Alignments for a candidate for aroC in Heliobacterium modesticaldum Ice1; ATCC 51547

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Heliobacterium modesticaldum Ice1; ATCC 51547

Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate WP_012281687.1 HM1_RS02475 chorismate synthase

Query= BRENDA::Q71Y87
         (388 letters)



>NCBI__GCF_000019165.1:WP_012281687.1
          Length = 393

 Score =  412 bits (1058), Expect = e-119
 Identities = 212/394 (53%), Positives = 277/394 (70%), Gaps = 10/394 (2%)

Query: 1   MRYLTAGESHGPGLTTIIEGLPAGMPLLAEDVNKELKRRQGGHGRGARMRIEKDQVQITA 60
           +RYLTAGESHGP LT I+EG+ AG+PL AED++++L RRQ GHGRG RM IEKD+  I +
Sbjct: 4   LRYLTAGESHGPALTVIVEGMVAGLPLKAEDLDEQLARRQKGHGRGGRMAIEKDRAAILS 63

Query: 61  GIRHGKTLGAPVAMFVENKDWKHWETVMSIEPVPEKNEKSRRVSRPRPGHADLVGGMKYG 120
           GIR GKTLG+P+ + +EN+DWK+W T+M+     E +   RRV++PRPGHADL G +KY 
Sbjct: 64  GIRGGKTLGSPICLQIENRDWKNWSTIMAAGA--EADLMGRRVTQPRPGHADLAGAIKYA 121

Query: 121 HNDMRNVLERSSARETTVRVAAGAVAKKLLHELGIEVAGHVLEIGGTRA------NLTRD 174
             D+RN+LERSSARET  RVAAGAVA++ L ELGI V  HV  IG   A          D
Sbjct: 122 QRDIRNILERSSARETAARVAAGAVARRFLAELGIGVCSHVTAIGDAAAVGGIIDRTESD 181

Query: 175 YAVSEIQETSEASPVRCLDGVAAEEMMQKIDDAKKNGDTIGGIVEVVVGGVPAGLGSYVQ 234
           +    +   +E S VRC D    + M+  ID AK  GD++GG++E+ V G+P G+GS+VQ
Sbjct: 182 WV--RLAAQAEQSTVRCADSALEQAMISAIDRAKSAGDSLGGVIELAVLGLPVGVGSHVQ 239

Query: 235 WDKKLDAKIARAIVSINAFKGAEFGVGFEAARKPGSEVMDEILWSKEDGYTRRTNNLGGF 294
            D++LD +IA A+++I A KG E G+GF AA +PGS+V DEI + +E GY RRTN  GG 
Sbjct: 240 SDRRLDGRIAGAMMAIPAIKGVEIGLGFAAALRPGSQVHDEIGYDRESGYGRRTNRAGGI 299

Query: 295 EGGMTNGMPIVVRGVMKPIPTLYKPLQSVDIDSKETFNASVERSDSCAVPAASVVAEAVV 354
           EGG++NG P+VVR  MKPIPTLY+PL +VDIDS++   ASVERSD+CAVPAA+VVAEAV+
Sbjct: 300 EGGISNGAPVVVRIAMKPIPTLYQPLMTVDIDSRQPVAASVERSDTCAVPAAAVVAEAVL 359

Query: 355 AWEVAVAVLEKFDGDRFDTLKKHVEEHRNLTKEF 388
           A  VA ++LE   GD    +++ V   R     F
Sbjct: 360 ALVVADSLLETTGGDTLAQVRERVAAMREQALRF 393


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: 431
Number of extensions: 16
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: 393
Length adjustment: 31
Effective length of query: 357
Effective length of database: 362
Effective search space:   129234
Effective search space used:   129234
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_012281687.1 HM1_RS02475 (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.6216.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.6e-126  406.2   1.7   6.4e-126  406.0   1.7    1.0  1  lcl|NCBI__GCF_000019165.1:WP_012281687.1  HM1_RS02475 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019165.1:WP_012281687.1  HM1_RS02475 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.0   1.7  6.4e-126  6.4e-126       1     349 [.       4     372 ..       4     374 .. 0.94

  Alignments for each domain:
  == domain 1  score: 406.0 bits;  conditional E-value: 6.4e-126
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               lr++t+GeSHg+al++i++G+ agl+l++ed+ ++l+rR++g++r+ rm  E+D+  ilsG++ GkT G
  lcl|NCBI__GCF_000019165.1:WP_012281687.1   4 LRYLTAGESHGPALTVIVEGMVAGLPLKAEDLDEQLARRQKGHGRGGRMAIEKDRAAILSGIRGGKTLG 72 
                                               699****************************************************************** PP

                                 TIGR00033  70 aPiallikNkd...........vrskdyedikelpRPgHadytylkKYgikd.regggrsSaReTaarv 126
                                               +Pi+l+i+N+d            +++ +    ++pRPgHad+++  KY  +d r++++rsSaReTaarv
  lcl|NCBI__GCF_000019165.1:WP_012281687.1  73 SPICLQIENRDwknwstimaagAEADLMGRRVTQPRPGHADLAGAIKYAQRDiRNILERSSARETAARV 141
                                               ***********999999976666666667799************************************* PP

                                 TIGR00033 127 aaGavakklLketagieivayvvklgeveleeesak......eiskerldkspvrcpdaeaekemeeei 189
                                               aaGava+++L+e  gi + ++v+ +g+ ++    ++           ++++s+vrc+d   e++m   i
  lcl|NCBI__GCF_000019165.1:WP_012281687.1 142 AAGAVARRFLAE-LGIGVCSHVTAIGDAAAVGGIIDrtesdwVRLAAQAEQSTVRCADSALEQAMISAI 209
                                               ************.88************776655555455555346778888****************** PP

                                 TIGR00033 190 dkakkdgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGsean 256
                                               d+ak++gds+Ggv+e+ v ++pvg+G  ++ +++ld+++a a+++i+A+KgveiG GF+aa ++Gs+++
  lcl|NCBI__GCF_000019165.1:WP_012281687.1 210 DRAKSAGDSLGGVIELAVLGLPVGVGshVQSDRRLDGRIAGAMMAIPAIKGVEIGLGFAAALRPGSQVH 278
                                               **************************777889************************************* PP

                                 TIGR00033 257 Delvle.ddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcv 324
                                               De+ ++ + ++ r+tn+ GGieGGi+nG +++vria+Kpipt+++pl+tvd++ ++++ a+++R+D c+
  lcl|NCBI__GCF_000019165.1:WP_012281687.1 279 DEIGYDrESGYGRRTNRAGGIEGGISNGAPVVVRIAMKPIPTLYQPLMTVDIDSRQPVAASVERSDTCA 347
                                               ******999************************************************************ PP

                                 TIGR00033 325 vpravpvvEamvalvladallekra 349
                                               vp+a++v+Ea++alv+ad lle ++
  lcl|NCBI__GCF_000019165.1:WP_012281687.1 348 VPAAAVVAEAVLALVVADSLLETTG 372
                                               *********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (393 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.90
//
[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