Alignments for a candidate for aroC in Desulfotomaculum ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Desulfotomaculum ruminis DSM 2154

Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate WP_013843078.1 DESRU_RS15750 chorismate synthase

Query= BRENDA::Q71Y87
         (388 letters)



>NCBI__GCF_000215085.1:WP_013843078.1
          Length = 387

 Score =  441 bits (1135), Expect = e-128
 Identities = 218/387 (56%), Positives = 283/387 (73%), Gaps = 2/387 (0%)

Query: 1   MRYLTAGESHGPGLTTIIEGLPAGMPLLAEDVNKELKRRQGGHGRGARMRIEKDQVQITA 60
           +R+LTAGESHGP LT I+EG+ AG+PL  E VN++L RRQGG+GRG RM+IE+DQ    +
Sbjct: 2   LRFLTAGESHGPVLTAIVEGMVAGLPLSREYVNRQLARRQGGYGRGGRMKIEQDQADFLS 61

Query: 61  GIRHGKTLGAPVAMFVENKDWKHWETVMSIEPVPEKNEKSRRVSRPRPGHADLVGGMKYG 120
           G+R G T G+P+ + V NKDW +W  +M+  P PE   + R V+RPRPGHADL G +KY 
Sbjct: 62  GVRGGLTTGSPITLQVVNKDWANWSEIMA--PGPEARLEERVVTRPRPGHADLAGAIKYN 119

Query: 121 HNDMRNVLERSSARETTVRVAAGAVAKKLLHELGIEVAGHVLEIGGTRANLTRDYAVSEI 180
             D+RN+LERSSARET VRVA G +A+ LL ELGI++ G V  IG   A L  +    ++
Sbjct: 120 QQDIRNILERSSARETAVRVAVGTIARALLAELGIQMTGWVRRIGSVEAVLEEEQTADQL 179

Query: 181 QETSEASPVRCLDGVAAEEMMQKIDDAKKNGDTIGGIVEVVVGGVPAGLGSYVQWDKKLD 240
           +E + AS + C DG A   M+++ID A+ NGD++GG+ E+ V  VPAGLGS+VQWD+KLD
Sbjct: 180 RELAGASQLLCPDGQAEAAMIREIDRARGNGDSLGGVFEIRVDHVPAGLGSHVQWDRKLD 239

Query: 241 AKIARAIVSINAFKGAEFGVGFEAARKPGSEVMDEILWSKEDGYTRRTNNLGGFEGGMTN 300
           +++A A++SI A KG E G+GF AA  PGS+V DEI +S E  Y R TN  GG EGG++N
Sbjct: 240 SRLAGALMSIQAIKGVEIGLGFGAAAVPGSQVHDEIFYSPEKSYYRATNRAGGIEGGISN 299

Query: 301 GMPIVVRGVMKPIPTLYKPLQSVDIDSKETFNASVERSDSCAVPAASVVAEAVVAWEVAV 360
           G P+VVR  MKPIPTLYKPL+SVD  SKE F ASVERSD+CAVPAA VV EAVVAWE+AV
Sbjct: 300 GEPLVVRAAMKPIPTLYKPLRSVDTGSKEPFTASVERSDACAVPAACVVGEAVVAWEIAV 359

Query: 361 AVLEKFDGDRFDTLKKHVEEHRNLTKE 387
           A+LEKF GD    L++ V++ R+  ++
Sbjct: 360 AILEKFGGDSLRELRERVDQWRSWIRQ 386


Lambda     K      H
   0.315    0.133    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: 438
Number of extensions: 21
Number of successful extensions: 3
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: 388
Length of database: 387
Length adjustment: 30
Effective length of query: 358
Effective length of database: 357
Effective search space:   127806
Effective search space used:   127806
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: 42 (22.0 bits)
S2: 50 (23.9 bits)

Align candidate WP_013843078.1 DESRU_RS15750 (chorismate synthase)
to HMM TIGR00033 (aroC: chorismate synthase (EC 4.2.3.5))

# 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/TIGR00033.hmm
# target sequence database:        /tmp/gapView.24624.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00033  [M=351]
Accession:   TIGR00033
Description: aroC: chorismate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.3e-126  405.6   0.0   9.5e-126  405.4   0.0    1.0  1  lcl|NCBI__GCF_000215085.1:WP_013843078.1  DESRU_RS15750 chorismate synthas


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000215085.1:WP_013843078.1  DESRU_RS15750 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.4   0.0  9.5e-126  9.5e-126       1     350 [.       2     367 ..       2     368 .. 0.94

  Alignments for each domain:
  == domain 1  score: 405.4 bits;  conditional E-value: 9.5e-126
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               lr++t+GeSHg+ l+ai++G+ agl+l+ e+++++l+rR+ g++r+ rm+ E+D+ ++lsGv+ G TtG
  lcl|NCBI__GCF_000215085.1:WP_013843078.1   2 LRFLTAGESHGPVLTAIVEGMVAGLPLSREYVNRQLARRQGGYGRGGRMKIEQDQADFLSGVRGGLTTG 70 
                                               699****************************************************************** PP

                                 TIGR00033  70 aPiallikNkd...........vrskdyed....ikelpRPgHadytylkKYgikd.regggrsSaReT 122
                                               +Pi+l++ Nkd            ++         + ++pRPgHad+++  KY+ +d r++++rsSaReT
  lcl|NCBI__GCF_000215085.1:WP_013843078.1  71 SPITLQVVNKDwanwseimapgPEA----RleerVVTRPRPGHADLAGAIKYNQQDiRNILERSSARET 135
                                               ***********98888874333333....2444599********************************* PP

                                 TIGR00033 123 aarvaaGavakklLketagieivayvvklgeveleeesak..eiskerldkspvrcpdaeaekemeeei 189
                                               a+rva+G++a++lL+e  gi+++++v+++g+ve+  e+ +  +  +e + +s++ cpd +ae++m  ei
  lcl|NCBI__GCF_000215085.1:WP_013843078.1 136 AVRVAVGTIARALLAE-LGIQMTGWVRRIGSVEAVLEEEQtaDQLRELAGASQLLCPDGQAEAAMIREI 203
                                               ****************.88************98654443334778999999****************** PP

                                 TIGR00033 190 dkakkdgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGsean 256
                                               d+a+ +gds+Ggv e+ v  vp+glG  +++++kld++la al+si+A+KgveiG GF aa v+Gs+++
  lcl|NCBI__GCF_000215085.1:WP_013843078.1 204 DRARGNGDSLGGVFEIRVDHVPAGLGshVQWDRKLDSRLAGALMSIQAIKGVEIGLGFGAAAVPGSQVH 272
                                               **************************9999*************************************** PP

                                 TIGR00033 257 Delvle.ddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcv 324
                                               De+ ++ ++ + r tn+ GGieGGi+nGe+++vr+a+Kpipt++kpl++vd+  ke+ +a+++R+D c+
  lcl|NCBI__GCF_000215085.1:WP_013843078.1 273 DEIFYSpEKSYYRATNRAGGIEGGISNGEPLVVRAAMKPIPTLYKPLRSVDTGSKEPFTASVERSDACA 341
                                               ***9998999*********************************************************** PP

                                 TIGR00033 325 vpravpvvEamvalvladallekras 350
                                               vp+a +v Ea+va  +a a+lek++ 
  lcl|NCBI__GCF_000215085.1:WP_013843078.1 342 VPAACVVGEAVVAWEIAVAILEKFGG 367
                                               **********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (387 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: 00:00:00.01
# Mc/sec: 8.11
//
[ok]

This GapMind analysis is from Apr 10 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