Alignments for a candidate for aroC in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroC in Desulfitobacterium hafniense DCB-2

Align Chorismate synthase; CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; EC 4.2.3.5 (characterized)
to candidate WP_015944646.1 DHAF_RS17635 chorismate synthase

Query= SwissProt::O66493
         (398 letters)



>NCBI__GCF_000021925.1:WP_015944646.1
          Length = 382

 Score =  375 bits (964), Expect = e-109
 Identities = 190/390 (48%), Positives = 265/390 (67%), Gaps = 11/390 (2%)

Query: 6   LRFLTAGESHGKGLTAILEGIPANLPLSEEEINHELRRRQRGYGRGGRMKIEKDTAEILS 65
           +R+LTAGESHG  L  ILEG+P+   + +E I+  L+ RQ+G GRGGRMKIEKD   ILS
Sbjct: 1   MRYLTAGESHGPKLVGILEGVPSGAKIDKETIDQALQERQKGPGRGGRMKIEKDQITILS 60

Query: 66  GVRFGKTLGSPIALFIRNRDWENWKEKMAIEGEPSPSVVPFTRPRPGHADLSGGIKYNQR 125
           GVR G T G+PIAL I NRDW NW++ MA   E          PRPGHADL+G +KY + 
Sbjct: 61  GVRGGLTTGAPIALEIINRDWANWEKIMAWGDEADLESRKVMTPRPGHADLTGYLKY-RT 119

Query: 126 DLRNILERASARETAARVAVGAVCKKFLSEFGIKIGSFVVSIGQKEVEELKDKSYFANPE 185
           ++RN+LERASARETA RVA+G +  + L   G++I   V+S+G+  ++           E
Sbjct: 120 EVRNVLERASARETAMRVAIGNIAVQILEALGVEIRGQVLSVGKVHMDS----------E 169

Query: 186 KLLSYHEKAEDSELRIPFPEKDEEFKTYIDEVKEKGESLGGVFEVFALNVPPGLGSHIQW 245
               Y ++ + SE ++  P+ +E     + E + +GESLGGV ++   N+ PGLGS++QW
Sbjct: 170 DTPEYWQRVQASEWKVGDPKGEEALDAQLQEARSQGESLGGVLQIQVRNLLPGLGSYVQW 229

Query: 246 DRRIDGRIAQAMMSIQAIKGVEIGLGFEAARRFGSQVHDEIGWSEGKGYFRHSNNLGGTE 305
           DR++DGR+AQA++S+QAIKGV  G+GF A + FGS+VHD IG+  G+GY+R+SNN GG E
Sbjct: 230 DRKLDGRLAQAVLSVQAIKGVAFGMGFTAGQHFGSEVHDPIGYDSGRGYYRYSNNAGGIE 289

Query: 306 GGITNGMPIVVRVAMKPIPTLKNPLRSVDIETKEEMKAGKERTDIVAVPAASVVGEAMLA 365
           GG+TNG P+++   MKPIPTL +PL +V++ETKE M+A  ER+D+ AVPAA VV + + A
Sbjct: 290 GGMTNGEPVIIEAVMKPIPTLYSPLSTVNLETKEVMEASVERSDVCAVPAALVVLKHVAA 349

Query: 366 IVLADALLEKLGGDFMEEVKKRFEDYVNHV 395
             +  A+LEK   D  +E+ K ++DY   V
Sbjct: 350 WEILQAILEKFPADTWDELDKAWQDYKRFV 379


Lambda     K      H
   0.317    0.137    0.394 

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: 469
Number of extensions: 24
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: 398
Length of database: 382
Length adjustment: 30
Effective length of query: 368
Effective length of database: 352
Effective search space:   129536
Effective search space used:   129536
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: 50 (23.9 bits)

Align candidate WP_015944646.1 DHAF_RS17635 (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.10978.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-113  364.8   0.0   2.4e-113  364.6   0.0    1.0  1  lcl|NCBI__GCF_000021925.1:WP_015944646.1  DHAF_RS17635 chorismate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_015944646.1  DHAF_RS17635 chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  364.6   0.0  2.4e-113  2.4e-113       1     348 [.       1     360 [.       1     363 [. 0.96

  Alignments for each domain:
  == domain 1  score: 364.6 bits;  conditional E-value: 2.4e-113
                                 TIGR00033   1 lrlttfGeSHgkalgaiidGlPaglelteediqkelkrRrpgqsrltrmrkEeDeveilsGvfeGkTtG 69 
                                               +r++t+GeSHg++l+ i++G+P+g ++++e+i ++l+ R++g +r+ rm+ E+D+++ilsGv+ G TtG
  lcl|NCBI__GCF_000021925.1:WP_015944646.1   1 MRYLTAGESHGPKLVGILEGVPSGAKIDKETIDQALQERQKGPGRGGRMKIEKDQITILSGVRGGLTTG 69 
                                               89******************************************************************* PP

                                 TIGR00033  70 aPiallikNkd...........vrskdyed.ikelpRPgHadytylkKYgikdregggrsSaReTaarv 126
                                               aPial i N+d              +d+e+ +  +pRPgHad+t+  KY+++ r+ ++r+SaReTa+rv
  lcl|NCBI__GCF_000021925.1:WP_015944646.1  70 APIALEIINRDwanwekimawgD-EADLESrKVMTPRPGHADLTGYLKYRTEVRNVLERASARETAMRV 137
                                               ***********999998866633.33333337789********************************** PP

                                 TIGR00033 127 aaGavakklLketagieivayvvklgeveleeesakeiskerldkspvrcpdaeaekemeeeidkakkd 195
                                               a G +a + L+   g+ei + v ++g+v++++e + e   +r+++s+ ++ d++ e+++ +++++a+++
  lcl|NCBI__GCF_000021925.1:WP_015944646.1 138 AIGNIAVQILEA-LGVEIRGQVLSVGKVHMDSEDTPE-YWQRVQASEWKVGDPKGEEALDAQLQEARSQ 204
                                               ***********9.88****************999987.7899999************************ PP

                                 TIGR00033 196 gdsvGgvvevvvsnvpvglG..eplfdkldaelasallsinAvKgveiGdGFeaasvrGseanDelvle 262
                                               g+s+Ggv++++v+n+  glG  +++++kld++la+a+ls++A+Kgv +G GF+a +  Gse++D++ ++
  lcl|NCBI__GCF_000021925.1:WP_015944646.1 205 GESLGGVLQIQVRNLLPGLGsyVQWDRKLDGRLAQAVLSVQAIKGVAFGMGFTAGQHFGSEVHDPIGYD 273
                                               ********************999*********************************************9 PP

                                 TIGR00033 263 .ddkirrktnnsGGieGGitnGedirvriavKpiptikkplktvdletkekakatkgRhDpcvvpravp 330
                                                  ++ r +nn GGieGG+tnGe++ +++++Kpipt++ pl tv+letke ++a+++R+D+c+vp+a +
  lcl|NCBI__GCF_000021925.1:WP_015944646.1 274 sGRGYYRYSNNAGGIEGGMTNGEPVIIEAVMKPIPTLYSPLSTVNLETKEVMEASVERSDVCAVPAALV 342
                                               8889***************************************************************** PP

                                 TIGR00033 331 vvEamvalvladallekr 348
                                               v   + a  +++a+lek+
  lcl|NCBI__GCF_000021925.1:WP_015944646.1 343 VLKHVAAWEILQAILEKF 360
                                               ***************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (382 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: 12.60
//
[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