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.16909.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.31
//
[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:

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:

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:

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:

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