Alignments for a candidate for aroB in Chlorobaculum parvum NCIB 8327

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Chlorobaculum parvum NCIB 8327

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_012502008.1 CPAR_RS03885 3-dehydroquinate synthase

Query= BRENDA::Q3M4V2
         (363 letters)



>NCBI__GCF_000020505.1:WP_012502008.1
          Length = 367

 Score =  255 bits (651), Expect = 1e-72
 Identities = 146/334 (43%), Positives = 207/334 (61%), Gaps = 9/334 (2%)

Query: 16  IAIAPASLDQIGQSLAGLKLGKKVLLVSNPTIFKHFGKVAVDSLEAAGFQVASYCLPAGE 75
           I +    +D IG+      LGKK +++ +    K +G   + S++  GF+     +PA E
Sbjct: 8   IIVRTPVIDSIGELYETRGLGKKSVVLFDENTRKLYGDKIIASMQRQGFRTVELVVPARE 67

Query: 76  RYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATWLRGINVVQVPTTLLA 135
             K++++  KLY   +E  ++RS  ++ +GGGV+GD+ G+ AA++ RGI VVQ+PTTLLA
Sbjct: 68  TSKSVSTAWKLYGQMIETDVDRSWNLLCVGGGVVGDLGGYIAASYYRGIPVVQLPTTLLA 127

Query: 136 MVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREFRAGMAEVIKYGVIWD 195
           M DS+IGGK  +NHP GKNLIG FH P  VLIDP  L+TLP RE   GMAEV+KYG I D
Sbjct: 128 MTDSSIGGKVAINHPLGKNLIGYFHMPALVLIDPAFLRTLPAREIFGGMAEVVKYGFIAD 187

Query: 196 AELFNQLEQSKRLDQL-RYIKPELMDAILTRSCQAKADVVGKDEKE-GGLRAILNYGHTV 253
            + F+ L  ++  D++ R  +P + DA+ +RS   KADVV KD +E  GLRA LN+GHT 
Sbjct: 188 RKFFDML--AEHWDEVTRLEEPWISDAV-SRSAFTKADVVEKDFRETSGLRATLNFGHTF 244

Query: 254 GHAVESLTNYRLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNALIEKAGLPTKLP-- 311
            H +E +  YR L+HGEAV IGM  A  ++  LG   +A+ +   ALI +   P  L   
Sbjct: 245 AHGLEKMAEYRNLRHGEAVTIGMACALYLSYRLGFLAEAELNEGLALIARFRFPRNLVNK 304

Query: 312 --AGLDIEGIIEALQLDKKVKDGKVRFVLPTQIG 343
               LD+E + +A+  DKK  D ++RFVL  +IG
Sbjct: 305 RFISLDLEELFDAMHSDKKKIDKQLRFVLLDRIG 338


Lambda     K      H
   0.319    0.136    0.388 

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: 334
Number of extensions: 23
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: 363
Length of database: 367
Length adjustment: 30
Effective length of query: 333
Effective length of database: 337
Effective search space:   112221
Effective search space used:   112221
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_012502008.1 CPAR_RS03885 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.20133.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.6e-121  389.6   0.0   7.4e-121  389.5   0.0    1.0  1  lcl|NCBI__GCF_000020505.1:WP_012502008.1  CPAR_RS03885 3-dehydroquinate sy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020505.1:WP_012502008.1  CPAR_RS03885 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.5   0.0  7.4e-121  7.4e-121       2     342 ..       7     355 ..       6     357 .. 0.97

  Alignments for each domain:
  == domain 1  score: 389.5 bits;  conditional E-value: 7.4e-121
                                 TIGR01357   2 kvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletv 68 
                                               +++v++ +++++ e +++    +k vv++de+++kl+++k+ +  +++g+++ +lvvp++e+sKs++t+
  lcl|NCBI__GCF_000020505.1:WP_012502008.1   7 HIIVRTPVIDSIGELYETrgLGKKSVVLFDENTRKLYGDKIIASMQRQGFRTVELVVPARETSKSVSTA 75 
                                               689999*******9999954459**************99999999999********************* PP

                                 TIGR01357  69 aklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplg 137
                                               +kl+ q++e +++r++ l+++GGGvvgDl+G++Aa+y+RGi++vq+PTtllam Dss+GGK++in+plg
  lcl|NCBI__GCF_000020505.1:WP_012502008.1  76 WKLYGQMIETDVDRSWNLLCVGGGVVGDLGGYIAASYYRGIPVVQLPTTLLAMTDSSIGGKVAINHPLG 144
                                               ********************************************************************* PP

                                 TIGR01357 138 kNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeel 206
                                               kNliG f++P +Vlid+++l+tlp re+  GmaEv+K+g+iad+++f+ l ++++++++l e+ +++++
  lcl|NCBI__GCF_000020505.1:WP_012502008.1 145 KNLIGYFHMPALVLIDPAFLRTLPAREIFGGMAEVVKYGFIADRKFFDMLAEHWDEVTRL-EEPWISDA 212
                                               *******************************************************99986.66****** PP

                                 TIGR01357 207 ikrsievKaevVeeDekes.glRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273
                                               ++rs  +Ka+vVe+D +e+ glRa+LNfGHt++H++E++++y+ l+HGeaV+iGm+++++ls +lg+l 
  lcl|NCBI__GCF_000020505.1:WP_012502008.1 213 VSRSAFTKADVVEKDFRETsGLRATLNFGHTFAHGLEKMAEYRnLRHGEAVTIGMACALYLSYRLGFLA 281
                                               ******************99************************************************* PP

                                 TIGR01357 274 aellerlvallkklglptklkk....klsveellkallkDKKnegskiklvlleeiGkaalas.evtee 337
                                               + +l++ +al+ ++  p++l +    +l++eel++a+ +DKK+ ++++++vll++iG+a+l++ ev++ 
  lcl|NCBI__GCF_000020505.1:WP_012502008.1 282 EAELNEGLALIARFRFPRNLVNkrfiSLDLEELFDAMHSDKKKIDKQLRFVLLDRIGHAFLHDrEVPKA 350
                                               *******************99889999***********************************9899998 PP

                                 TIGR01357 338 ellea 342
                                               ++l+a
  lcl|NCBI__GCF_000020505.1:WP_012502008.1 351 DVLHA 355
                                               88876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (367 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: 7.32
//
[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