Alignments for a candidate for serA in Alkalihalobacterium alkalinitrilicum DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for serA in Alkalihalobacterium alkalinitrilicum DSM 22532

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate WP_078430830.1 BK574_RS10245 phosphoglycerate dehydrogenase

Query= CharProtDB::CH_004924
         (525 letters)



>NCBI__GCF_002019605.1:WP_078430830.1
          Length = 524

 Score =  634 bits (1636), Expect = 0.0
 Identities = 314/524 (59%), Positives = 403/524 (76%)

Query: 1   MFRVLVSDKMSNDGLQPLIESDFIEIVQKNVADAEDELHTFDALLVRSATKVTEDLFNKM 60
           M+ +LVSD MS +GL PL+ES+ +  +QKNV + + ELHTFDA+LVRSAT VT +L  KM
Sbjct: 1   MYNILVSDAMSKEGLLPLLESEQVNCIQKNVTEVQQELHTFDAILVRSATTVTAELIEKM 60

Query: 61  TSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQANIS 120
            +LKI+ RAGVGVDNIDI+ ATK G++V+NAP+GNTISTAEHTF+MI +L R IPQAN S
Sbjct: 61  PNLKIIARAGVGVDNIDIEAATKAGIVVVNAPDGNTISTAEHTFSMICALARKIPQANQS 120

Query: 121 VKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKKIG 180
           +K  EWNR A+ G+EL GKTLGIVG GRIGS++A+R  AF M   VFDPFLT+ RA+K+G
Sbjct: 121 IKLGEWNRKAFQGTELRGKTLGIVGFGRIGSQLAKRAKAFEMQPLVFDPFLTKARAEKLG 180

Query: 181 VNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAALLE 240
           V   T EEVLE ADIITVHTPLTK+TKG+L  E I KTK+GV LINCARGGIIDE AL  
Sbjct: 181 VVPATLEEVLEKADIITVHTPLTKDTKGILGMENIGKTKRGVYLINCARGGIIDEVALKH 240

Query: 241 ALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQFA 300
            LENGHVAGAALDVFE EP +DN L++   VIATPH+ ASTKEAQLNVAAQVSEEVL F 
Sbjct: 241 YLENGHVAGAALDVFEEEPAIDNALIELDNVIATPHIAASTKEAQLNVAAQVSEEVLLFL 300

Query: 301 KGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKLET 360
           +G PV ++INLP ++K+ + KIKPY+++   +G+++SQCMK PVQ++ + Y G +  LET
Sbjct: 301 EGNPVSNSINLPTLSKEVYGKIKPYYELTKTMGNILSQCMKTPVQEIEVFYGGEVTNLET 360

Query: 361 SFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGDRS 420
           S  T++L++GFL  RVD++VN+VNA  +AKERGI F EK  ++  GY N I   V G+  
Sbjct: 361 SITTRSLMAGFLSARVDASVNDVNASLIAKERGIVFGEKFLNNAYGYANIIHAIVHGENR 420

Query: 421 TFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINIAT 480
           TF +  TY+  +G RIV INGF +DF+P GHL+YIQH D  GVIG++G++L + ++NIAT
Sbjct: 421 TFEIKGTYVKEYGPRIVSINGFIVDFFPAGHLIYIQHNDRPGVIGKMGQMLAEYELNIAT 480

Query: 481 MQVGRKEKGGEAIMMLSFDRHLEDKIVKELTNVPDIVSVKLIDL 524
           MQVGRKE GGEAIMM++ D+ + D ++  + ++ +I     I+L
Sbjct: 481 MQVGRKEIGGEAIMMVAIDKAVTDDVLSAVRSIEEITLADKIEL 524


Lambda     K      H
   0.317    0.134    0.374 

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: 739
Number of extensions: 15
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: 525
Length of database: 524
Length adjustment: 35
Effective length of query: 490
Effective length of database: 489
Effective search space:   239610
Effective search space used:   239610
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_078430830.1 BK574_RS10245 (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.3682612.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-203  662.7  10.4   2.4e-203  662.6  10.4    1.0  1  NCBI__GCF_002019605.1:WP_078430830.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002019605.1:WP_078430830.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  662.6  10.4  2.4e-203  2.4e-203       1     525 []       3     524 .]       3     524 .] 0.98

  Alignments for each domain:
  == domain 1  score: 662.6 bits;  conditional E-value: 2.4e-203
                             TIGR01327   1 kvlvadklseegie.llkekelevdvktglskeellekikdydalivRSatkvteelleaaekLkvigRaGvG 72 
                                           ++lv+d +s+eg+  ll++++++  ++++++  e+ ++++++da++vRSat+vt+el+e++++Lk+i+RaGvG
  NCBI__GCF_002019605.1:WP_078430830.1   3 NILVSDAMSKEGLLpLLESEQVNC-IQKNVT--EVQQELHTFDAILVRSATTVTAELIEKMPNLKIIARAGVG 72 
                                           59**********998999999887.777776..56778*********************************** PP

                             TIGR01327  73 vDNidieaatkkGilvvNaPegntisaaElalalllalaRkipqadksvkekkWerkkflGtElygktlGviG 145
                                           vDNidieaatk Gi+vvNaP+gntis+aE+++ ++ alaRkipqa++s+k ++W+rk+f GtEl+gktlG++G
  NCBI__GCF_002019605.1:WP_078430830.1  73 VDNIDIEAATKAGIVVVNAPDGNTISTAEHTFSMICALARKIPQANQSIKLGEWNRKAFQGTELRGKTLGIVG 145
                                           ************************************************************************* PP

                             TIGR01327 146 lGriGsevakrakalgmkvlayDPyiseekaeklgvellkdldellaeaDvitvHvPltketkgligkeelak 218
                                           +GriGs++akraka++m+ l++DP++++++aeklgv   ++l+e+l++aD+itvH+Pltk+tkg++g e++ k
  NCBI__GCF_002019605.1:WP_078430830.1 146 FGRIGSQLAKRAKAFEMQPLVFDPFLTKARAEKLGVV-PATLEEVLEKADIITVHTPLTKDTKGILGMENIGK 217
                                           ************************************9.788******************************** PP

                             TIGR01327 219 mKkgviivNcaRGGiidEkALvealeegkvraaalDvfekEPptdnklleldnvvvtpHlgAsteEaqenvav 291
                                           +K+gv+++NcaRGGiidE AL ++le+g+v++aalDvfe+EP+ dn l+eldnv++tpH++Ast+Eaq nva+
  NCBI__GCF_002019605.1:WP_078430830.1 218 TKRGVYLINCARGGIIDEVALKHYLENGHVAGAALDVFEEEPAIDNALIELDNVIATPHIAASTKEAQLNVAA 290
                                           ************************************************************************* PP

                             TIGR01327 292 evaeevlealkgevvesavNlpaldaeeleklkpyldlaeklGklasqllkeavkkvevtleGelaeeesell 364
                                           +v+eevl +l+g++v++++Nlp+l++e+  k+kpy +l++++G++ sq++k+ v+++ev + Ge+++ e+++ 
  NCBI__GCF_002019605.1:WP_078430830.1 291 QVSEEVLLFLEGNPVSNSINLPTLSKEVYGKIKPYYELTKTMGNILSQCMKTPVQEIEVFYGGEVTNLETSIT 363
                                           ************************************************************************* PP

                             TIGR01327 365 tsallkgllkevleeevnlvnAkavakergitveeskeeesedyknllevkveadkgevsvagtvleekepri 437
                                           t++l++g+l+++++++vn vnA  +akergi + e+  +++  y n+++  v++++ ++++ gt+++e  pri
  NCBI__GCF_002019605.1:WP_078430830.1 364 TRSLMAGFLSARVDASVNDVNASLIAKERGIVFGEKFLNNAYGYANIIHAIVHGENRTFEIKGTYVKEYGPRI 436
                                           ************************************************************************* PP

                             TIGR01327 438 veidgfevdlepegilliiknkDkpGvigkvgsllgeagiNiasmqlgrkekggealmllslDeevseevlee 510
                                           v i+gf vd+ p g+l++i+++D+pGvigk+g++l+e+++Nia+mq+grke ggea+m++ +D++v+++vl++
  NCBI__GCF_002019605.1:WP_078430830.1 437 VSINGFIVDFFPAGHLIYIQHNDRPGVIGKMGQMLAEYELNIATMQVGRKEIGGEAIMMVAIDKAVTDDVLSA 509
                                           ************************************************************************* PP

                             TIGR01327 511 ikevpeiksvklvel 525
                                           +++++ei+ +  +el
  NCBI__GCF_002019605.1:WP_078430830.1 510 VRSIEEITLADKIEL 524
                                           *******99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (525 nodes)
Target sequences:                          1  (524 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: 23.45
//
[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