Alignments for a candidate for CBS in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for CBS in Echinicola vietnamensis KMM 6221, DSM 17526

Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate Echvi_4660 Echvi_4660 cystathionine beta-synthase

Query= SwissProt::P9WP51
         (464 letters)



>FitnessBrowser__Cola:Echvi_4660
          Length = 456

 Score =  362 bits (928), Expect = e-104
 Identities = 208/469 (44%), Positives = 287/469 (61%), Gaps = 25/469 (5%)

Query: 3   IAQHISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLK 62
           I   I + IG TPLV+LN +     GT+  KVEY NPG S KDR+A+KMI+ AE +G LK
Sbjct: 2   IYNSIIDTIGDTPLVKLNRLNKGIKGTIYVKVEYFNPGNSVKDRMAIKMIDDAEKAGILK 61

Query: 63  PGGTIVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPP 122
           PGGTI+E TSGNTG+GLALV   RGYKC+F   DK S++K +VL A GAEVVVCPT V P
Sbjct: 62  PGGTIIEGTSGNTGMGLALVGIARGYKCIFTMADKQSKEKIDVLKAMGAEVVVCPTNVSP 121

Query: 123 HDPASYYSVSDRLVRDIDGAWKPDQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGT 182
            DP SYYSV+ +L +DI  ++ P+QY N     +HY TTGPEIW DTEGK+THF AG+GT
Sbjct: 122 DDPRSYYSVAKKLNKDIPNSFYPNQYDNLSNWKAHYETTGPEIWKDTEGKITHFAAGVGT 181

Query: 183 GGTITGAGRYLKEVSGGRVRIVGADPEGSV---------YSGGAGRPYLVEGVGEDFWPA 233
           GGT++G  +YLKE +   V  VG D  GSV         +      PYL EG+GED  PA
Sbjct: 182 GGTMSGTAKYLKEQNPSIVS-VGIDTYGSVFKKYKETGEFDENEIYPYLTEGIGEDILPA 240

Query: 234 AYDPSVPDEIIAVSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVA-EEAGPDALIVV 292
             D S+ D  + V+D DS  MTRRL+REE + VG SCG AV  AL+ A +       +V+
Sbjct: 241 NVDFSMIDHFVKVTDKDSAVMTRRLSREEGLFVGWSCGSAVHGALEYARQHLTEQDTMVI 300

Query: 293 LLPDGGRGYMSKIFNDAWMSSYGFLRSRLDGSTEQSTVGDVLRRKSGALPALVHTHPSET 352
           +LPD G  Y+ K++ND WM ++GFL       T   T  D++  ++G+   LV     E 
Sbjct: 301 ILPDHGTRYLGKVYNDDWMKNHGFLE-----DTTFGTARDIISSRNGSY-ELVVAKKGEK 354

Query: 353 VRDAIGILREYGVSQMPVVGAEPPVMAGEVAGSVSERELLSAVFEGRAKLADA-VSAHMS 411
           V+ AI ++ E  VSQ+PV      V  G V GS+++ +LL+ + + + +L DA V   M 
Sbjct: 355 VKAAIHLMNERSVSQIPV------VEDGNVIGSLTDTKLLTKIIQ-KPELKDAPVEEVME 407

Query: 412 PPLRMIGAGELVSAAGKALRDWDALMVVEEGKPVGVITRYDLLGFLSEG 460
             ++ +     +      +    A++V ++   + +IT++D+LG +++G
Sbjct: 408 DSMKFVALDSTLDVLSSMVDKDKAVLVRDDLHQIHIITKHDILGAITKG 456


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: 548
Number of extensions: 18
Number of successful extensions: 5
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: 456
Length adjustment: 33
Effective length of query: 431
Effective length of database: 423
Effective search space:   182313
Effective search space used:   182313
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 Echvi_4660 Echvi_4660 (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.9973.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.2e-160  520.2   2.8   2.5e-160  520.0   2.8    1.0  1  lcl|FitnessBrowser__Cola:Echvi_4660  Echvi_4660 cystathionine beta-sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_4660  Echvi_4660 cystathionine beta-synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  520.0   2.8  2.5e-160  2.5e-160       2     454 ..       3     451 ..       2     454 .. 0.95

  Alignments for each domain:
  == domain 1  score: 520.0 bits;  conditional E-value: 2.5e-160
                            TIGR01137   2 adnildliGntPlvrlnkvskglkaevlakveffnaGGsvkdrialrmiedaeksGrlkpgdtliePtsGntGi 75 
                                           ++i+d iG+tPlv+ln+++kg+k++++ kve+fn+G svkdr+a +mi+daek G lkpg+t+ie tsGntG+
  lcl|FitnessBrowser__Cola:Echvi_4660   3 YNSIIDTIGDTPLVKLNRLNKGIKGTIYVKVEYFNPGNSVKDRMAIKMIDDAEKAGILKPGGTIIEGTSGNTGM 76 
                                          679*********************************************************************** PP

                            TIGR01137  76 GlalvaaikGykciivlPekvseekvdvlkalGaeivrtPtaaafdsPesyigvakrlekeipgavildqyana 149
                                          Glalv+  +Gykci+++ +k s+ek+dvlka+Gae+v++Pt++++d+P sy++vak+l+k+ip+++ ++qy+n 
  lcl|FitnessBrowser__Cola:Echvi_4660  77 GLALVGIARGYKCIFTMADKQSKEKIDVLKAMGAEVVVCPTNVSPDDPRSYYSVAKKLNKDIPNSFYPNQYDNL 150
                                          ************************************************************************** PP

                            TIGR01137 150 snPlahydttgeeileqlegkldalvagvGtGGtitGiarklkekedkvrivGadPeGsila...epeelnkte 220
                                          sn +ahy+ttg+ei++++egk++++ agvGtGGt++G+a++lke+++++  vG+d  Gs++    e  e+++ e
  lcl|FitnessBrowser__Cola:Echvi_4660 151 SNWKAHYETTGPEIWKDTEGKITHFAAGVGTGGTMSGTAKYLKEQNPSIVSVGIDTYGSVFKkykETGEFDENE 224
                                          ************************************************************76111566789999 PP

                            TIGR01137 221 ktdykveGiGydfiPtvldrkvvdeiiktddkesfkmarrlikeegllvgGssGsavvaalkvaeeelkeddvi 294
                                          + +y+ eGiG+d +P+ +d +++d+++k+ dk+s  m+rrl +eegl+vg s+Gsav +al++a+++l+e+d +
  lcl|FitnessBrowser__Cola:Echvi_4660 225 IYPYLTEGIGEDILPANVDFSMIDHFVKVTDKDSAVMTRRLSREEGLFVGWSCGSAVHGALEYARQHLTEQDTM 298
                                          99************************************************************************ PP

                            TIGR01137 295 vvllpdsirnyltkflndeWlkdkgflddesltkkdvlkvfgnarvkdlalkalvtvketetvadaieilrekG 368
                                          v++lpd +  yl k+ nd+W+k++gfl+d +  ++        +  ++++  +lv  k+ e+v++ai++++e+ 
  lcl|FitnessBrowser__Cola:Echvi_4660 299 VIILPDHGTRYLGKVYNDDWMKNHGFLEDTTFGTARDI-----ISSRNGS-YELVVAKKGEKVKAAIHLMNERS 366
                                          ****************************9766555442.....2344454.457778999************** PP

                            TIGR01137 369 fdqlPvvkeagkvlgsvtlrellsallakkakledavkkklskklkkidegeklsdlskvlekadaalvveeek 442
                                          ++q+Pvv e+g+v+gs t ++ll+++++k   ++ +v++++ + +k +   ++l  ls++++k++a+lv ++ +
  lcl|FitnessBrowser__Cola:Echvi_4660 367 VSQIPVV-EDGNVIGSLTDTKLLTKIIQKPELKDAPVEEVMEDSMKFVALDSTLDVLSSMVDKDKAVLVRDDLH 439
                                          ******9.689****************99999999*************************************** PP

                            TIGR01137 443 pigvvtkidlls 454
                                          +i+++tk d+l+
  lcl|FitnessBrowser__Cola:Echvi_4660 440 QIHIITKHDILG 451
                                          **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (457 nodes)
Target sequences:                          1  (456 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.00
//
[ok]

This GapMind analysis is from Apr 09 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