Alignments for a candidate for cysK in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_5721 Cysteine synthase B (EC 2.5.1.47)

Query= BRENDA::P29848
         (303 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5721
          Length = 300

 Score =  408 bits (1048), Expect = e-119
 Identities = 202/290 (69%), Positives = 235/290 (81%)

Query: 3   TLEQTIGNTPLVKLQRLGPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGD 62
           T+   +GNTPLV+LQRL     + + +KLEGNNPAGSVKDR ALSMI   E RG+I+PGD
Sbjct: 7   TIADCVGNTPLVRLQRLPGVTTNTLLLKLEGNNPAGSVKDRPALSMITRGELRGQIRPGD 66

Query: 63  VLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGA 122
            LIEATSGNTGIALAM AA+KGY+M L+MPDN S ER+AAM AYGAELILVT+EQGMEGA
Sbjct: 67  TLIEATSGNTGIALAMAAAIKGYKMILIMPDNSSAERKAAMTAYGAELILVTQEQGMEGA 126

Query: 123 RDLALAMSERGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGTITGV 182
           RDLA  M   G GK+LDQF N DNP AHYT+TGPEIWRQT G ITHFVSSMGTTGTI G 
Sbjct: 127 RDLAERMQAEGRGKVLDQFANGDNPEAHYTSTGPEIWRQTDGTITHFVSSMGTTGTIMGT 186

Query: 183 SRFLREQEKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDEVLDIHQNDAENTMR 242
           SR+L+EQ   V I+GLQP EGS+IPGIRRWP EY+P I+ A  VD ++D+ Q++AE+T R
Sbjct: 187 SRYLKEQNPNVQIIGLQPMEGSAIPGIRRWPEEYLPKIYQADRVDRIIDMAQSEAEDTTR 246

Query: 243 ELAVREGIFCGVSSGGAVAGALRVARATPGAIVVAIICDRGDRYLSTGVF 292
            LA  EGIFCGVSSGGAVAG LR+++    A++VAIICDRGDRYLSTG+F
Sbjct: 247 RLAREEGIFCGVSSGGAVAGMLRLSKEVENAVIVAIICDRGDRYLSTGIF 296


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: 373
Number of extensions: 8
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: 303
Length of database: 300
Length adjustment: 27
Effective length of query: 276
Effective length of database: 273
Effective search space:    75348
Effective search space used:    75348
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 Pf6N2E2_5721 (Cysteine synthase B (EC 2.5.1.47))
to HMM TIGR01138 (cysM: cysteine synthase B (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/TIGR01138.hmm
# target sequence database:        /tmp/gapView.4543.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01138  [M=290]
Accession:   TIGR01138
Description: cysM: cysteine synthase B
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   4.3e-165  534.3   0.2   4.9e-165  534.1   0.2    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5721  Cysteine synthase B (EC 2.5.1.47


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5721  Cysteine synthase B (EC 2.5.1.47)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  534.1   0.2  4.9e-165  4.9e-165       1     290 []       7     296 ..       7     296 .. 1.00

  Alignments for each domain:
  == domain 1  score: 534.1 bits;  conditional E-value: 4.9e-165
                                      TIGR01138   1 tilklvGntplvrlkrllpeedsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlie 64 
                                                    ti+++vGntplvrl+rl++ + +++l+klegnnpaGsvkdrpalsmi++ e+rG+i++Gd+lie
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5721   7 TIADCVGNTPLVRLQRLPGVTTNTLLLKLEGNNPAGSVKDRPALSMITRGELRGQIRPGDTLIE 70 
                                                    89************************************************************** PP

                                      TIGR01138  65 atsGntGialamvaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelv 128
                                                    atsGntGialam+aa+kGyk++l+mpdn+s+erkaa++ayGaelilv++e+GmeGardla++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5721  71 ATSGNTGIALAMAAAIKGYKMILIMPDNSSAERKAAMTAYGAELILVTQEQGMEGARDLAERMQ 134
                                                    **************************************************************** PP

                                      TIGR01138 129 rkgeeklldqfnnpdnpkahytstGieiwqqtkGrithfvsslGttGtimGvsrflkeqnpavq 192
                                                     +g++k+ldqf+n+dnp+ahytstG+eiw+qt+G ithfvss+GttGtimG+sr+lkeqnp+vq
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5721 135 AEGRGKVLDQFANGDNPEAHYTSTGPEIWRQTDGTITHFVSSMGTTGTIMGTSRYLKEQNPNVQ 198
                                                    **************************************************************** PP

                                      TIGR01138 193 ivGlqpaegsaieGlrrieseylpgifdaslvdrvvdveqedaediarelakkegifvGvssGg 256
                                                    i+Glqp+egsai+G+rr+++eylp+i++a +vdr++d+ q++aed+ r+la++egif+GvssGg
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5721 199 IIGLQPMEGSAIPGIRRWPEEYLPKIYQADRVDRIIDMAQSEAEDTTRRLAREEGIFCGVSSGG 262
                                                    **************************************************************** PP

                                      TIGR01138 257 avaaalrlarelekavvvaiicdrGdrylstgvf 290
                                                    ava++lrl++e+e+av+vaiicdrGdrylstg+f
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5721 263 AVAGMLRLSKEVENAVIVAIICDRGDRYLSTGIF 296
                                                    ********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (300 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.85
//
[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