Alignments for a candidate for serA in Haloechinothrix alba DSM 45207

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Haloechinothrix alba DSM 45207

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate WP_089299963.1 CHB84_RS03225 phosphoglycerate dehydrogenase

Query= BRENDA::P9WNX3
         (528 letters)



>NCBI__GCF_900188115.1:WP_089299963.1
          Length = 532

 Score =  646 bits (1666), Expect = 0.0
 Identities = 339/519 (65%), Positives = 410/519 (78%), Gaps = 1/519 (0%)

Query: 2   SLPVVLIADKLAPSTVAALGDQVEVRWVDGPDRDKLLAAVPEADALLVRSATTVDAEVLA 61
           S PVVL+A+KLAPS + A GD+VE+R VDG DR  LL AV +ADAL+VRSAT VDAEVL 
Sbjct: 5   SRPVVLLAEKLAPSVMDAFGDEVEIRHVDGTDRAALLEAVADADALVVRSATQVDAEVLT 64

Query: 62  AAPKLKIVARAGVGLDNVDVDAATARGVLVVNAPTSNIHSAAEHALALLLAASRQIPAAD 121
           A  KL +V RAGVGLDNV+V AAT RGVLVVNAPTSNI SAAEHA+ALLL+  R++PAAD
Sbjct: 65  AGKKLTVVGRAGVGLDNVEVPAATERGVLVVNAPTSNIVSAAEHAVALLLSVVRRVPAAD 124

Query: 122 ASLREHTWKRSSFSGTEIFGKTVGVVGLGRIGQLVAQRIAAFGAYVVAYDPYVSPARAAQ 181
            SLR   WKRSS++G E+ GKTVGVVGLG+IGQL AQR+AAFG  ++AYDPY + ARAAQ
Sbjct: 125 QSLRGGEWKRSSYTGVELNGKTVGVVGLGKIGQLFAQRVAAFGTTLIAYDPYATAARAAQ 184

Query: 182 LGIELLSLDDLLARADFISVHLPKTPETAGLIDKEALAKTKPGVIIVNAARGGLVDEAAL 241
           LG+EL+SLD+LL R+D IS+HLPKTPETAGLID +ALAK K G I++NAARGGLVDE AL
Sbjct: 185 LGVELVSLDELLQRSDIISIHLPKTPETAGLIDADALAKVKQGAIVINAARGGLVDEQAL 244

Query: 242 ADAITGGHVRAAGLDVFATEPCTDSPLFELAQVVVTPHLGASTAEAQDRAGTDVAESVRL 301
           ADA+  G V  AG+DVF TEP T+SPLF L  VVVTPHLGAST+EAQDRAGTDVA SVRL
Sbjct: 245 ADAVKEGRVGGAGVDVFVTEPTTESPLFGLPNVVVTPHLGASTSEAQDRAGTDVAHSVRL 304

Query: 302 ALAGEFVPDAVNV-GGGVVNEEVAPWLDLVRKLGVLAGVLSDELPVSLSVQVRGELAAEE 360
           AL G+FVPDAVNV GGG V++EV P+L L +KLG++    SD+ P S+ V V GEL++E+
Sbjct: 305 ALRGDFVPDAVNVAGGGAVSDEVRPYLPLTQKLGIVLSAFSDKAPTSVQVVVSGELSSED 364

Query: 361 VEVLRLSALRGLFSAVIEDAVTFVNAPALAAERGVTAEICKASESPNHRSVVDVRAVGAD 420
           V+VL L+ALRG+F  V+ED VTFVNAP LA E GV  E+   SES  +RS V VRAV AD
Sbjct: 365 VDVLPLAALRGVFDGVVEDQVTFVNAPRLAEELGVQFEVTTQSESEIYRSEVTVRAVHAD 424

Query: 421 GSVVTVSGTLYGPQLSQKIVQINGRHFDLRAQGINLIIHYVDRPGALGKIGTLLGTAGVN 480
           G+ ++VSG + G    +K+V++NGRHFD+RA+G  L++ Y DRPG LG+IGTLLG AGVN
Sbjct: 425 GTTLSVSGAITGLDEVEKLVEVNGRHFDIRAEGHMLLLEYPDRPGVLGRIGTLLGEAGVN 484

Query: 481 IQAAQLSEDAEGPGATILLRLDQDVPDDVRTAIAAAVDA 519
           I+ AQ+S+ AEG  A +L+R+D+ V   V   I AAV A
Sbjct: 485 IETAQVSQTAEGTSAVLLMRVDRTVDTSVLEPIGAAVGA 523


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: 764
Number of extensions: 25
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: 528
Length of database: 532
Length adjustment: 35
Effective length of query: 493
Effective length of database: 497
Effective search space:   245021
Effective search space used:   245021
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_089299963.1 CHB84_RS03225 (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.19099.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.8e-188  613.5   4.9     2e-188  613.3   4.9    1.0  1  lcl|NCBI__GCF_900188115.1:WP_089299963.1  CHB84_RS03225 phosphoglycerate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900188115.1:WP_089299963.1  CHB84_RS03225 phosphoglycerate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  613.3   4.9    2e-188    2e-188       2     524 ..       9     530 ..       8     531 .. 0.98

  Alignments for each domain:
  == domain 1  score: 613.3 bits;  conditional E-value: 2e-188
                                 TIGR01327   2 vlvadklseegiellkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaG 70 
                                               vl+a+kl+++ ++++ ++ +e++  +g ++++lle++ d+dal+vRSat+v++e+l a +kL v+gRaG
  lcl|NCBI__GCF_900188115.1:WP_089299963.1   9 VLLAEKLAPSVMDAFGDE-VEIRHVDGTDRAALLEAVADADALVVRSATQVDAEVLTAGKKLTVVGRAG 76 
                                               99*************977.8************************************************* PP

                                 TIGR01327  71 vGvDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygk 139
                                               vG+DN++++aat++G+lvvNaP++n++saaE+a+alll+++R++p+ad+s++ ++W+r++++G+El gk
  lcl|NCBI__GCF_900188115.1:WP_089299963.1  77 VGLDNVEVPAATERGVLVVNAPTSNIVSAAEHAVALLLSVVRRVPAADQSLRGGEWKRSSYTGVELNGK 145
                                               ********************************************************************* PP

                                 TIGR01327 140 tlGviGlGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketk 208
                                               t+Gv+GlG+iG+  a+r++a+g +++ayDPy + ++a++lgve l +ldell+++D+i++H+P+t+et+
  lcl|NCBI__GCF_900188115.1:WP_089299963.1 146 TVGVVGLGKIGQLFAQRVAAFGTTLIAYDPYATAARAAQLGVE-LVSLDELLQRSDIISIHLPKTPETA 213
                                               *******************************************.556********************** PP

                                 TIGR01327 209 gligkeelakmKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpH 277
                                               gli++++lak+K+g+i++N+aRGG++dE+AL++a++eg+v +a++Dvf +EP+t+++l+ l+nvvvtpH
  lcl|NCBI__GCF_900188115.1:WP_089299963.1 214 GLIDADALAKVKQGAIVINAARGGLVDEQALADAVKEGRVGGAGVDVFVTEPTTESPLFGLPNVVVTPH 282
                                               ********************************************************************* PP

                                 TIGR01327 278 lgAsteEaqenvavevaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavk 346
                                               lgAst+Eaq++++++va++v+ al+g++v++avN+      ++++++pyl l++klG + s ++++a++
  lcl|NCBI__GCF_900188115.1:WP_089299963.1 283 LGASTSEAQDRAGTDVAHSVRLALRGDFVPDAVNVAG-GGAVSDEVRPYLPLTQKLGIVLSAFSDKAPT 350
                                               ***********************************99.677889************************* PP

                                 TIGR01327 347 kvevtleGelaeeeselltsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevk 415
                                               +v+v ++Gel++e++++l  a+l+g+++ v+e++v++vnA+ +a+e g+++e+++++ese y++ ++v+
  lcl|NCBI__GCF_900188115.1:WP_089299963.1 351 SVQVVVSGELSSEDVDVLPLAALRGVFDGVVEDQVTFVNAPRLAEELGVQFEVTTQSESEIYRSEVTVR 419
                                               ********************************************************************9 PP

                                 TIGR01327 416 veadkg.evsvagtvlee.kepriveidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasm 482
                                               +  ++g + sv+g++ +  + +++ve++g ++d+++eg++l++++ D+pGv+g++g+llgeag+Ni ++
  lcl|NCBI__GCF_900188115.1:WP_089299963.1 420 AVHADGtTLSVSGAITGLdEVEKLVEVNGRHFDIRAEGHMLLLEYPDRPGVLGRIGTLLGEAGVNIETA 488
                                               776666499*****99864789*********************************************** PP

                                 TIGR01327 483 qlgrkekggealmllslDeevseevleeikevpeiksvklve 524
                                               q++++++g +a++l+++D++v+  vle i +   +++v+ v+
  lcl|NCBI__GCF_900188115.1:WP_089299963.1 489 QVSQTAEGTSAVLLMRVDRTVDTSVLEPIGAAVGARTVRSVT 530
                                               *****************************9999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (532 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: 12.83
//
[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