADQTGRIVI--YDKYYTDLIAEGTFLYFNNLDRPGI 480

Query: 463 VGKVGVLLGEHGINIAGMQVGR--REPG-GHSIMFLDIDHMISDEVLDEIRKMENVRAAK 519
           +GKVG +LG+H INIA   + R  +E G   ++ F+ +D  +   VLDEI  ++ +  AK
Sbjct: 481 IGKVGTILGKHSINIADFDLARNVKEDGEADAVAFVRVDSKVPAGVLDEILALDGMLEAK 540

Query: 520 SI 521
            I
Sbjct: 541 VI 542


Lambda     K      H
   0.316    0.134    0.364 

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: 764
Number of extensions: 48
Number of successful extensions: 6
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: 523
Length of database: 544
Length adjustment: 35
Effective length of query: 488
Effective length of database: 509
Effective search space:   248392
Effective search space used:   248392
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_013010554.1 DACET_RS06335 (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.13846.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.2e-192  625.9   7.0   3.7e-192  625.6   7.0    1.0  1  lcl|NCBI__GCF_000025725.1:WP_013010554.1  DACET_RS06335 phosphoglycerate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025725.1:WP_013010554.1  DACET_RS06335 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  625.6   7.0  3.7e-192  3.7e-192       1     524 [.       5     543 ..       5     544 .] 0.96

  Alignments for each domain:
  == domain 1  score: 625.6 bits;  conditional E-value: 3.7e-192
                                 TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 
                                               kvl++d++s++g++ l ++k++evd++ g+++ +l ++i +yda+i+RS t+vt+el+e+  kLk+igR
  lcl|NCBI__GCF_000025725.1:WP_013010554.1   5 KVLITDHISQDGVNiLKSDKDIEVDIQAGIKNPDLKKIIGNYDAIITRSGTTVTAELIENPGKLKIIGR 73 
                                               7*************6677899************************************************ PP

                                 TIGR01327  69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137
                                               aGvG+DN+dieaa+ kGi+v+NaP+gnt++a El++ ++l+++Rk+p a++ +k+++W+rk+f+G+ ly
  lcl|NCBI__GCF_000025725.1:WP_013010554.1  74 AGVGLDNVDIEAASMKGIIVMNAPTGNTLAACELTMGMMLSVVRKLPLANQVTKSGEWDRKRFMGIQLY 142
                                               ********************************************************************* PP

                                 TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206
                                               +ktl v+GlGriG +vakr+ka++mkv+ayDPyi +++ae+lgvel ++l+e +++aD+it H+Plt+e
  lcl|NCBI__GCF_000025725.1:WP_013010554.1 143 QKTLAVVGLGRIGGNVAKRCKAFDMKVVAYDPYIKKSRAESLGVELCNSLEEAISQADIITFHTPLTDE 211
                                               ********************************************************************* PP

                                 TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvt 275
                                               tk+li k+e+akmK+gv+i+NcaRGGi++E  Lv+a ++gkv+aa+lDvf +EPp ++++++ +n++vt
  lcl|NCBI__GCF_000025725.1:WP_013010554.1 212 TKNLITKDEIAKMKDGVVIINCARGGIVNELDLVDACKSGKVTAAGLDVFMSEPPVNHPFFDVENIYVT 280
                                               ********************************************************************* PP

                                 TIGR01327 276 pHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkea 344
                                               pH+gA+t+E q  vav++ae+v++al+g + ++avN+p ++++  e+++ y++l e++G++a ql+k++
  lcl|NCBI__GCF_000025725.1:WP_013010554.1 281 PHIGANTAEGQYGVAVIIAEQVVNALHGRSYKNAVNIPFMKTQLPEDMQKYFELLENIGHMAAQLTKGR 349
                                               ********************************************************************* PP

                                 TIGR01327 345 vkkvevtleG.....elaee......eselltsallkgllkevleeevnlvnAkavakergitveeske 402
                                               ++++e+++ G     ++ e       + ++ t a lkg+++ +++e+v ++nA++vaker+i++ e+k+
  lcl|NCBI__GCF_000025725.1:WP_013010554.1 350 PERIEIQMVGhkfeeDFGERtfdtpfNFQPFTVAGLKGFMEVAVAENVSFINAPYVAKERNIDIIETKS 418
                                               ********99422222322222111246899************************************** PP

                                 TIGR01327 403 eesedyknllevkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsl 471
                                               ++ ++y++l+ vkv++d +e+  agtv+++++ riv  d++  dl +eg+ l+++n D+pG+igkvg++
  lcl|NCBI__GCF_000025725.1:WP_013010554.1 419 AHYDKYNDLVMVKVKTDVEEKIYAGTVFADQTGRIVIYDKYYTDLIAEGTFLYFNNLDRPGIIGKVGTI 487
                                               ********************************************************************* PP

                                 TIGR01327 472 lgeagiNiasmqlgrk.ekgg..ealmllslDeevseevleeikevpeiksvklve 524
                                               lg++ iNia++ l+r+ +++g  +a++ +++D++v+++vl+ei +++ + ++k+++
  lcl|NCBI__GCF_000025725.1:WP_013010554.1 488 LGKHSINIADFDLARNvKEDGeaDAVAFVRVDSKVPAGVLDEILALDGMLEAKVIT 543
                                               ***************9533332379***************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (544 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: 7.51
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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