Alignments for a candidate for aroB in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Chlorobaculum tepidum TLS

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate NP_662292.1 CT1406 3-dehydroquinate synthase

Query= BRENDA::Q3M4V2
         (363 letters)



>NCBI__GCF_000006985.1:NP_662292.1
          Length = 368

 Score =  256 bits (655), Expect = 5e-73
 Identities = 148/358 (41%), Positives = 216/358 (60%), Gaps = 8/358 (2%)

Query: 9   LPTQSYEIAIAPASLDQIGQSLAGLKLGKKVLLVSNPTIFKHFGKVAVDSLEAAGFQVAS 68
           + T S  I +    +D +G+  A   LGKK +L+ +    + FG   ++S++  GF+   
Sbjct: 1   MQTPSSHIIVRTPVIDSVGELYATRGLGKKTVLLFDENTRRLFGDAIIESMQRQGFRTIE 60

Query: 69  YCLPAGERYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATWLRGINVVQ 128
             +PA E  K++++  KLY   +E  ++RS  ++  GGGV+GD+ G+ AA++ RGI VVQ
Sbjct: 61  LVVPARETSKSVSTAWKLYGQMIEADVDRSWNLLCAGGGVVGDLGGYIAASYYRGIPVVQ 120

Query: 129 VPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREFRAGMAEVI 188
           +PTTLLAM DS+IGGK  +NHP GKNLIG FH P  VLIDP  L+TLP RE   GM+EV+
Sbjct: 121 LPTTLLAMTDSSIGGKVAINHPLGKNLIGFFHMPELVLIDPAYLRTLPSREIYGGMSEVV 180

Query: 189 KYGVIWDAELFNQLEQSKRLDQLRYIKPELMDAILTRSCQAKADVVGKDEKE-GGLRAIL 247
           KYG I D E F+ L  +K  D++  ++   +   ++RS   KA+VV KD +E  GLRA L
Sbjct: 181 KYGFIADREFFDLL--TKHWDEVVRLEEPWLSKAVSRSAFIKANVVEKDFRETSGLRATL 238

Query: 248 NYGHTVGHAVESLTNYRLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNALIEK---- 303
           N+GHT  H +E +  YR L+HGEAV IGMV A  ++   G   +AD     AL+ +    
Sbjct: 239 NFGHTFAHGLEKMAGYRNLRHGEAVTIGMVCALFLSHRPGFLAEADLREGLALLARFRFP 298

Query: 304 AGLPTKLPAGLDIEGIIEALQLDKKVKDGKVRFVLPTQIGVVTVTD-EVTSDHIRQVL 360
            GL  K    LD + ++E++  DKK  D ++RFVL  +IG   + D ++T   + Q +
Sbjct: 299 RGLVNKRFLSLDRDELVESMLSDKKKIDKQLRFVLLDRIGHAFLHDKDITKTDVLQAI 356


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: 357
Number of extensions: 24
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: 368
Length adjustment: 30
Effective length of query: 333
Effective length of database: 338
Effective search space:   112554
Effective search space used:   112554
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 NP_662292.1 CT1406 (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.19258.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   7.4e-121  389.5   0.0   8.4e-121  389.3   0.0    1.0  1  lcl|NCBI__GCF_000006985.1:NP_662292.1  CT1406 3-dehydroquinate synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_662292.1  CT1406 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.3   0.0  8.4e-121  8.4e-121       2     343 ..       7     356 ..       6     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: 389.3 bits;  conditional E-value: 8.4e-121
                              TIGR01357   2 kvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvakl 71 
                                            +++v++ +++++ e +a+    +k+v+++de++++l+++ + e  +++g+++++lvvp++e+sKs++t++kl
  lcl|NCBI__GCF_000006985.1:NP_662292.1   7 HIIVRTPVIDSVGELYATrgLGKKTVLLFDENTRRLFGDAIIESMQRQGFRTIELVVPARETSKSVSTAWKL 78 
                                            689999******9999995445***************99998888888************************ PP

                              TIGR01357  72 ldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGa 143
                                            + q++e++++r++ l++ GGGvvgDl+G++Aa+y+RGi++vq+PTtllam Dss+GGK++in+plgkNliG 
  lcl|NCBI__GCF_000006985.1:NP_662292.1  79 YGQMIEADVDRSWNLLCAGGGVVGDLGGYIAASYYRGIPVVQLPTTLLAMTDSSIGGKVAINHPLGKNLIGF 150
                                            ************************************************************************ PP

                              TIGR01357 144 fyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKa 215
                                            f++P++Vlid+++l+tlp+re++ Gm+Ev+K+g+iad+e+f+ l+k+++++++l e+ +l+++++rs  +Ka
  lcl|NCBI__GCF_000006985.1:NP_662292.1 151 FHMPELVLIDPAYLRTLPSREIYGGMSEVVKYGFIADREFFDLLTKHWDEVVRL-EEPWLSKAVSRSAFIKA 221
                                            *************************************************99986.66*************** PP

                              TIGR01357 216 evVeeDekes.glRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallk 285
                                            +vVe+D +e+ glRa+LNfGHt++H++E++++y+ l+HGeaV+iGmv+++ ls++ g+l + +l++ +all 
  lcl|NCBI__GCF_000006985.1:NP_662292.1 222 NVVEKDFRETsGLRATLNFGHTFAHGLEKMAGYRnLRHGEAVTIGMVCALFLSHRPGFLAEADLREGLALLA 293
                                            *********99************************************************************* PP

                              TIGR01357 286 klglptklkk....klsveellkallkDKKnegskiklvlleeiGkaalas.evteeelleal 343
                                            ++  p+ l +    +l+ +el++++l+DKK+ ++++++vll++iG+a+l++ ++t++++l+a+
  lcl|NCBI__GCF_000006985.1:NP_662292.1 294 RFRFPRGLVNkrflSLDRDELVESMLSDKKKIDKQLRFVLLDRIGHAFLHDkDITKTDVLQAI 356
                                            *****9998889999**********************************99899999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (368 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: 7.85
//
[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