Alignments for a candidate for CBS in Nocardiopsis lucentensis DSM 44048

GapMind for Amino acid biosynthesis

Alignments for a candidate for CBS in Nocardiopsis lucentensis DSM 44048

Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate WP_017598059.1 D471_RS0107595 cystathionine beta-synthase

Query= SwissProt::P9WP51
         (464 letters)



>NCBI__GCF_000341125.1:WP_017598059.1
          Length = 455

 Score =  614 bits (1584), Expect = e-180
 Identities = 298/458 (65%), Positives = 357/458 (77%), Gaps = 4/458 (0%)

Query: 1   MRIAQHISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQ 60
           MR+   + +L+G TPLVRL  V    A T+ AKVEY NPGGS KDRIA++M+EAAE SG+
Sbjct: 1   MRVHDSLIDLVGDTPLVRLRKVTEGLAPTILAKVEYFNPGGSVKDRIALRMVEAAEKSGE 60

Query: 61  LKPGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAV 120
           L+ GGTIVEPTSGNTG+GLA+VAQ +GY+CVFVCPDKV  DK  VL AYGAEVVVCPT V
Sbjct: 61  LRAGGTIVEPTSGNTGIGLAMVAQEKGYRCVFVCPDKVGADKLAVLRAYGAEVVVCPTTV 120

Query: 121 PPHDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGI 180
            P  P SYYSVSDRL  +I GAWKP+QY N   P SHY +TGPEIW  TEG+VTHFVAGI
Sbjct: 121 APEHPDSYYSVSDRLAEEIPGAWKPNQYENQNNPESHYHSTGPEIWDQTEGRVTHFVAGI 180

Query: 181 GTGGTITGAGRYLKEVSGGRVRIVGADPEGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVP 240
           GTGGTI+G GRYLKEVS GR +++GADPEGSVYSGG+GRPYLVEGVGED WP  YD  + 
Sbjct: 181 GTGGTISGTGRYLKEVSDGRGKVIGADPEGSVYSGGSGRPYLVEGVGEDIWPGTYDTGIC 240

Query: 241 DEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRG 300
           D+I+AVSD +SF MTRRLAREEA+LVGGSCG+AV AAL+VAE+AGPD +IVVLLPDGGRG
Sbjct: 241 DDIVAVSDKESFLMTRRLAREEALLVGGSCGLAVEAALRVAEDAGPDDVIVVLLPDGGRG 300

Query: 301 YMSKIFNDAWMSSYGFLRSRLDGSTEQSTVGDVLRRKSGALPALVHTHPSETVRDAIGIL 360
           Y+ KIFND WM+ YGF    L   TE++T G VL  K G +P  VHTHP E++  A+ I+
Sbjct: 301 YLGKIFNDEWMADYGF----LSAETEEATAGQVLNGKGGEMPDFVHTHPHESIGTAVAIM 356

Query: 361 REYGVSQMPVVGAEPPVMAGEVAGSVSERELLSAVFEGRAKLADAVSAHMSPPLRMIGAG 420
           REYGVSQ+PV+  EPPVMA EV GS++ER++L A+F+GRA+L D+V  HM  PL  +G G
Sbjct: 357 REYGVSQLPVMKEEPPVMAAEVVGSIAERDVLDALFDGRAQLDDSVETHMGKPLATVGTG 416

Query: 421 ELVSAAGKALRDWDALMVVEEGKPVGVITRYDLLGFLS 458
             V    + LR   AL+V+ +G+PVG++TR DLL  LS
Sbjct: 417 TPVGDCVRLLRGSGALVVLRDGRPVGILTRQDLLAHLS 454


Lambda     K      H
   0.316    0.135    0.398 

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: 882
Number of extensions: 38
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: 464
Length of database: 455
Length adjustment: 33
Effective length of query: 431
Effective length of database: 422
Effective search space:   181882
Effective search space used:   181882
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: 51 (24.3 bits)

Align candidate WP_017598059.1 D471_RS0107595 (cystathionine beta-synthase)
to HMM TIGR01137 (cystathionine beta-synthase (EC 4.2.1.22))

# 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/TIGR01137.hmm
# target sequence database:        /tmp/gapView.3675478.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01137  [M=457]
Accession:   TIGR01137
Description: cysta_beta: cystathionine beta-synthase
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-193  630.0   0.0   1.2e-193  629.9   0.0    1.0  1  NCBI__GCF_000341125.1:WP_017598059.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000341125.1:WP_017598059.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  629.9   0.0  1.2e-193  1.2e-193       2     456 ..       4     453 ..       3     454 .. 0.97

  Alignments for each domain:
  == domain 1  score: 629.9 bits;  conditional E-value: 1.2e-193
                             TIGR01137   2 adnildliGntPlvrlnkvskglkaevlakveffnaGGsvkdrialrmiedaeksGrlkpgdtliePtsGntG 74 
                                           +d+++dl+G+tPlvrl+kv++gl++++lakve+fn+GGsvkdrialrm+e+aeksG+l+ g+t++ePtsGntG
  NCBI__GCF_000341125.1:WP_017598059.1   4 HDSLIDLVGDTPLVRLRKVTEGLAPTILAKVEYFNPGGSVKDRIALRMVEAAEKSGELRAGGTIVEPTSGNTG 76 
                                           789********************************************************************** PP

                             TIGR01137  75 iGlalvaaikGykciivlPekvseekvdvlkalGaeivrtPtaaafdsPesyigvakrlekeipgavildqya 147
                                           iGla+va+ kGy+c++v+P+kv  +k+ vl+a+Gae+v++Pt +a+++P+sy++v++rl +eipga++++qy+
  NCBI__GCF_000341125.1:WP_017598059.1  77 IGLAMVAQEKGYRCVFVCPDKVGADKLAVLRAYGAEVVVCPTTVAPEHPDSYYSVSDRLAEEIPGAWKPNQYE 149
                                           ************************************************************************* PP

                             TIGR01137 148 nasnPlahydttgeeileqlegkldalvagvGtGGtitGiarklk.ekedkvrivGadPeGsilaepeelnkt 219
                                           n++nP++hy++tg+ei++q+eg+++++vag+GtGGti+G++r+lk +++++ +++GadPeGs+++++     +
  NCBI__GCF_000341125.1:WP_017598059.1 150 NQNNPESHYHSTGPEIWDQTEGRVTHFVAGIGTGGTISGTGRYLKeVSDGRGKVIGADPEGSVYSGG-----S 217
                                           *********************************************88999*****************.....9 PP

                             TIGR01137 220 ektdykveGiGydfiPtvldrkvvdeiiktddkesfkmarrlikeegllvgGssGsavvaalkvaeeelkedd 292
                                           ++ +y+veG+G+d +P  +d  + d+i++++dkesf m+rrl++ee+llvgGs+G av aal+vae+++ +d 
  NCBI__GCF_000341125.1:WP_017598059.1 218 GR-PYLVEGVGEDIWPGTYDTGICDDIVAVSDKESFLMTRRLAREEALLVGGSCGLAVEAALRVAEDAGPDD- 288
                                           99.9****************************************************************9999. PP

                             TIGR01137 293 vivvllpdsirnyltkflndeWlkdkgfldd..esltkkdvlkvfgnarvkdlalkalvtvketetvadaiei 363
                                           vivvllpd++r+yl k++ndeW++d+gfl+   e++t  +v      ++ k+++++  v++++ e ++ a+ i
  NCBI__GCF_000341125.1:WP_017598059.1 289 VIVVLLPDGGRGYLGKIFNDEWMADYGFLSAetEEATAGQV------LNGKGGEMPDFVHTHPHESIGTAVAI 355
                                           *****************************983344444444......56899********************* PP

                             TIGR01137 364 lrekGfdqlPvvk.....eagkvlgsvtlrellsallakkakledavkkklskklkkidegeklsdlskvlek 431
                                           +re+G++qlPv+k     +a++v+gs+++r++l+al+ ++a+l+d+v+ ++ k+l ++++g+ ++d  ++l+ 
  NCBI__GCF_000341125.1:WP_017598059.1 356 MREYGVSQLPVMKeeppvMAAEVVGSIAERDVLDALFDGRAQLDDSVETHMGKPLATVGTGTPVGDCVRLLRG 428
                                           *************9*********************************************************** PP

                             TIGR01137 432 adaalvveeekpigvvtkidllsfl 456
                                           + a++v+ +++p+g++t++dll++l
  NCBI__GCF_000341125.1:WP_017598059.1 429 SGALVVLRDGRPVGILTRQDLLAHL 453
                                           **********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (457 nodes)
Target sequences:                          1  (455 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: 00:00:00.00
# Mc/sec: 24.64
//
[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