Alignments for a candidate for serA in Ferroglobus placidus DSM 10642

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Ferroglobus placidus DSM 10642

Align D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized, see rationale)
to candidate WP_012966581.1 FERP_RS10600 phosphoglycerate dehydrogenase

Query= uniprot:Q6LWW6
         (523 letters)



>NCBI__GCF_000025505.1:WP_012966581.1
          Length = 527

 Score =  476 bits (1224), Expect = e-138
 Identities = 253/519 (48%), Positives = 355/519 (68%), Gaps = 7/519 (1%)

Query: 3   KILITDPLHESAVEILKQAG-EVEVATGLTVEELKLKIKDVDALVIRSGTTATREIIEAS 61
           K+L+   + + A+E+LK  G EV+V   ++ EELK  IKD DAL++RS    TREIIE  
Sbjct: 2   KVLVASNIAKEAIELLKAEGMEVDVRADISEEELKEVIKDYDALIVRSKPKVTREIIERG 61

Query: 62  ENLKVIARAGVGVDNVDLDAATEKGIVVVNAPDASSISVAELLFGMMLAAARNIPQATAS 121
           E LK+I RAGVGVDN+D+DAATE+GI+VVNAP  ++IS AEL  G++++AAR IPQA  S
Sbjct: 62  EKLKIIGRAGVGVDNIDVDAATERGIIVVNAPGGNTISTAELTMGLIISAARKIPQADRS 121

Query: 122 IKSGKWDRKSFKGMEIYGKTLGIVGLGRIGQQVAKRAQAFGMTIVAYDPYIPEDVASELG 181
           +K GKW+RK F+G+E+ GKTLGI+GLGRIG +VAKRA++F M ++AYDPYI  + A  +G
Sbjct: 122 VKEGKWERKKFEGLELRGKTLGIIGLGRIGFEVAKRAKSFEMRVIAYDPYISPERAKSIG 181

Query: 182 IKLLTVDELCTVSDFITLHVPLTPKTKHMIGKEQIALMKSNMVIMNCARGGLIDEAALYD 241
           ++L++ D L   SD IT+HVP T +T+ MI  E+   MK N++I+NCARGG++DE ALY+
Sbjct: 182 VELVSFDYLIENSDIITVHVPKTKETEKMISYEEFRKMKDNVIIVNCARGGIVDEDALYE 241

Query: 242 ALNSGKIKAAALDVFEQEPPK-ESPLLTLNNLIGTPHQGASTEEAQLSAGTIVAEQTVKI 300
           AL SGK+  AALDV+E+EPP    PL  L N+I TPH GAST+EAQ S G I+A   + +
Sbjct: 242 ALKSGKVYMAALDVYEKEPPNFNHPLFKLENVITTPHIGASTKEAQKSVGMIIARDIINL 301

Query: 301 LKGESAENVVNLPMVPTEKMKKLKPYMVLAEKMGSMAIQYLDNSIELLEITYMGGLAKEK 360
            KG    N VNLP +  E  + L PY+ LAEKMG +A   L  + + ++ITY G LA + 
Sbjct: 302 YKGLPVINAVNLPSLKPEDFEYLMPYITLAEKMGKIASARLGGNFKEVKITYRGKLANKD 361

Query: 361 TEILKRSFLKGILAPILLAGVNLVNAPVIAKSRNIKIAEGTMSESD-YGNSIKISAKGEN 419
           T  + R+ LKG+L  IL A +NLV++  IAK R I+I E  +  +D Y + +++  KGE 
Sbjct: 362 TAYVARALLKGLLETILGANINLVSSMPIAKQRGIRIEESRIESTDSYESLLEVEVKGEK 421

Query: 420 DEISIIG-SIEHNEVVFREINGYRMDIKPEGTICIIKHIDRPGMVGKVGVLLGEHGINIA 478
             IS+ G S   ++     I+ Y++D  P G   I  H D+PG++G+VG L G++ INIA
Sbjct: 422 -SISLAGTSFGRDDYRIIRIDRYKVDFVPRGHYIISLHEDKPGVIGRVGTLFGQYNINIA 480

Query: 479 GMQVGR--REPGGHSIMFLDIDHMISDEVLDEIRKMENV 515
           GM VGR   +PGG  +M L +D   ++EVL+++ K++ +
Sbjct: 481 GMIVGRYGDKPGGVQLMLLLVDDPPTEEVLEKMVKLDGI 519


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: 738
Number of extensions: 51
Number of successful extensions: 7
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_012966581.1 FERP_RS10600 (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.2756615.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-221  720.7   2.8   6.3e-221  720.6   2.8    1.0  1  NCBI__GCF_000025505.1:WP_012966581.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025505.1:WP_012966581.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  720.6   2.8  6.3e-221  6.3e-221       1     524 [.       2     526 ..       2     527 .] 0.99

  Alignments for each domain:
  == domain 1  score: 720.6 bits;  conditional E-value: 6.3e-221
                             TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 
                                           kvlva ++++e+iellk +++evdv+ ++s+eel e+ikdydalivRS+ kvt+e++e+ ekLk+igRaGvGv
  NCBI__GCF_000025505.1:WP_012966581.1   2 KVLVASNIAKEAIELLKAEGMEVDVRADISEEELKEVIKDYDALIVRSKPKVTREIIERGEKLKIIGRAGVGV 74 
                                           79*********************************************************************** PP

                             TIGR01327  74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGl 146
                                           DNid++aat++Gi+vvNaP gntis+aEl++ l++++aRkipqad+svke+kWerkkf G+El+gktlG+iGl
  NCBI__GCF_000025505.1:WP_012966581.1  75 DNIDVDAATERGIIVVNAPGGNTISTAELTMGLIISAARKIPQADRSVKEGKWERKKFEGLELRGKTLGIIGL 147
                                           ************************************************************************* PP

                             TIGR01327 147 GriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakm 219
                                           GriG evakrak+++m+v+ayDPyis+e+a+++gve l ++d l++++D+itvHvP+tket+++i+ ee+ km
  NCBI__GCF_000025505.1:WP_012966581.1 148 GRIGFEVAKRAKSFEMRVIAYDPYISPERAKSIGVE-LVSFDYLIENSDIITVHVPKTKETEKMISYEEFRKM 219
                                           ************************************.556********************************* PP

                             TIGR01327 220 KkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt.dnklleldnvvvtpHlgAsteEaqenvav 291
                                           K++viivNcaRGGi+dE+AL+eal++gkv +aalDv+ekEPp+ +++l++l+nv++tpH+gAst+Eaq+ v++
  NCBI__GCF_000025505.1:WP_012966581.1 220 KDNVIIVNCARGGIVDEDALYEALKSGKVYMAALDVYEKEPPNfNHPLFKLENVITTPHIGASTKEAQKSVGM 292
                                           ******************************************98999************************** PP

                             TIGR01327 292 evaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesell 364
                                           ++a +++++ kg +v +avNlp+l+ e++e l+py++laek+Gk+as  l+++ k+v++t++G+la++++  +
  NCBI__GCF_000025505.1:WP_012966581.1 293 IIARDIINLYKGLPVINAVNLPSLKPEDFEYLMPYITLAEKMGKIASARLGGNFKEVKITYRGKLANKDTAYV 365
                                           ************************************************************************* PP

                             TIGR01327 365 tsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepri 437
                                            +allkgll+ +l +++nlv+ + +ak+rgi++ees+ e++++y++llev+v+++k ++s+agt ++ + +ri
  NCBI__GCF_000025505.1:WP_012966581.1 366 ARALLKGLLETILGANINLVSSMPIAKQRGIRIEESRIESTDSYESLLEVEVKGEK-SISLAGTSFGRDDYRI 437
                                           *****************************************************975.799************* PP

                             TIGR01327 438 veidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrk..ekggealmllslDeevseevl 508
                                           ++id+++vd+ p+g+++i+ ++DkpGvig+vg+l+g+++iNia+m +gr   + gg +lmll +D++++eevl
  NCBI__GCF_000025505.1:WP_012966581.1 438 IRIDRYKVDFVPRGHYIISLHEDKPGVIGRVGTLFGQYNINIAGMIVGRYgdKPGGVQLMLLLVDDPPTEEVL 510
                                           *************************************************755999****************** PP

                             TIGR01327 509 eeikevpeiksvklve 524
                                           e++ +++ i +++++ 
  NCBI__GCF_000025505.1:WP_012966581.1 511 EKMVKLDGIIDATYIY 526
                                           ************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: 17.13
//
[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