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

GapMind for Amino acid biosynthesis

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

Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate WP_005459144.1 SACCYDRAFT_RS20705 cystathionine beta-synthase

Query= SwissProt::P9WP51
         (464 letters)



>NCBI__GCF_000244975.1:WP_005459144.1
          Length = 457

 Score =  679 bits (1753), Expect = 0.0
 Identities = 332/458 (72%), Positives = 382/458 (83%), Gaps = 4/458 (0%)

Query: 1   MRIAQHISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQ 60
           M  A+H+++L+G TPLV+LN++  D    V AKVEYLNPGGS KDRIA +MIEAAEASG+
Sbjct: 1   MDYAEHVTDLVGNTPLVKLNALTQDVEPLVLAKVEYLNPGGSVKDRIAQRMIEAAEASGE 60

Query: 61  LKPGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAV 120
           L+PGGTIVEPTSGNTGVGLA+VAQR+GY+CVFVCPDKVSEDKRNVL AYGAEVVVCPTAV
Sbjct: 61  LRPGGTIVEPTSGNTGVGLAMVAQRKGYRCVFVCPDKVSEDKRNVLKAYGAEVVVCPTAV 120

Query: 121 PPHDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGI 180
           PP  P SYYSVSDRL R+I+GAWKP+QYANP  P SHY +TGPEIW  TEGKVTHFVAG+
Sbjct: 121 PPEHPESYYSVSDRLTREIEGAWKPNQYANPHNPESHYHSTGPEIWKQTEGKVTHFVAGV 180

Query: 181 GTGGTITGAGRYLKEVSGGRVRIVGADPEGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVP 240
           GTGGTI+G GRYLKEVS GRV++VGADPEGSVYSGG GRPYLVEGVGEDFWP  YD  V 
Sbjct: 181 GTGGTISGTGRYLKEVSEGRVKVVGADPEGSVYSGGTGRPYLVEGVGEDFWPDTYDCGVA 240

Query: 241 DEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRG 300
           DEII VSD+DSF +TRRLAREE +LVGGSCGMAV AAL++A+  GPD +IVVLLPDGGRG
Sbjct: 241 DEIIPVSDADSFTVTRRLAREEGLLVGGSCGMAVAAALELAKRCGPDDVIVVLLPDGGRG 300

Query: 301 YMSKIFNDAWMSSYGFLRSRLDGSTEQSTVGDVLRRKSGALPALVHTHPSETVRDAIGIL 360
           Y+ K+FND WMSSYGF    L   ++ +TV DVLRRK G LP LVHTHP+ETV +A+ IL
Sbjct: 301 YLGKVFNDTWMSSYGF----LSPESQDATVSDVLRRKDGTLPDLVHTHPNETVAEAVAIL 356

Query: 361 REYGVSQMPVVGAEPPVMAGEVAGSVSERELLSAVFEGRAKLADAVSAHMSPPLRMIGAG 420
           RE+GVSQMPVV AEPPVMA EV G+V+ER+LL A+F G+A LAD +  HMSPPL  IGAG
Sbjct: 357 REFGVSQMPVVSAEPPVMAAEVVGAVNERDLLEALFTGKAALADRLEQHMSPPLPTIGAG 416

Query: 421 ELVSAAGKALRDWDALMVVEEGKPVGVITRYDLLGFLS 458
           E + AA KAL      +V+E+GKP GV+TR+DLL FLS
Sbjct: 417 EQIGAAMKALGAASGALVLEDGKPAGVVTRHDLLAFLS 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: 888
Number of extensions: 36
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: 457
Length adjustment: 33
Effective length of query: 431
Effective length of database: 424
Effective search space:   182744
Effective search space used:   182744
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_005459144.1 SACCYDRAFT_RS20705 (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.3183584.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-203  662.6   0.0   1.5e-203  662.4   0.0    1.0  1  NCBI__GCF_000244975.1:WP_005459144.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000244975.1:WP_005459144.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  662.4   0.0  1.5e-203  1.5e-203       2     457 .]       4     454 ..       3     454 .. 0.98

  Alignments for each domain:
  == domain 1  score: 662.4 bits;  conditional E-value: 1.5e-203
                             TIGR01137   2 adnildliGntPlvrlnkvskglkaevlakveffnaGGsvkdrialrmiedaeksGrlkpgdtliePtsGntG 74 
                                           a+++ dl+GntPlv+ln +++++++ vlakve++n+GGsvkdria+rmie+ae+sG+l+pg+t++ePtsGntG
  NCBI__GCF_000244975.1:WP_005459144.1   4 AEHVTDLVGNTPLVKLNALTQDVEPLVLAKVEYLNPGGSVKDRIAQRMIEAAEASGELRPGGTIVEPTSGNTG 76 
                                           5799********************************************************************* PP

                             TIGR01137  75 iGlalvaaikGykciivlPekvseekvdvlkalGaeivrtPtaaafdsPesyigvakrlekeipgavildqya 147
                                           +Gla+va++kGy+c++v+P+kvse+k++vlka+Gae+v++Pta+ +++Pesy++v++rl++ei+ga++++qya
  NCBI__GCF_000244975.1:WP_005459144.1  77 VGLAMVAQRKGYRCVFVCPDKVSEDKRNVLKAYGAEVVVCPTAVPPEHPESYYSVSDRLTREIEGAWKPNQYA 149
                                           ************************************************************************* PP

                             TIGR01137 148 nasnPlahydttgeeileqlegkldalvagvGtGGtitGiarklk.ekedkvrivGadPeGsilaepeelnkt 219
                                           n++nP++hy++tg+ei++q+egk++++vagvGtGGti+G++r+lk ++e++v++vGadPeGs+++++     t
  NCBI__GCF_000244975.1:WP_005459144.1 150 NPHNPESHYHSTGPEIWKQTEGKVTHFVAGVGTGGTISGTGRYLKeVSEGRVKVVGADPEGSVYSGG-----T 217
                                           *********************************************8899******************.....* PP

                             TIGR01137 220 ektdykveGiGydfiPtvldrkvvdeiiktddkesfkmarrlikeegllvgGssGsavvaalkvaeeelkedd 292
                                           ++ +y+veG+G+df+P+ +d  v+deii ++d +sf+++rrl++eegllvgGs+G+av+aal+ a++ + +d 
  NCBI__GCF_000244975.1:WP_005459144.1 218 GR-PYLVEGVGEDFWPDTYDCGVADEIIPVSDADSFTVTRRLAREEGLLVGGSCGMAVAAALELAKRCGPDD- 288
                                           **.9**************************************************************999988. PP

                             TIGR01137 293 vivvllpdsirnyltkflndeWlkdkgflddesltkkdvlkvfgnarvkdlalkalvtvketetvadaieilr 365
                                           vivvllpd++r+yl k++nd W++++gfl++es+  + +      +r+kd++l+ lv+++++etva+a+ ilr
  NCBI__GCF_000244975.1:WP_005459144.1 289 VIVVLLPDGGRGYLGKVFNDTWMSSYGFLSPESQDATVSD----VLRRKDGTLPDLVHTHPNETVAEAVAILR 357
                                           *****************************99765443332....36799************************ PP

                             TIGR01137 366 ekGfdqlPvvk.....eagkvlgsvtlrellsallakkakledavkkklskklkkidegeklsdlskvlekad 433
                                           e G++q+Pvv+     +a++v+g v +r+ll+al+++ka l+d +++++s +l +i++ge++++++k+l  a+
  NCBI__GCF_000244975.1:WP_005459144.1 358 EFGVSQMPVVSaeppvMAAEVVGAVNERDLLEALFTGKAALADRLEQHMSPPLPTIGAGEQIGAAMKALGAAS 430
                                           ************************************************************************* PP

                             TIGR01137 434 aalvveeekpigvvtkidllsfla 457
                                            alv+e++kp gvvt+ dll+fl+
  NCBI__GCF_000244975.1:WP_005459144.1 431 GALVLEDGKPAGVVTRHDLLAFLS 454
                                           **********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (457 nodes)
Target sequences:                          1  (457 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: 19.55
//
[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