Alignments for a candidate for serA in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Nitriliruptor alkaliphilus DSM 45188

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_052666323.1 NITAL_RS11360 phosphoglycerate dehydrogenase

Query= BRENDA::Q9Z564
         (529 letters)



>NCBI__GCF_000969705.1:WP_052666323.1
          Length = 527

 Score =  528 bits (1361), Expect = e-154
 Identities = 272/525 (51%), Positives = 374/525 (71%), Gaps = 2/525 (0%)

Query: 7   VLIAEELSPATVDALGPDFEIRHCNGADRAELLPAIADVDAILVRSATKVDAEAVAAAKK 66
           +L+A++L+ A VDAL  D ++    G  + ELL  +   DAI+VRS T +DA+ +AAA +
Sbjct: 3   ILVADKLAQAGVDALAVDHQVDVNTGLSKDELLVTVPGYDAIVVRSQTIIDADVIAAATE 62

Query: 67  LKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNIPQANAALK 126
           LKVV RAGVGLDNVD+ AAT++GV+V NAP SN+V+AAE    L+++ ARN+PQA+AAL 
Sbjct: 63  LKVVGRAGVGLDNVDIDAATRSGVVVCNAPQSNVVSAAEHTLALLLSLARNVPQAHAALV 122

Query: 127 NGEWKRSKYTGVELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYVQPARAAQMGVK 186
            G W+RS++ G EL +KTLGV+GLGRIG LVAQR  AFGM++VAYDP+V P RAA++GV+
Sbjct: 123 EGRWERSRWNGTELHDKTLGVLGLGRIGTLVAQRAHAFGMRLVAYDPFVAPDRAARIGVR 182

Query: 187 VL-SLDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGIVDEEALYSA 245
           ++ ++DE+L  +DFIT+HLPKTPETLG+   +   K+K + R++N ARGGIV EE L  A
Sbjct: 183 LVDTVDEVLAEADFITIHLPKTPETLGMFDADRFAKMKSTARLLNVARGGIVVEEDLAKA 242

Query: 246 LKEGRVAGAGLDVYAKEPCTDSPLFEFDQVVATPHLGASTDEAQEKAGIAVAKSVRLALA 305
           L++G +AGA +DV+  EP TDSPLF     + TPHLGAST+EAQ++AG+ VA++V LAL 
Sbjct: 243 LQDGVIAGAAVDVFDAEPKTDSPLFGLPNAIVTPHLGASTEEAQDRAGVQVAEAVDLALK 302

Query: 306 GELVPDAVNVQGGVIAEDVKPGLPLAERLGRIFTALAGE-VAVRLDVEVYGEITQHDVKV 364
           GELVP AVNVQGG + + VKP LPL E+LGR+  ALA E +   + VE  G I   D +V
Sbjct: 303 GELVPSAVNVQGGPVPDAVKPFLPLGEKLGRLLAALAEEGLTGEVTVEAAGAIADEDTRV 362

Query: 365 LELSALKGVFEDVVDETVSYVNAPLFAQERGVEVRLTTSSESPEHRNVVIVRGTLSDGEE 424
           + LS +KG+   VV E V++VNAPLFA+ERG+ VR  +   S ++ +V+ V G   +G  
Sbjct: 363 VALSVIKGLLAAVVSEPVTFVNAPLFAEERGLSVREISDPHSEDYVSVLRVSGLTREGRT 422

Query: 425 VSVSGTLAGPKHLQKIVAIGEYDVDLALADHMVVLRYEDRPGVVGTVGRIIGEAGLNIAG 484
           V V+GT+  P   ++++ + +  VD+  +DHM   RYEDRPG++GTVG   GEAG+NIA 
Sbjct: 423 VRVAGTIVHPGDRERLIEVWDTPVDVEPSDHMAFFRYEDRPGIIGTVGTGFGEAGVNIAA 482

Query: 485 MQVARATVGGEALAVLTVDDTVPSGVLAEVAAEIGATSARSVNLV 529
            QV R   GGEA+  L++D+ VP  VLA +   IGA   R++ L+
Sbjct: 483 AQVGRLAAGGEAIMALSLDEAVPREVLAALTERIGAREGRAITLI 527


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: 777
Number of extensions: 34
Number of successful extensions: 3
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: 527
Length adjustment: 35
Effective length of query: 494
Effective length of database: 492
Effective search space:   243048
Effective search space used:   243048
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_052666323.1 NITAL_RS11360 (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.14490.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-190  620.2   1.0   1.9e-190  620.0   1.0    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052666323.1  NITAL_RS11360 phosphoglycerate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052666323.1  NITAL_RS11360 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  620.0   1.0  1.9e-190  1.9e-190       1     516 [.       2     517 ..       2     526 .. 0.96

  Alignments for each domain:
  == domain 1  score: 620.0 bits;  conditional E-value: 1.9e-190
                                 TIGR01327   1 kvlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRa 69 
                                               ++lvadkl+++g+++l+ ++ +vdv+tglsk+ell +++ yda++vRS+t +++++++aa++Lkv+gRa
  lcl|NCBI__GCF_000969705.1:WP_052666323.1   2 RILVADKLAQAGVDALAVDH-QVDVNTGLSKDELLVTVPGYDAIVVRSQTIIDADVIAAATELKVVGRA 69 
                                               69************998665.9*********************************************** PP

                                 TIGR01327  70 GvGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElyg 138
                                               GvG+DN+di+aat+ G++v NaP++n +saaE++lalll+laR++pqa++ + e++Wer+++ GtEl +
  lcl|NCBI__GCF_000969705.1:WP_052666323.1  70 GVGLDNVDIDAATRSGVVVCNAPQSNVVSAAEHTLALLLSLARNVPQAHAALVEGRWERSRWNGTELHD 138
                                               ********************************************************************* PP

                                 TIGR01327 139 ktlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltket 207
                                               ktlGv+GlGriG+ va+ra+a+gm+++ayDP++++++a+++gv+l++++de+laeaD+it+H+P+t+et
  lcl|NCBI__GCF_000969705.1:WP_052666323.1 139 KTLGVLGLGRIGTLVAQRAHAFGMRLVAYDPFVAPDRAARIGVRLVDTVDEVLAEADFITIHLPKTPET 207
                                               ********************************************************************* PP

                                 TIGR01327 208 kgligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtp 276
                                                g+ +++++akmK++++++N+aRGGi+ E+ L++al++g +++aa+Dvf  EP td++l+ l+n +vtp
  lcl|NCBI__GCF_000969705.1:WP_052666323.1 208 LGMFDADRFAKMKSTARLLNVARGGIVVEEDLAKALQDGVIAGAAVDVFDAEPKTDSPLFGLPNAIVTP 276
                                               ********************************************************************* PP

                                 TIGR01327 277 HlgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllk.ea 344
                                               HlgAsteEaq++++v+vae v  alkge v+savN+      + + +kp+l l+eklG l   l++ + 
  lcl|NCBI__GCF_000969705.1:WP_052666323.1 277 HLGASTEEAQDRAGVQVAEAVDLALKGELVPSAVNVQGG--PVPDAVKPFLPLGEKLGRLLAALAEeGL 343
                                               ************************************995..55566************87766665056 PP

                                 TIGR01327 345 vkkvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknlle 413
                                               + +v+v+  G +a+e++ ++  +++kgll +v++e v++vnA+  a+erg++v+e ++ +sedy ++l+
  lcl|NCBI__GCF_000969705.1:WP_052666323.1 344 TGEVTVEAAGAIADEDTRVVALSVIKGLLAAVVSEPVTFVNAPLFAEERGLSVREISDPHSEDYVSVLR 412
                                               789****************************************************************** PP

                                 TIGR01327 414 vkveadkg.evsvagtvlee.kepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNia 480
                                               v   +++g +v vagt+++  + +r++e+ +  vd+ep++++ +++++D+pG+ig vg+ +geag+Nia
  lcl|NCBI__GCF_000969705.1:WP_052666323.1 413 VSGLTREGrTVRVAGTIVHPgDRERLIEVWDTPVDVEPSDHMAFFRYEDRPGIIGTVGTGFGEAGVNIA 481
                                               *9777766599*****9987689********************************************** PP

                                 TIGR01327 481 smqlgrkekggealmllslDeevseevleeikevpe 516
                                               ++q+gr ++ggea+m lslDe+v+ evl++++e   
  lcl|NCBI__GCF_000969705.1:WP_052666323.1 482 AAQVGRLAAGGEAIMALSLDEAVPREVLAALTERIG 517
                                               ******************************998555 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 12.49
//
[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