Alignments for a candidate for aroG in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Chlorobaculum tepidum TLS

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate NP_661874.1 CT0981 phospho-2-dehydro-3-deoxyheptonate aldolase

Query= BRENDA::Q9K169
         (351 letters)



>NCBI__GCF_000006985.1:NP_661874.1
          Length = 353

 Score =  375 bits (963), Expect = e-109
 Identities = 184/334 (55%), Positives = 241/334 (72%), Gaps = 6/334 (1%)

Query: 9   DIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHDP 68
           D+++  +  L  P A   +LP+++  +  V++ RQE+ +++ G+D R+LVI+GPCSIHD 
Sbjct: 6   DLRVSRIITLSSPKALKEKLPVTEHIADTVYKARQEVENILTGKDSRMLVIVGPCSIHDI 65

Query: 69  KAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQA 128
           KAA +YA RL  LRK+ E+E  IVMRVYFEKPRTT+GWKG INDPHL+ T+DI  GL  A
Sbjct: 66  KAARDYASRLFALRKELESEFCIVMRVYFEKPRTTIGWKGFINDPHLNDTYDIEHGLFHA 125

Query: 129 RSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGFK 188
           R LL+ LN MG+PA+TEFLD I+PQY ADLISW AIGART ESQ HR++ASGLS PVGFK
Sbjct: 126 RKLLIELNEMGLPAATEFLDPISPQYVADLISWAAIGARTIESQTHRQMASGLSMPVGFK 185

Query: 189 NGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGG-KEPNYDAEH 247
           N TDG L++AIDAI +A H H FL + + GHS+++ T GNP  H++LRGG  +PNYDA+ 
Sbjct: 186 NATDGRLQVAIDAIRSAMHQHSFLGIDQDGHSSVITTKGNPFGHLVLRGGSSKPNYDADS 245

Query: 248 VSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESHL 307
           ++ A +QLR A +T  L++DCSHANS K    Q++V  DI AQ EQ   +I+GVM+ES++
Sbjct: 246 IAHAEKQLRKADLTPHLLVDCSHANSGKKCGNQLKVWADILAQKEQGNTSIVGVMIESNI 305

Query: 308 VEGRQDKPE-----VYGKSITDACIGWGATEELL 336
             G Q  P       YG SITD C+ W  TE +L
Sbjct: 306 FSGNQPFPVDPRELQYGVSITDECVSWEETERML 339


Lambda     K      H
   0.318    0.135    0.396 

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: 364
Number of extensions: 15
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: 351
Length of database: 353
Length adjustment: 29
Effective length of query: 322
Effective length of database: 324
Effective search space:   104328
Effective search space used:   104328
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate NP_661874.1 CT0981 (phospho-2-dehydro-3-deoxyheptonate aldolase)
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

# 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/TIGR00034.hmm
# target sequence database:        /tmp/gapView.3020.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00034  [M=342]
Accession:   TIGR00034
Description: aroFGH: 3-deoxy-7-phosphoheptulonate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   8.4e-156  503.9   0.0     1e-155  503.7   0.0    1.0  1  lcl|NCBI__GCF_000006985.1:NP_661874.1  CT0981 phospho-2-dehydro-3-deoxy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_661874.1  CT0981 phospho-2-dehydro-3-deoxyheptonate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  503.7   0.0    1e-155    1e-155       2     335 ..       6     343 ..       5     351 .. 0.98

  Alignments for each domain:
  == domain 1  score: 503.7 bits;  conditional E-value: 1e-155
                              TIGR00034   2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkk 73 
                                            dlr+ +i  l +P++lk+k p+te+ a++v k+r+e+++il+Gkd+r+lv++GPcsihd +aa +ya+rl +
  lcl|NCBI__GCF_000006985.1:NP_661874.1   6 DLRVSRIITLSSPKALKEKLPVTEHIADTVYKARQEVENILTGKDSRMLVIVGPCSIHDIKAARDYASRLFA 77 
                                            899********************************************************************* PP

                              TIGR00034  74 laeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtisp 145
                                            l+++l++++ ivmrvyfekPrtt+GWkG+indP+ln+++d+++Gl  arkll++l+e+glp+ate+ld+isp
  lcl|NCBI__GCF_000006985.1:NP_661874.1  78 LRKELESEFCIVMRVYFEKPRTTIGWKGFINDPHLNDTYDIEHGLFHARKLLIELNEMGLPAATEFLDPISP 149
                                            ************************************************************************ PP

                              TIGR00034 146 qyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaive 217
                                            qy+adl+sw+aiGart esq+hr++asgls+pvgfkn+tdG l+vaidair+a ++h fl+++++G++++++
  lcl|NCBI__GCF_000006985.1:NP_661874.1 150 QYVADLISWAAIGARTIESQTHRQMASGLSMPVGFKNATDGRLQVAIDAIRSAMHQHSFLGIDQDGHSSVIT 221
                                            ************************************************************************ PP

                              TIGR00034 218 tkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGe 288
                                            tkGn+ gh++lrGG + pnyda+++a+++++l+ka+l+++l++d+sh+ns k+  +ql+v +++ +q ++G+
  lcl|NCBI__GCF_000006985.1:NP_661874.1 222 TKGNPFGHLVLRGGSSkPNYDADSIAHAEKQLRKADLTPHLLVDCSHANSGKKCGNQLKVWADILAQKEQGN 293
                                            **************999******************************************************* PP

                              TIGR00034 289 kaiiGvmiesnleeGnqsl...keelkyGksvtdacigwedteallrkla 335
                                            ++i+Gvmiesn+  Gnq      +el+yG+s+td+c++we+te++lr+ a
  lcl|NCBI__GCF_000006985.1:NP_661874.1 294 TSIVGVMIESNIFSGNQPFpvdPRELQYGVSITDECVSWEETERMLRDGA 343
                                            *****************97655689*********************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (353 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: 6.78
//
[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