Alignments for a candidate for cysK in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for cysK in Klebsiella michiganensis M5al

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 BWI76_RS20685 BWI76_RS20685 cysteine synthase B

Query= BRENDA::P29848
         (303 letters)



>FitnessBrowser__Koxy:BWI76_RS20685
          Length = 303

 Score =  569 bits (1467), Expect = e-167
 Identities = 283/303 (93%), Positives = 293/303 (96%)

Query: 1   MNTLEQTIGNTPLVKLQRLGPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKP 60
           MNTLE TIGNTPLVKLQR+GPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKP
Sbjct: 1   MNTLEYTIGNTPLVKLQRMGPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKP 60

Query: 61  GDVLIEATSGNTGIALAMIAALKGYRMKLLMPDNMSQERRAAMRAYGAELILVTKEQGME 120
           GDVLIEATSGNTGIALAMIAALKGY+MKLLMPDNMSQERRAAMRAYGAELILVTKEQGME
Sbjct: 61  GDVLIEATSGNTGIALAMIAALKGYQMKLLMPDNMSQERRAAMRAYGAELILVTKEQGME 120

Query: 121 GARDLALAMSERGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTSGRITHFVSSMGTTGTIT 180
           GARDLALAM++RGEGKLLDQFNNPDNPYAHYTTTGPEIWRQT GRITHFVSSMGTTGTIT
Sbjct: 121 GARDLALAMAQRGEGKLLDQFNNPDNPYAHYTTTGPEIWRQTDGRITHFVSSMGTTGTIT 180

Query: 181 GVSRFLREQEKPVTIVGLQPEEGSSIPGIRRWPAEYMPGIFNASLVDEVLDIHQNDAENT 240
           GVSRFLREQ+K V+IVGLQPEEGSSIPGIRRWPAEYMPGIFNA LVD VLDIHQ DAENT
Sbjct: 181 GVSRFLREQDKAVSIVGLQPEEGSSIPGIRRWPAEYMPGIFNAQLVDVVLDIHQQDAENT 240

Query: 241 MRELAVREGIFCGVSSGGAVAGALRVARATPGAIVVAIICDRGDRYLSTGVFGEEHFSQG 300
           MR LAV+EGIFCGVSSGGAV GALRVAR  PGA+VVAI+CDRGDRYLSTGVFGEEHF+QG
Sbjct: 241 MRMLAVKEGIFCGVSSGGAVVGALRVARENPGAVVVAIVCDRGDRYLSTGVFGEEHFTQG 300

Query: 301 AGI 303
           AGI
Sbjct: 301 AGI 303


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: 491
Number of extensions: 9
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: 303
Length adjustment: 27
Effective length of query: 276
Effective length of database: 276
Effective search space:    76176
Effective search space used:    76176
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 BWI76_RS20685 BWI76_RS20685 (cysteine synthase B)
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.2774.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   5.3e-169  547.1   0.2   5.9e-169  547.0   0.2    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS20685  BWI76_RS20685 cysteine synthase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS20685  BWI76_RS20685 cysteine synthase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  547.0   0.2  5.9e-169  5.9e-169       1     290 []       3     292 ..       3     292 .. 1.00

  Alignments for each domain:
  == domain 1  score: 547.0 bits;  conditional E-value: 5.9e-169
                               TIGR01138   1 tilklvGntplvrlkrllpeedsevlvklegnnpaGsvkdrpalsmiveaekrGeikeGdvlieatsGntG 71 
                                             t++ ++Gntplv+l+r++p+++se++vklegnnpaGsvkdr+alsmiveaekrGeik+GdvlieatsGntG
  lcl|FitnessBrowser__Koxy:BWI76_RS20685   3 TLEYTIGNTPLVKLQRMGPDNGSEIWVKLEGNNPAGSVKDRAALSMIVEAEKRGEIKPGDVLIEATSGNTG 73 
                                             7899******************************************************************* PP

                               TIGR01138  72 ialamvaalkGykvkllmpdnvseerkaalkayGaelilvdkeeGmeGardlarelvrkgeeklldqfnnp 142
                                             ialam+aalkGy++kllmpdn+s+er+aa++ayGaelilv+ke+GmeGardla  ++++ge+klldqfnnp
  lcl|FitnessBrowser__Koxy:BWI76_RS20685  74 IALAMIAALKGYQMKLLMPDNMSQERRAAMRAYGAELILVTKEQGMEGARDLALAMAQRGEGKLLDQFNNP 144
                                             *********************************************************************** PP

                               TIGR01138 143 dnpkahytstGieiwqqtkGrithfvsslGttGtimGvsrflkeqnpavqivGlqpaegsaieGlrriese 213
                                             dnp+ahyt+tG+eiw+qt+Grithfvss+GttGti+Gvsrfl+eq++av ivGlqp+egs+i+G+rr+++e
  lcl|FitnessBrowser__Koxy:BWI76_RS20685 145 DNPYAHYTTTGPEIWRQTDGRITHFVSSMGTTGTITGVSRFLREQDKAVSIVGLQPEEGSSIPGIRRWPAE 215
                                             *********************************************************************** PP

                               TIGR01138 214 ylpgifdaslvdrvvdveqedaediarelakkegifvGvssGgavaaalrlarelekavvvaiicdrGdry 284
                                             y+pgif+a lvd v+d++q+dae+++r la+kegif+GvssGgav++alr+are++ avvvai+cdrGdry
  lcl|FitnessBrowser__Koxy:BWI76_RS20685 216 YMPGIFNAQLVDVVLDIHQQDAENTMRMLAVKEGIFCGVSSGGAVVGALRVARENPGAVVVAIVCDRGDRY 286
                                             *********************************************************************** PP

                               TIGR01138 285 lstgvf 290
                                             lstgvf
  lcl|FitnessBrowser__Koxy:BWI76_RS20685 287 LSTGVF 292
                                             *****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (303 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: 8.49
//
[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