Alignments for a candidate for serA in Geotalea uraniireducens Rf4

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Geotalea uraniireducens Rf4

Align D-3-phosphoglycerate dehydrogenase; PGDH; EC 1.1.1.95 (uncharacterized)
to candidate WP_011940656.1 GURA_RS19650 phosphoglycerate dehydrogenase

Query= curated2:O29445
         (527 letters)



>NCBI__GCF_000016745.1:WP_011940656.1
          Length = 539

 Score =  403 bits (1035), Expect = e-116
 Identities = 209/516 (40%), Positives = 333/516 (64%), Gaps = 5/516 (0%)

Query: 1   MKVLVAEPISEEAIDYMRKNG-LEVEVKTGMSREELIREVPKYEAIVVRSQTKVDAEVIQ 59
           MKV+V + ++ E +  + ++  +E++++ G+ +EEL+  +  YEAI+ RS T VD +++ 
Sbjct: 1   MKVIVTDEVAPEGLALLAQDPRVEMDIRLGLKKEELLAIIGDYEAIITRSGTNVDRDLLD 60

Query: 60  AAKNLKIIGRAGVGVDNIDINAATQRGIVVVNAPGGNTISTAEHAIALMLAAARKIPQAD 119
           AAK LK++ RAGVG+DN+D++ A+ RG++VVNAP GNT S AEH +AL+LA  R I +A+
Sbjct: 61  AAKKLKMVARAGVGIDNVDVDYASARGVIVVNAPFGNTNSAAEHTMALLLAFYRNITKAN 120

Query: 120 RSVKEGKWERKKFMGIELRGKTAGVIGLGRVGFEVAKRCKALEMNVLAYDPFVSKERAEQ 179
            S+K G+W+R  F G EL+G+TAGVIGLG+VG  VA R KA E  VLA DP+V+ +RA  
Sbjct: 121 ASLKSGEWKRAPFTGYELKGRTAGVIGLGKVGGRVATRLKAFECEVLACDPYVAVKRAHD 180

Query: 180 IGVKLVDFDTLLASSDVITVHVPRTKETIGLIGKGQFEKMKDGVIVVNAARGGIVDEAAL 239
           +GV+LV  + +  + D+IT+H P   ET+ +IG+ +   MK+GV+++NAARGGI +E AL
Sbjct: 181 LGVRLVSHEEIYRNCDIITIHTPLNGETLDMIGEKEIAMMKEGVVLINAARGGIFNEQAL 240

Query: 240 YEAIKAGKVAAAALDVYEKEPPSPD--NPLLKLDNVVTTPHIAASTREAQLNVGMIIAED 297
             A++ GKVA AA+DV+ +EPP  +    L+    +V TPH+ A+T EAQ+NV + ++ +
Sbjct: 241 LNALQTGKVAGAAVDVWSEEPPRTELLKELIAQQRLVVTPHLGANTFEAQINVAVDVSRE 300

Query: 298 IVNMAKGLPVRNAVNLPSIEPSDFEFMMPFLTLAEKMGKIASVRLGGAIRKVKVTCSGKL 357
           I+N     P+ NAVN+P  + +  E M PFL L + M  +A   +     K+    +G +
Sbjct: 301 ILNYLDDQPLENAVNIPRFDLTLMEQMRPFLNLVKVMCDLAFQLVDDNPAKLAFGYAGAI 360

Query: 358 ATKNTEFVTRALLKGLFEPILSNEINLVSAKPVAVERGITIEESKVESVEHYESLLEVWV 417
           A  +   +T   L  +   ++  E+N+V+A  +A   GI +EE K    + + +++ + V
Sbjct: 361 AHYDCSPLTVCGLAAILNLVVDQEVNMVNAPLIAENMGIVVEEHKSTRADAFSNMVTLTV 420

Query: 418 ESNGKEMYLAGTCFGNEYRILKIDVYNVNFVPKGHYIISLHEDKPGVIGRVGTLFGRNNI 477
           E  GK   L+GT F    RI+++  Y ++F P+GH ++  + D+PG+IGR+GT+ G  +I
Sbjct: 421 EGQGKRRLLSGTLFEGAPRIVRLRDYAMDFSPEGHMLLLNYIDRPGMIGRIGTILGTRDI 480

Query: 478 NIAGMIVGRSGDKPGGIQLMLLLVDDPPTPEVLEEM 513
           NIA M +GR   K  G  +++L +D    P+V+EE+
Sbjct: 481 NIASMNLGRREKK--GEAMVILSLDSAVPPDVVEEL 514


Lambda     K      H
   0.317    0.136    0.376 

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: 725
Number of extensions: 39
Number of successful extensions: 2
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: 527
Length of database: 539
Length adjustment: 35
Effective length of query: 492
Effective length of database: 504
Effective search space:   247968
Effective search space used:   247968
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_011940656.1 GURA_RS19650 (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.3694733.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.1e-195  634.6   0.8     8e-195  634.4   0.8    1.0  1  NCBI__GCF_000016745.1:WP_011940656.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016745.1:WP_011940656.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  634.4   0.8    8e-195    8e-195       1     521 [.       2     524 ..       2     528 .. 0.98

  Alignments for each domain:
  == domain 1  score: 634.4 bits;  conditional E-value: 8e-195
                             TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvG 72 
                                           kv+v+d++++eg++ l ++ ++e+d++ gl+keell++i dy+a+i+RS t+v+++ll+aa+kLk+++RaGvG
  NCBI__GCF_000016745.1:WP_011940656.1   2 KVIVTDEVAPEGLAlLAQDPRVEMDIRLGLKKEELLAIIGDYEAIITRSGTNVDRDLLDAAKKLKMVARAGVG 74 
                                           79************7788899**************************************************** PP

                             TIGR01327  73 vDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviG 145
                                           +DN+d+++a+++G++vvNaP gnt saaE+++allla  R+i++a++s+k+++W+r  f+G El+g+t GviG
  NCBI__GCF_000016745.1:WP_011940656.1  75 IDNVDVDYASARGVIVVNAPFGNTNSAAEHTMALLLAFYRNITKANASLKSGEWKRAPFTGYELKGRTAGVIG 147
                                           ************************************************************************* PP

                             TIGR01327 146 lGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelak 218
                                           lG++G +va+r ka++ +vla DPy++ ++a++lgv+l+ + +e+ +++D+it+H+Pl+ et ++ig++e+a 
  NCBI__GCF_000016745.1:WP_011940656.1 148 LGKVGGRVATRLKAFECEVLACDPYVAVKRAHDLGVRLV-SHEEIYRNCDIITIHTPLNGETLDMIGEKEIAM 219
                                           *************************************55.59******************************* PP

                             TIGR01327 219 mKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt...dnklleldnvvvtpHlgAsteEaqen 288
                                           mK+gv+++N+aRGGi +E+AL++al++gkv++aa+Dv+++EPp     ++l++++++vvtpHlgA+t Eaq n
  NCBI__GCF_000016745.1:WP_011940656.1 220 MKEGVVLINAARGGIFNEQALLNALQTGKVAGAAVDVWSEEPPRtelLKELIAQQRLVVTPHLGANTFEAQIN 292
                                           *******************************************97777899999******************* PP

                             TIGR01327 289 vavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeees 361
                                           vav+v+ e+l++l +++ e+avN+p  d   +e+++p+l+l++ +  la ql+++++ k++  + G +a+++ 
  NCBI__GCF_000016745.1:WP_011940656.1 293 VAVDVSREILNYLDDQPLENAVNIPRFDLTLMEQMRPFLNLVKVMCDLAFQLVDDNPAKLAFGYAGAIAHYDC 365
                                           ************************************************************************* PP

                             TIGR01327 362 elltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleeke 434
                                           ++lt   l+ +l+ v+++evn+vnA+ +a++ gi vee+k+  ++ ++n+++++ve++ +++ ++gt++e+ +
  NCBI__GCF_000016745.1:WP_011940656.1 366 SPLTVCGLAAILNLVVDQEVNMVNAPLIAENMGIVVEEHKSTRADAFSNMVTLTVEGQGKRRLLSGTLFEG-A 437
                                           **********************************************************************5.* PP

                             TIGR01327 435 priveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseev 507
                                           priv+++++ +d++peg++l++++ D+pG+ig++g++lg+ +iNiasm+lgr+ek+gea+++lslD++v+++v
  NCBI__GCF_000016745.1:WP_011940656.1 438 PRIVRLRDYAMDFSPEGHMLLLNYIDRPGMIGRIGTILGTRDINIASMNLGRREKKGEAMVILSLDSAVPPDV 510
                                           ************************************************************************* PP

                             TIGR01327 508 leeikevpeiksvk 521
                                           +ee+++ ++++ ++
  NCBI__GCF_000016745.1:WP_011940656.1 511 VEELRNATNATFIR 524
                                           ******99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (539 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 0.03s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.71
//
[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