Alignments for a candidate for serA in Thermus aquaticus YT-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Thermus aquaticus YT-1

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_053768202.1 BVI061214_RS09620 phosphoglycerate dehydrogenase

Query= BRENDA::Q9Z564
         (529 letters)



>NCBI__GCF_001280255.1:WP_053768202.1
          Length = 521

 Score =  338 bits (867), Expect = 3e-97
 Identities = 217/521 (41%), Positives = 307/521 (58%), Gaps = 26/521 (4%)

Query: 7   VLIAEELSPATVDALGPDFEIRHCNGADRAELLPAIADVDAILVRSATKVDAEAVAAAKK 66
           VL+++E+    V   G   + R   G  R ELL  I   DA++ RS T+VDAE +   K+
Sbjct: 4   VLVSDEMRLGEVKYPGVLLDYRP--GIGREELLEIIPAYDALITRSRTQVDAELLKRGKR 61

Query: 67  LKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNIPQANAALK 126
           LKVV R GVG+DNVD+ AA++ G++VVN P +N  +AAELA GL+++ AR I  ++  ++
Sbjct: 62  LKVVGRGGVGVDNVDLEAASRLGILVVNVPEANTRSAAELAFGLLLSAARGIALSDRKIR 121

Query: 127 NGEWKRSKYTGVELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYVQPARAAQMGVK 186
            GEW R K+ G+EL  KTLG+VGLGRIG  VA+    F M+V+AYDPY+   RA  +GV+
Sbjct: 122 AGEWDR-KFLGLELKGKTLGIVGLGRIGGQVARFAKGFEMRVLAYDPYIPRTRAESLGVE 180

Query: 187 VLS-LDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGIVDEEALYSA 245
           +L  L++LL  S F+TVH P T ET G+IG   L  +     +VNAARGGIVDE+AL   
Sbjct: 181 LLEHLEDLLRQSHFLTVHTPLTEETRGMIGRRELYLLPRGAVVVNAARGGIVDEKALLEV 240

Query: 246 LKEGRVAGAGLDVYAKE-PCTDSPLFEFDQVVATPHLGASTDEAQEKAGIAVAKSVRLAL 304
           L+EG +  AGLDV+++E P  D PL +  +VV T HLGA+T EAQE+ G A+ + V   L
Sbjct: 241 LEEGHLFAAGLDVFSEEPPPKDHPLLKHPRVVLTAHLGANTLEAQERVGEAILERVVRTL 300

Query: 305 AGELV--------PDAVNVQGGVIAEDVKPGLPLAERLGRIFTALAGEVAVRLDVEVYGE 356
            G+L         P+A+    G         LPL E LGR+   +       L+V   G+
Sbjct: 301 EGDLSYALNTGFDPEALQALRGF--------LPLGEALGRLLAQITRGRPQVLEVAFLGQ 352

Query: 357 ITQHDVKVLELSALKGVFEDVV-DETVSYVNAPLFAQERGVEVRLTTSSESPEHRNVVIV 415
             + D + +  +  KG+   V+  E V+ V+A    +ERG+ +      E+ E+  ++ V
Sbjct: 353 Y-EKDPEPVASAVAKGLLSRVLGPEAVNLVSARPLLKERGIRLVTQRQEEAGEYTRLLEV 411

Query: 416 RGTLSDGEEVSVSGTLAGPKHLQKIVAIGEYDVDLALADHMVVLRYEDRPGVVGTVGRII 475
           R T +D E     G + G K   ++V I +Y +++    +M+V    DRPGVVG VG ++
Sbjct: 412 RLT-TDQETRRARGVVIGGK--PRLVGIDDYSLEVVPEGYMLVCVNYDRPGVVGQVGTLL 468

Query: 476 GEAGLNIAGMQVARATVGGEALAVLTVDDTVPSGVLAEVAA 516
           GEAG+NIAGMQ+ R   GG AL VLTVD      VL  + A
Sbjct: 469 GEAGVNIAGMQLGRDVPGGRALFVLTVDQKPAPEVLEALRA 509


Lambda     K      H
   0.315    0.133    0.362 

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: 753
Number of extensions: 37
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: 529
Length of database: 521
Length adjustment: 35
Effective length of query: 494
Effective length of database: 486
Effective search space:   240084
Effective search space used:   240084
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_053768202.1 BVI061214_RS09620 (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.1528964.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-185  602.8   0.0   3.6e-185  602.6   0.0    1.0  1  NCBI__GCF_001280255.1:WP_053768202.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280255.1:WP_053768202.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  602.6   0.0  3.6e-185  3.6e-185       1     524 [.       3     520 ..       3     521 .] 0.98

  Alignments for each domain:
  == domain 1  score: 602.6 bits;  conditional E-value: 3.6e-185
                             TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvGv 73 
                                           +vlv+d++    +++     + +d++ g+ +eelle+i+ ydali+RS+t+v++ell++ ++Lkv+gR+GvGv
  NCBI__GCF_001280255.1:WP_053768202.1   3 RVLVSDEMRLGEVKYPG---VLLDYRPGIGREELLEIIPAYDALITRSRTQVDAELLKRGKRLKVVGRGGVGV 72 
                                           79*******99999877...89*************************************************** PP

                             TIGR01327  74 DNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviGl 146
                                           DN+d+eaa++ GilvvN Pe+nt saaEla+ lll++aR i  +d+++++++W+r kflG+El+gktlG++Gl
  NCBI__GCF_001280255.1:WP_053768202.1  73 DNVDLEAASRLGILVVNVPEANTRSAAELAFGLLLSAARGIALSDRKIRAGEWDR-KFLGLELKGKTLGIVGL 144
                                           *******************************************************.9**************** PP

                             TIGR01327 147 GriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelakm 219
                                           GriG +va+ ak+++m+vlayDPyi++ +ae+lgvell++l++ll+++ ++tvH+Plt+et+g+ig++el  +
  NCBI__GCF_001280255.1:WP_053768202.1 145 GRIGGQVARFAKGFEMRVLAYDPYIPRTRAESLGVELLEHLEDLLRQSHFLTVHTPLTEETRGMIGRRELYLL 217
                                           ************************************************************************* PP

                             TIGR01327 220 KkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPpt.dnklleldnvvvtpHlgAsteEaqenvav 291
                                            +g+++vN+aRGGi+dEkAL+e+leeg++ aa+lDvf++EPp  d++ll++++vv+t+HlgA+t Eaqe+v+ 
  NCBI__GCF_001280255.1:WP_053768202.1 218 PRGAVVVNAARGGIVDEKALLEVLEEGHLFAAGLDVFSEEPPPkDHPLLKHPRVVLTAHLGANTLEAQERVGE 290
                                           ****************************************976599*************************** PP

                             TIGR01327 292 evaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesell 364
                                            + e+v+++l+g+  ++a+N++  d e+l+ l+++l l+e lG l  q++ ++++ +ev++ G+  ++  e++
  NCBI__GCF_001280255.1:WP_053768202.1 291 AILERVVRTLEGDL-SYALNTGF-DPEALQALRGFLPLGEALGRLLAQITRGRPQVLEVAFLGQYEKDP-EPV 360
                                           ************97.58***998.9****************************************9998.99* PP

                             TIGR01327 365 tsallkgllkevle.eevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepr 436
                                            sa+ kgll+ vl  e+vnlv+A+ + kergi++  +++ee+ +y+ llev++++d++++   g v+++ +pr
  NCBI__GCF_001280255.1:WP_053768202.1 361 ASAVAKGLLSRVLGpEAVNLVSARPLLKERGIRLVTQRQEEAGEYTRLLEVRLTTDQETRRARGVVIGG-KPR 432
                                           *************8457***************************************************5.*** PP

                             TIGR01327 437 iveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevle 509
                                           +v id++++++ peg++l++ n D+pGv+g+vg+llgeag+Nia+mqlgr+  gg al++l++D+++ +evle
  NCBI__GCF_001280255.1:WP_053768202.1 433 LVGIDDYSLEVVPEGYMLVCVNYDRPGVVGQVGTLLGEAGVNIAGMQLGRDVPGGRALFVLTVDQKPAPEVLE 505
                                           ************************************************************************* PP

                             TIGR01327 510 eikevpeiksvklve 524
                                           +++++p +++v l e
  NCBI__GCF_001280255.1:WP_053768202.1 506 ALRALPVLERVDLAE 520
                                           ******999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (521 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: 21.66
//
[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