Alignments for a candidate for serA in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Nocardiopsis lucentensis DSM 44048

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_017598160.1 D471_RS0108145 phosphoglycerate dehydrogenase

Query= BRENDA::Q9Z564
         (529 letters)



>NCBI__GCF_000341125.1:WP_017598160.1
          Length = 529

 Score =  723 bits (1866), Expect = 0.0
 Identities = 361/525 (68%), Positives = 445/525 (84%)

Query: 4   KPVVLIAEELSPATVDALGPDFEIRHCNGADRAELLPAIADVDAILVRSATKVDAEAVAA 63
           KP VL+AE+LSPA +  L  DFE+RH +GADR++LLPA+ADVDA++VRSAT++DAEA+AA
Sbjct: 3   KPAVLVAEKLSPAGIALLEEDFEVRHVDGADRSQLLPALADVDAVIVRSATQIDAEALAA 62

Query: 64  AKKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNIPQANA 123
           A +L+VVARAGVGLDNVDV AATKAGV+VVNAPTSNI++AAE A  L++A+ARN   A+ 
Sbjct: 63  ASRLQVVARAGVGLDNVDVDAATKAGVLVVNAPTSNIISAAEQAINLLLASARNTAPAHN 122

Query: 124 ALKNGEWKRSKYTGVELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYVQPARAAQM 183
           AL NGEWKRSKYTGVEL EK +GVVGLGRIGALVAQR+SAFG KV+AYDP+VQPARAAQ+
Sbjct: 123 ALINGEWKRSKYTGVELYEKVVGVVGLGRIGALVAQRLSAFGTKVIAYDPFVQPARAAQI 182

Query: 184 GVKVLSLDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGIVDEEALY 243
           GV++ +LD+LLE SDFIT+HLPK  +TLGLI DEAL KVKPSVR++NAARGGI+DE+ALY
Sbjct: 183 GVEMTTLDDLLERSDFITIHLPKNKDTLGLISDEALSKVKPSVRVINAARGGILDEDALY 242

Query: 244 SALKEGRVAGAGLDVYAKEPCTDSPLFEFDQVVATPHLGASTDEAQEKAGIAVAKSVRLA 303
            ALK+GRVAGAG+DV+AKEPCTDSPLFEF+ VV  PHLGAST EAQEKAG  VA+SV+LA
Sbjct: 243 RALKDGRVAGAGIDVFAKEPCTDSPLFEFENVVVAPHLGASTTEAQEKAGTQVARSVKLA 302

Query: 304 LAGELVPDAVNVQGGVIAEDVKPGLPLAERLGRIFTALAGEVAVRLDVEVYGEITQHDVK 363
           L+GE VPDAVNVQG  +AE++KPGLPL E+LGR+FT+LAG +A R+DVEV GEI  HDVK
Sbjct: 303 LSGEFVPDAVNVQGTGVAEEIKPGLPLTEKLGRVFTSLAGTIASRIDVEVRGEIAAHDVK 362

Query: 364 VLELSALKGVFEDVVDETVSYVNAPLFAQERGVEVRLTTSSESPEHRNVVIVRGTLSDGE 423
           VLEL+ALKGVF DVV++TV++VNAPL A+ERGVEV L TS +  + RN++ VRG L+DG+
Sbjct: 363 VLELAALKGVFADVVEDTVTFVNAPLLAKERGVEVNLVTSDDHSDWRNLISVRGVLADGQ 422

Query: 424 EVSVSGTLAGPKHLQKIVAIGEYDVDLALADHMVVLRYEDRPGVVGTVGRIIGEAGLNIA 483
            VSVSGTL GP+ ++K+V I  Y ++++L+DHMV L YEDRPG+VG VG ++G+A +NIA
Sbjct: 423 RVSVSGTLTGPRQVEKLVEINNYGMEISLSDHMVFLSYEDRPGIVGKVGALLGDAQVNIA 482

Query: 484 GMQVARATVGGEALAVLTVDDTVPSGVLAEVAAEIGATSARSVNL 528
           GMQV R   GG+AL  LTVD  VP  VLA +++EI A   R ++L
Sbjct: 483 GMQVIRDQEGGKALIALTVDSAVPDEVLASISSEIEADITRQIDL 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: 838
Number of extensions: 33
Number of successful extensions: 1
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: 529
Length adjustment: 35
Effective length of query: 494
Effective length of database: 494
Effective search space:   244036
Effective search space used:   244036
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_017598160.1 D471_RS0108145 (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.14159.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.8e-188  612.1   8.3   5.4e-188  611.9   8.3    1.0  1  lcl|NCBI__GCF_000341125.1:WP_017598160.1  D471_RS0108145 phosphoglycerate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_017598160.1  D471_RS0108145 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  611.9   8.3  5.4e-188  5.4e-188       2     513 ..       6     515 ..       5     527 .. 0.98

  Alignments for each domain:
  == domain 1  score: 611.9 bits;  conditional E-value: 5.4e-188
                                 TIGR01327   2 vlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaG 70 
                                               vlva+kls++gi+ll+e+ +ev+  +g ++ +ll ++ d+da+ivRSat++++e l+aa++L+v++RaG
  lcl|NCBI__GCF_000341125.1:WP_017598160.1   6 VLVAEKLSPAGIALLEED-FEVRHVDGADRSQLLPALADVDAVIVRSATQIDAEALAAASRLQVVARAG 73 
                                               9************99966.8************************************************* PP

                                 TIGR01327  71 vGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygk 139
                                               vG+DN+d++aatk G+lvvNaP++n+isaaE a+ llla aR+   a++ + +++W+r+k++G+Ely+k
  lcl|NCBI__GCF_000341125.1:WP_017598160.1  74 VGLDNVDVDAATKAGVLVVNAPTSNIISAAEQAINLLLASARNTAPAHNALINGEWKRSKYTGVELYEK 142
                                               ********************************************************************* PP

                                 TIGR01327 140 tlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketk 208
                                                +Gv+GlGriG  va+r  a+g kv+ayDP++ +++a+++gve +++ld+ll+++D+it+H+P++k+t 
  lcl|NCBI__GCF_000341125.1:WP_017598160.1 143 VVGVVGLGRIGALVAQRLSAFGTKVIAYDPFVQPARAAQIGVE-MTTLDDLLERSDFITIHLPKNKDTL 210
                                               *******************************************.778********************** PP

                                 TIGR01327 209 gligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpH 277
                                               gli+ e+l k+K++v+++N+aRGGi+dE+AL+ al++g+v++a++Dvf+kEP+td++l+e++nvvv+pH
  lcl|NCBI__GCF_000341125.1:WP_017598160.1 211 GLISDEALSKVKPSVRVINAARGGILDEDALYRALKDGRVAGAGIDVFAKEPCTDSPLFEFENVVVAPH 279
                                               ********************************************************************* PP

                                 TIGR01327 278 lgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavk 346
                                               lgAst+Eaqe+++++va +v+ al ge+v++avN+    + ++e++kp l l+eklG + + l+++  +
  lcl|NCBI__GCF_000341125.1:WP_017598160.1 280 LGASTTEAQEKAGTQVARSVKLALSGEFVPDAVNVQG--TGVAEEIKPGLPLTEKLGRVFTSLAGTIAS 346
                                               ***********************************98..678899************************ PP

                                 TIGR01327 347 kvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevk 415
                                               +++v+++Ge+a++++++l+ a+lkg++ +v+e++v++vnA+ +akerg++v+  ++++++d++nl++v+
  lcl|NCBI__GCF_000341125.1:WP_017598160.1 347 RIDVEVRGEIAAHDVKVLELAALKGVFADVVEDTVTFVNAPLLAKERGVEVNLVTSDDHSDWRNLISVR 415
                                               ********************************************************************8 PP

                                 TIGR01327 416 .veadkgevsvagtvlee.kepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482
                                                v ad ++vsv+gt+ +  + +++vei+++ ++++ ++++++++++D+pG++gkvg+llg+a++Nia+m
  lcl|NCBI__GCF_000341125.1:WP_017598160.1 416 gVLADGQRVSVSGTLTGPrQVEKLVEINNYGMEISLSDHMVFLSYEDRPGIVGKVGALLGDAQVNIAGM 484
                                               6788889*********986889*********************************************** PP

                                 TIGR01327 483 qlgrkekggealmllslDeevseevleeike 513
                                               q+ r+++gg+al+ l++D++v++evl+ i +
  lcl|NCBI__GCF_000341125.1:WP_017598160.1 485 QVIRDQEGGKALIALTVDSAVPDEVLASISS 515
                                               **************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (529 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: 11.20
//
[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