Alignments for a candidate for serA in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Saccharomonospora cyanea NA-134

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_005454228.1 SACCYDRAFT_RS05095 phosphoglycerate dehydrogenase

Query= BRENDA::P9WNX3
         (528 letters)



>NCBI__GCF_000244975.1:WP_005454228.1
          Length = 531

 Score =  642 bits (1657), Expect = 0.0
 Identities = 337/525 (64%), Positives = 403/525 (76%)

Query: 2   SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLA 61
           S PVVL+A+KLAPS VA  GD+VEVR VDG DR  LL AV EADALLVRSAT VD EVLA
Sbjct: 5   SQPVVLLAEKLAPSAVAVFGDEVEVRHVDGTDRPALLQAVKEADALLVRSATKVDREVLA 64

Query: 62  AAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAAD 121
            APKLK+VARAGVGLDNVDV AAT RGVLVVNAPTSNI SAAEHA+ALL+A +R++PAAD
Sbjct: 65  EAPKLKVVARAGVGLDNVDVPAATERGVLVVNAPTSNIVSAAEHAVALLMAVARRVPAAD 124

Query: 122 ASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQ 181
            SLR   WKRS+++G E+ GKTVGVVG G+IGQLVA R+AAF   ++AYDPYVS ARAAQ
Sbjct: 125 QSLRSGEWKRSAYTGVELSGKTVGVVGFGKIGQLVAARLAAFDTKLLAYDPYVSAARAAQ 184

Query: 182 LGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAAL 241
           LG+EL+SLD+LL R+D IS+HLPKTPET GLID  ALAK KPGV++VNAARGGL+DE AL
Sbjct: 185 LGVELVSLDELLERSDAISIHLPKTPETKGLIDAAALAKVKPGVLVVNAARGGLIDENAL 244

Query: 242 ADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRL 301
           A+A+  G V  AG+DVFA EP T SPLFEL  VVVTPHLGAST EAQDRAGTDVA S  L
Sbjct: 245 AEALREGRVGGAGIDVFAEEPTTSSPLFELPNVVVTPHLGASTREAQDRAGTDVARSTLL 304

Query: 302 ALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEEV 361
           AL G+FVPDAVNV  G V EEV P+L L +KLG +    S + P S+SV   GELA E+V
Sbjct: 305 ALRGDFVPDAVNVASGTVGEEVRPYLSLTQKLGTVLSAFSTKAPASVSVTAAGELATEDV 364

Query: 362 EVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGADG 421
            VL+L+ALRG+F+ V+ED VTFVNAP LA E GV   +    ES N+RS V VR V  DG
Sbjct: 365 SVLQLAALRGVFAGVVEDQVTFVNAPRLAEELGVQVSVSTEPESQNYRSQVTVRVVHDDG 424

Query: 422 SVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNI 481
           S  +VSG + G    +K++++NGRHFD+RA+G  L++ Y DRPG +G++GTLLG AG+NI
Sbjct: 425 SSHSVSGAVTGKDEVEKLIEVNGRHFDIRAEGHMLLLEYPDRPGIMGRVGTLLGEAGINI 484

Query: 482 QAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDAYKLEVVD 526
           +AAQ+S+  +   A +LLR+D+ V   +   I A VDA  +  VD
Sbjct: 485 EAAQISQTTDRSDAVMLLRVDRAVGGHMLEPIGATVDARMIRAVD 529


Lambda     K      H
   0.317    0.133    0.370 

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: 756
Number of extensions: 28
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: 528
Length of database: 531
Length adjustment: 35
Effective length of query: 493
Effective length of database: 496
Effective search space:   244528
Effective search space used:   244528
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_005454228.1 SACCYDRAFT_RS05095 (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.3578.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-194  634.1   3.3   1.1e-194  633.9   3.3    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005454228.1  SACCYDRAFT_RS05095 phosphoglycer


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005454228.1  SACCYDRAFT_RS05095 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  633.9   3.3  1.1e-194  1.1e-194       2     524 ..       9     529 ..       8     530 .. 0.98

  Alignments for each domain:
  == domain 1  score: 633.9 bits;  conditional E-value: 1.1e-194
                                 TIGR01327   2 vlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaG 70 
                                               vl+a+kl++++++++ ++ +ev+  +g ++ +ll+++k++dal+vRSatkv++e+l++a+kLkv++RaG
  lcl|NCBI__GCF_000244975.1:WP_005454228.1   9 VLLAEKLAPSAVAVFGDE-VEVRHVDGTDRPALLQAVKEADALLVRSATKVDREVLAEAPKLKVVARAG 76 
                                               99**************77.8************************************************* PP

                                 TIGR01327  71 vGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygk 139
                                               vG+DN+d++aat++G+lvvNaP++n++saaE+a+all+a+aR++p+ad+s+++++W+r++++G+El gk
  lcl|NCBI__GCF_000244975.1:WP_005454228.1  77 VGLDNVDVPAATERGVLVVNAPTSNIVSAAEHAVALLMAVARRVPAADQSLRSGEWKRSAYTGVELSGK 145
                                               ********************************************************************* PP

                                 TIGR01327 140 tlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketk 208
                                               t+Gv+G+G+iG+ va r +a++ k+layDPy+s ++a++lgve l +ldell+++D+i++H+P+t+etk
  lcl|NCBI__GCF_000244975.1:WP_005454228.1 146 TVGVVGFGKIGQLVAARLAAFDTKLLAYDPYVSAARAAQLGVE-LVSLDELLERSDAISIHLPKTPETK 213
                                               *******************************************.556********************** PP

                                 TIGR01327 209 gligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpH 277
                                               gli++ +lak+K+gv +vN+aRGG+idE+AL+eal eg+v +a++Dvf++EP+t+++l+el+nvvvtpH
  lcl|NCBI__GCF_000244975.1:WP_005454228.1 214 GLIDAAALAKVKPGVLVVNAARGGLIDENALAEALREGRVGGAGIDVFAEEPTTSSPLFELPNVVVTPH 282
                                               ********************************************************************* PP

                                 TIGR01327 278 lgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavk 346
                                               lgAst+Eaq++++++va + l al+g++v++avN+ +    + e+++pyl+l++klG++ s ++ +a+ 
  lcl|NCBI__GCF_000244975.1:WP_005454228.1 283 LGASTREAQDRAGTDVARSTLLALRGDFVPDAVNVAS--GTVGEEVRPYLSLTQKLGTVLSAFSTKAPA 349
                                               ***********************************99..667788************************ PP

                                 TIGR01327 347 kvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevk 415
                                               +v+vt  Gela+e++++l+ a+l+g++  v+e++v++vnA+ +a+e g++v++s+e es++y++ ++v+
  lcl|NCBI__GCF_000244975.1:WP_005454228.1 350 SVSVTAAGELATEDVSVLQLAALRGVFAGVVEDQVTFVNAPRLAEELGVQVSVSTEPESQNYRSQVTVR 418
                                               ********************************************************************* PP

                                 TIGR01327 416 veadkg.evsvagtvlee.kepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482
                                               v  d+g ++sv+g+v ++ + ++++e++g ++d+++eg++l++++ D+pG++g+vg+llgeagiNi ++
  lcl|NCBI__GCF_000244975.1:WP_005454228.1 419 VVHDDGsSHSVSGAVTGKdEVEKLIEVNGRHFDIRAEGHMLLLEYPDRPGIMGRVGTLLGEAGINIEAA 487
                                               999888689*******985679*********************************************** PP

                                 TIGR01327 483 qlgrkekggealmllslDeevseevleeikevpeiksvklve 524
                                               q+++++ + +a+mll++D++v  ++le i +  +++ +++v+
  lcl|NCBI__GCF_000244975.1:WP_005454228.1 488 QISQTTDRSDAVMLLRVDRAVGGHMLEPIGATVDARMIRAVD 529
                                               *****************************9999999888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (531 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: 00:00:00.02
# Mc/sec: 12.95
//
[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