Alignments for a candidate for serA in Methylosarcina fibrata AML-C10

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Methylosarcina fibrata AML-C10

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_020565839.1 A3OW_RS0123135 phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>NCBI__GCF_000372865.1:WP_020565839.1
          Length = 527

 Score =  387 bits (994), Expect = e-112
 Identities = 216/527 (40%), Positives = 322/527 (61%), Gaps = 8/527 (1%)

Query: 1   MSKILITDPLHESAVEIL-KQAG-EVEVATGLTVEELKLKIKDVDALVIRSGTTATREII 58
           M KILI+D L E+ +  L +Q+G +V + TGL  E L   I D DAL+IRS T  T +++
Sbjct: 1   MKKILISDKLSEAGINYLNEQSGIQVHIETGLKEEGLCNIIGDYDALLIRSDTQVTPKVL 60

Query: 59  EASENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQA 118
           +A++ LK+I RAG+GVDNVD+  ATE GI+V+N PDA++ + AEL    M++ +R++P A
Sbjct: 61  QAAKKLKLIGRAGIGVDNVDIPMATELGIIVMNTPDANATTTAELAIAHMMSLSRHLPTA 120

Query: 119 TASIKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVAS 178
             S+++GKW+R    G EI  KTL I+G G IG+ VA+R     M ++AYDP++  ++  
Sbjct: 121 DRSVRAGKWERSKLMGSEIAHKTLAILGFGTIGRIVAQRGLGLKMKVIAYDPFVAPEIFQ 180

Query: 179 ELGIKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAA 238
           +LG++ + +DEL + +D++TLH PL  KT+++IGK Q  +MK   +++NCARGGLI+E A
Sbjct: 181 DLGVESVGLDELVSRADYLTLHCPLIEKTRNIIGKPQFDIMKKGAMLINCARGGLINEEA 240

Query: 239 LYDALNSGKIKAAALDVFEQEPPKESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTV 298
           LYDAL SGKI  AALDV++ EPP  SPLL L+N++ TPH GAST EAQ++    +A Q V
Sbjct: 241 LYDALKSGKIAGAALDVYDNEPPAGSPLLELDNIVFTPHLGASTAEAQVAVSVEIARQAV 300

Query: 299 KILKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAK 358
             LK   A N +NLP    E++KK   Y+ LA  +G +        IE LE+   G  A+
Sbjct: 301 TFLKTGEAINALNLPRQSAEEIKKSFEYVNLATILGKVLAGLATQPIEKLEVALFGRAAE 360

Query: 359 EKTEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSE-SDYGNSIKISAKG 417
                +    L GIL+      VN VNA  IAK + I + E    E  DY + IK++  G
Sbjct: 361 VDVRPVSVGALVGILSGQFSTPVNRVNAENIAKRQGISLIESKTEEPQDYISLIKLTGHG 420

Query: 418 ENDEISIIGSI---EHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHG 474
               IS+ G +    H  +V   IN + +++ PEGT+ + +H D+PG++  +  +LG   
Sbjct: 421 GQHSISLSGVLLGGRHPRLVC--INHFDIEVVPEGTLVVTQHNDKPGVISAISAVLGNAN 478

Query: 475 INIAGMQVGRREPGGHSIMFLDIDHMISDEVLDEIRKMENVRAAKSI 521
           INI  MQVG  +    ++  + +   +SD +L ++  +  V+ A  I
Sbjct: 479 INITRMQVGTADDQQQAMAVISVSEPLSDALLQQLCGVPAVQKATQI 525


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: 701
Number of extensions: 34
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: 523
Length of database: 527
Length adjustment: 35
Effective length of query: 488
Effective length of database: 492
Effective search space:   240096
Effective search space used:   240096
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_020565839.1 A3OW_RS0123135 (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.24438.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-185  603.5   4.1   2.2e-185  603.3   4.1    1.0  1  lcl|NCBI__GCF_000372865.1:WP_020565839.1  A3OW_RS0123135 phosphoglycerate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000372865.1:WP_020565839.1  A3OW_RS0123135 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  603.3   4.1  2.2e-185  2.2e-185       1     525 []       3     527 .]       3     527 .] 0.99

  Alignments for each domain:
  == domain 1  score: 603.3 bits;  conditional E-value: 2.2e-185
                                 TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigR 68 
                                               k+l++dklse+gi+ l ++++++v+++tgl++e l ++i dydal++RS t+vt ++l+aa+kLk igR
  lcl|NCBI__GCF_000372865.1:WP_020565839.1   3 KILISDKLSEAGINyLNEQSGIQVHIETGLKEEGLCNIIGDYDALLIRSDTQVTPKVLQAAKKLKLIGR 71 
                                               79************8888999************************************************ PP

                                 TIGR01327  69 aGvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtEly 137
                                               aG+GvDN+di+ at+ Gi+v+N+P++n  ++aEla+a++++l+R++p+ad+sv+++kWer+k +G+E+ 
  lcl|NCBI__GCF_000372865.1:WP_020565839.1  72 AGIGVDNVDIPMATELGIIVMNTPDANATTTAELAIAHMMSLSRHLPTADRSVRAGKWERSKLMGSEIA 140
                                               ********************************************************************* PP

                                 TIGR01327 138 gktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltke 206
                                               +ktl ++G+G iG +va+r  +l+mkv+ayDP++++e +++lgve +  ldel+++aD +t+H Pl ++
  lcl|NCBI__GCF_000372865.1:WP_020565839.1 141 HKTLAILGFGTIGRIVAQRGLGLKMKVIAYDPFVAPEIFQDLGVE-SVGLDELVSRADYLTLHCPLIEK 208
                                               *********************************************.666******************** PP

                                 TIGR01327 207 tkgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvt 275
                                               t+++igk +++ mKkg++++NcaRGG+i+E+AL++al++gk+++aalDv+ +EPp  ++lleldn+v t
  lcl|NCBI__GCF_000372865.1:WP_020565839.1 209 TRNIIGKPQFDIMKKGAMLINCARGGLINEEALYDALKSGKIAGAALDVYDNEPPAGSPLLELDNIVFT 277
                                               ********************************************************************* PP

                                 TIGR01327 276 pHlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkea 344
                                               pHlgAst+Eaq +v+ve+a + + +lk+  + +a+Nlp ++aee++k   y++la  lGk+   l+ + 
  lcl|NCBI__GCF_000372865.1:WP_020565839.1 278 PHLGASTAEAQVAVSVEIARQAVTFLKTGEAINALNLPRQSAEEIKKSFEYVNLATILGKVLAGLATQP 346
                                               ********************************************************************* PP

                                 TIGR01327 345 vkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknlle 413
                                               ++k+ev+l G  ae ++ +++  +l g+l+ + ++ vn vnA+ +ak +gi++ esk+ee +dy +l++
  lcl|NCBI__GCF_000372865.1:WP_020565839.1 347 IEKLEVALFGRAAEVDVRPVSVGALVGILSGQFSTPVNRVNAENIAKRQGISLIESKTEEPQDYISLIK 415
                                               ********************************************************************* PP

                                 TIGR01327 414 vkveadkgevsvagtvleekepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482
                                               ++ ++ ++++s++g +l++ +pr+v i++f++++ peg+l++++++DkpGvi+ ++++lg+a+iNi  m
  lcl|NCBI__GCF_000372865.1:WP_020565839.1 416 LTGHGGQHSISLSGVLLGGRHPRLVCINHFDIEVVPEGTLVVTQHNDKPGVISAISAVLGNANINITRM 484
                                               ********************************************************************* PP

                                 TIGR01327 483 qlgrkekggealmllslDeevseevleeikevpeiksvklvel 525
                                               q+g    +++a++++s+ e++s+ +l+++  vp++++++ + l
  lcl|NCBI__GCF_000372865.1:WP_020565839.1 485 QVGTADDQQQAMAVISVSEPLSDALLQQLCGVPAVQKATQIVL 527
                                               *************************************999875 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.67
//
[ok]

This GapMind analysis is from Apr 10 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