Alignments for a candidate for aroC in Ammonifex degensii KC4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Ammonifex degensii KC4

Align chorismate synthase (EC 4.2.3.5) (characterized)
to candidate WP_015738682.1 ADEG_RS03360 chorismate synthase

Query= BRENDA::Q71Y87
         (388 letters)



>NCBI__GCF_000024605.1:WP_015738682.1
          Length = 388

 Score =  418 bits (1074), Expect = e-121
 Identities = 213/376 (56%), Positives = 275/376 (73%), Gaps = 3/376 (0%)

Query: 1   MRYLTAGESHGPGLTTIIEGLPAGMPLLAEDVNKELKRRQGGHGRGARMRIEKDQVQITA 60
           +RYLTAGESHG  L TIIEG+PAG+ L A+ ++++L+RRQGG+GRGAR RIE+D+V+I +
Sbjct: 2   LRYLTAGESHGQALLTIIEGMPAGLWLTADYIDRQLERRQGGYGRGARQRIERDRVEILS 61

Query: 61  GIRHGKTLGAPVAMFVENKDWKHWETVMSIEPVPEKNEKSRRVSRPRPGHADLVGGMKYG 120
           G+R G TLG+P+A+ + N+DW++W  VM+  P  E     R ++RPRPGHADL G +KY 
Sbjct: 62  GVRGGFTLGSPIALKIANRDWENWREVMN--PGLEARLDERVITRPRPGHADLAGALKYA 119

Query: 121 HNDMRNVLERSSARETTVRVAAGAVAKKLLHELGIEVAGHVLEIGGTRANLTRDYAVSEI 180
             D+RNVLER+SARET  RVAAGAVA++ L ELGI +AG V++IG  +A    +    EI
Sbjct: 120 FYDLRNVLERASARETVARVAAGAVARRFLEELGITLAGQVVQIGEVKAT-PAEGTPEEI 178

Query: 181 QETSEASPVRCLDGVAAEEMMQKIDDAKKNGDTIGGIVEVVVGGVPAGLGSYVQWDKKLD 240
           +  ++ASPV C D  A+  M++ I+ A+K GDT+GGI EV V GVP GLGSYV WD++LD
Sbjct: 179 RSQADASPVYCPDPQASAAMVEAIERAEKAGDTLGGIFEVRVYGVPPGLGSYVHWDRRLD 238

Query: 241 AKIARAIVSINAFKGAEFGVGFEAARKPGSEVMDEILWSKEDGYTRRTNNLGGFEGGMTN 300
            ++A+A++SI   KG E G+GF  A  PGS   DEI +S   GY R TN  GG EGG+TN
Sbjct: 239 GRLAQALMSIPGIKGVEIGLGFALASLPGSRAHDEIFYSPVQGYYRVTNRAGGLEGGVTN 298

Query: 301 GMPIVVRGVMKPIPTLYKPLQSVDIDSKETFNASVERSDSCAVPAASVVAEAVVAWEVAV 360
           G PIVVR VMKPIPTL KPL+SVD+ +KE   A+ ER+D CAVPAA V+ EAVVAWE+A 
Sbjct: 299 GEPIVVRAVMKPIPTLRKPLRSVDMFTKEPVAAAYERADICAVPAACVIGEAVVAWEIAA 358

Query: 361 AVLEKFDGDRFDTLKK 376
           A LEKF GD    LK+
Sbjct: 359 ACLEKFGGDTMAELKE 374


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: 456
Number of extensions: 20
Number of successful extensions: 4
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: 388
Length adjustment: 30
Effective length of query: 358
Effective length of database: 358
Effective search space:   128164
Effective search space used:   128164
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_015738682.1 ADEG_RS03360 (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.29158.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.1e-127  410.3   0.0   3.5e-127  410.1   0.0    1.0  1  lcl|NCBI__GCF_000024605.1:WP_015738682.1  ADEG_RS03360 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000024605.1:WP_015738682.1  ADEG_RS03360 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.1   0.0  3.5e-127  3.5e-127       1     350 [.       2     366 ..       2     367 .. 0.96

  Alignments for each domain:
  == domain 1  score: 410.1 bits;  conditional E-value: 3.5e-127
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               lr++t+GeSHg+al +ii+G+Pagl lt+++i ++l+rR+ g++r++r+r E+D+veilsGv+ G T G
  lcl|NCBI__GCF_000024605.1:WP_015738682.1   2 LRYLTAGESHGQALLTIIEGMPAGLWLTADYIDRQLERRQGGYGRGARQRIERDRVEILSGVRGGFTLG 70 
                                               699****************************************************************** PP

                                 TIGR00033  70 aPiallikNkd...........vrskdyedikelpRPgHadytylkKYgikd.regggrsSaReTaarv 126
                                               +Pial i N+d           ++++  e + ++pRPgHad+++  KY ++d r+ ++r+SaReT+arv
  lcl|NCBI__GCF_000024605.1:WP_015738682.1  71 SPIALKIANRDwenwrevmnpgLEARLDERVITRPRPGHADLAGALKYAFYDlRNVLERASARETVARV 139
                                               ***********9888887666666666666*************************************** PP

                                 TIGR00033 127 aaGavakklLketagieivayvvklgeveleeesak.eiskerldkspvrcpdaeaekemeeeidkakk 194
                                               aaGava+++L+e  gi +++ vv++gev+++  + + e+++ ++d+spv cpd++a+++m+e i++a+k
  lcl|NCBI__GCF_000024605.1:WP_015738682.1 140 AAGAVARRFLEE-LGITLAGQVVQIGEVKATPAEGTpEEIRSQADASPVYCPDPQASAAMVEAIERAEK 207
                                               ************.88************88776665568899**************************** PP

                                 TIGR00033 195 dgdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvl 261
                                               +gd++Gg+ ev v++vp glG  ++++++ld++la+al+si+ +KgveiG GF++as +Gs+a+De+ +
  lcl|NCBI__GCF_000024605.1:WP_015738682.1 208 AGDTLGGIFEVRVYGVPPGLGsyVHWDRRLDGRLAQALMSIPGIKGVEIGLGFALASLPGSRAHDEIFY 276
                                               *********************999*******************************************99 PP

                                 TIGR00033 262 e.ddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvprav 329
                                               +  +++ r+tn+ GG+eGG+tnGe+i+vr+++Kpipt++kpl++vd+ tke++ a+++R D c+vp+a 
  lcl|NCBI__GCF_000024605.1:WP_015738682.1 277 SpVQGYYRVTNRAGGLEGGVTNGEPIVVRAVMKPIPTLRKPLRSVDMFTKEPVAAAYERADICAVPAAC 345
                                               9899***************************************************************** PP

                                 TIGR00033 330 pvvEamvalvladallekras 350
                                               ++ Ea+va  +a a+lek++ 
  lcl|NCBI__GCF_000024605.1:WP_015738682.1 346 VIGEAVVAWEIAAACLEKFGG 366
                                               ****************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (388 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: 10.93
//
[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