Alignments for a candidate for cysK in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Pedobacter sp. GW460-11-11-14-LB5

Align S-sulfo-L-cysteine synthase (O-acetyl-L-serine-dependent) (EC 2.5.1.144); cysteine synthase (EC 2.5.1.47) (characterized)
to candidate CA265_RS10150 CA265_RS10150 cysteine synthase B

Query= BRENDA::P29848
         (303 letters)



>FitnessBrowser__Pedo557:CA265_RS10150
          Length = 290

 Score =  310 bits (795), Expect = 2e-89
 Identities = 161/289 (55%), Positives = 204/289 (70%), Gaps = 9/289 (3%)

Query: 8   IGNTPLVKLQRLGPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDVLIEA 67
           IGNTP+ +LQ+L  +    ++ KLEGNNP GSVKDRA+L+MI  A +RG++ PG  L+EA
Sbjct: 8   IGNTPMAELQKLNINPAVRVFAKLEGNNPGGSVKDRASLNMIRSAIERGDVVPGTKLVEA 67

Query: 68  TSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGARDLAL 127
           TSGNTGIALAMIA+L    ++L+MP N ++ER+  M A+GA++ L+   + +E  RD A 
Sbjct: 68  TSGNTGIALAMIASLYNLEIELVMPANSTRERKVTMEAFGAKVTLL---ESIEDCRDYA- 123

Query: 128 AMSERGEGK---LLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGTITGVSR 184
              E+G  K   LL+QF NPDN  AHY TTGPEIWR T G ITHFVSSMGTTGTI G SR
Sbjct: 124 --EEKGVSKGYFLLNQFANPDNYLAHYKTTGPEIWRDTEGEITHFVSSMGTTGTIMGCSR 181

Query: 185 FLREQEKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDEVLDIHQNDAENTMREL 244
           F +E+   + I+G QP EGSSIPGIRRWP EY+P IF+   VD V+DI Q +A    R +
Sbjct: 182 FFKEKNNDIQIIGCQPTEGSSIPGIRRWPEEYLPKIFDPLRVDRVMDIAQEEATLMSRRM 241

Query: 245 AVREGIFCGVSSGGAVAGALRVARATPGAIVVAIICDRGDRYLSTGVFG 293
           A  EG+F G+SSGGA A AL++A       +V I CDRGDRYLS+ +FG
Sbjct: 242 AKEEGLFAGMSSGGACAAALKLASELDKGTIVFIACDRGDRYLSSDLFG 290


Lambda     K      H
   0.316    0.134    0.386 

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: 307
Number of extensions: 14
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: 303
Length of database: 290
Length adjustment: 26
Effective length of query: 277
Effective length of database: 264
Effective search space:    73128
Effective search space used:    73128
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: 48 (23.1 bits)

Align candidate CA265_RS10150 CA265_RS10150 (cysteine synthase B)
to HMM TIGR01136 (cysteine synthase (EC 2.5.1.47))

# 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/TIGR01136.hmm
# target sequence database:        /tmp/gapView.32074.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01136  [M=299]
Accession:   TIGR01136
Description: cysKM: cysteine 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.3e-108  346.4   0.0   8.2e-108  346.2   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS10150  CA265_RS10150 cysteine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS10150  CA265_RS10150 cysteine synthase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.2   0.0  8.2e-108  8.2e-108       2     299 .]       5     289 ..       4     289 .. 0.97

  Alignments for each domain:
  == domain 1  score: 346.2 bits;  conditional E-value: 8.2e-108
                                  TIGR01136   2 eeliGntPlvrln.lseelkaevlvKlEsrnPsgSvKdRialsmildAekrgllkkgktiieatSGNt 68 
                                                 +liGntP+ +l+ l+ + +++v++KlE++nP+gSvKdR++l+mi +A +rg + +g++++eatSGNt
  lcl|FitnessBrowser__Pedo557:CA265_RS10150   5 IDLIGNTPMAELQkLNINPAVRVFAKLEGNNPGGSVKDRASLNMIRSAIERGDVVPGTKLVEATSGNT 72 
                                                589**********999999************************************************* PP

                                  TIGR01136  69 GiaLAmvaaakgyklilvmpetmslERrkllkayGaelvlteaeegmkgaiekakelaeeepekyvll 136
                                                GiaLAm+a   ++++ lvmp++ + ER+ +++a+Ga++ l e+    + +++ a+e   +++  y+ll
  lcl|FitnessBrowser__Pedo557:CA265_RS10150  73 GIALAMIASLYNLEIELVMPANSTRERKVTMEAFGAKVTLLES---IEDCRDYAEEKGVSKG--YFLL 135
                                                ****************************************876...5678999999998866..99** PP

                                  TIGR01136 137 kqfeNpaNpeaHrkttgpEilkdtdgkidafvagvGtgGtitGvgrvlkekkpnvkivavePaespvl 204
                                                +qf+Np+N  aH+kttgpEi++dt+g+i++fv+++Gt+Gti+G +r++kek+++++i++++P+e++  
  lcl|FitnessBrowser__Pedo557:CA265_RS10150 136 NQFANPDNYLAHYKTTGPEIWRDTEGEITHFVSSMGTTGTIMGCSRFFKEKNNDIQIIGCQPTEGSS- 202
                                                ******************************************************************9. PP

                                  TIGR01136 205 segkpgphkiqgigagfiPkildeelldevikvededaietarrlakeegilvGiSsGaavaaalkva 272
                                                + g      i++++++++Pki+d   +d+v+++ +e+a+ ++rr+akeeg+++G+SsG+a+aaalk+a
  lcl|FitnessBrowser__Pedo557:CA265_RS10150 203 IPG------IRRWPEEYLPKIFDPLRVDRVMDIAQEEATLMSRRMAKEEGLFAGMSSGGACAAALKLA 264
                                                888......9********************************************************** PP

                                  TIGR01136 273 kklekedkkivvilpdagerYLstelf 299
                                                 +l+  + +iv i++d+g+rYLs++lf
  lcl|FitnessBrowser__Pedo557:CA265_RS10150 265 SELD--KGTIVFIACDRGDRYLSSDLF 289
                                                ***8..69*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (290 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.77
//
[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