Alignments for a candidate for aroG in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Saccharomonospora cyanea NA-134

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_005458359.1 SACCYDRAFT_RS17975 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::O68903
         (455 letters)



>NCBI__GCF_000244975.1:WP_005458359.1
          Length = 467

 Score =  797 bits (2059), Expect = 0.0
 Identities = 393/463 (84%), Positives = 423/463 (91%), Gaps = 8/463 (1%)

Query: 1   MNWTVDVPVDTLP-------ELRSRLDDALGRPAAQQPEWPDADLARRVRAVLESVPPIT 53
           +NWTVDVP+D LP       ELR RLDDAL RPAAQQPEWPD ++  RVR VLESVPPIT
Sbjct: 5   VNWTVDVPIDALPSLPPLPAELRKRLDDALSRPAAQQPEWPDPEVVSRVRTVLESVPPIT 64

Query: 54  VPAEIDRLRENLAAVARGEAFMLQGGDCAETFADNTEPHIRANVRTLLQMAVVLTYGASL 113
           VPAE+DRLRE LA VARGEAF+LQGGDCAETF  NTEPHIRAN+RTLLQMAVVLTYGASL
Sbjct: 65  VPAEVDRLRERLAMVARGEAFLLQGGDCAETFESNTEPHIRANLRTLLQMAVVLTYGASL 124

Query: 114 PVVKIGRIAGQYAKPRSSGTDALGLPSYRGDIVNSLVPTPEARVADPGRMIRAYANAGAA 173
           PVVK+GRIAGQYAKPRS+ TDALGLP YRGDIVNSL P PE RV DPGRMIRAYANAGAA
Sbjct: 125 PVVKVGRIAGQYAKPRSNSTDALGLPVYRGDIVNSLAPDPELRVPDPGRMIRAYANAGAA 184

Query: 174 MNLLRAMTTAGMADLHRLHDWNKDFVRTSPAGERYEALAAEIDRGLRFMSACGVNDSSLH 233
           MNL+RA+T AGMADL ++H WNKDFVRTSPAGERYEALA+EIDRGLRFM+ACGV D+SLH
Sbjct: 185 MNLVRALTGAGMADLAQVHAWNKDFVRTSPAGERYEALASEIDRGLRFMAACGVTDTSLH 244

Query: 234 TTEIFASHEALLLDYERALLRL-DTRGDEPKLYDLSSHFLWIGERTKQLDGAHIAFAELL 292
           +TEIFASHEALLLDYERA+LRL D   D P LY+LSSHFLWIGERT+QLDGAHIAFAELL
Sbjct: 245 STEIFASHEALLLDYERAMLRLDDPSADNPSLYNLSSHFLWIGERTRQLDGAHIAFAELL 304

Query: 293 ANPIGLKIGPSTTPEMAVEYVERLDPHNQPGRLTLIIRMGNGKVRDVLPAIVEKVTASGH 352
           ANPIG+KIGP+TTPE AVEYVERLDP N+PGRLTLI RMGNGKVR+VLPAIVEKV ASGH
Sbjct: 305 ANPIGIKIGPTTTPEQAVEYVERLDPRNEPGRLTLISRMGNGKVREVLPAIVEKVEASGH 364

Query: 353 KVIWQCDPMHGNTHESSTGYKTRHFDRIVDEVQGFFEVHRRLGTHPGGIHIELTGEDVTE 412
           KVIWQCDPMHGNTHESS GYKTRHFDRIVDEVQGFFEVHRRLG++PGGIH+ELTGEDVTE
Sbjct: 365 KVIWQCDPMHGNTHESSNGYKTRHFDRIVDEVQGFFEVHRRLGSYPGGIHVELTGEDVTE 424

Query: 413 CLGGAQEISDTDLAGRYETACDPRLNTQQSLELAFLVAEMLRS 455
           CLGGAQ+ISD DL+GRYETACDPRLNTQQSLELAFLVAEMLR+
Sbjct: 425 CLGGAQDISDLDLSGRYETACDPRLNTQQSLELAFLVAEMLRA 467


Lambda     K      H
   0.319    0.135    0.404 

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: 769
Number of extensions: 30
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: 455
Length of database: 467
Length adjustment: 33
Effective length of query: 422
Effective length of database: 434
Effective search space:   183148
Effective search space used:   183148
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_005458359.1 SACCYDRAFT_RS17975 (3-deoxy-7-phosphoheptulonate synthase class II)
to HMM TIGR01358 (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/TIGR01358.hmm
# target sequence database:        /tmp/gapView.7590.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01358  [M=443]
Accession:   TIGR01358
Description: DAHP_synth_II: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-218  711.5   0.0   1.8e-218  711.3   0.0    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005458359.1  SACCYDRAFT_RS17975 3-deoxy-7-pho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005458359.1  SACCYDRAFT_RS17975 3-deoxy-7-phosphoheptulonate synthase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  711.3   0.0  1.8e-218  1.8e-218       4     440 ..      31     466 ..      28     467 .] 0.99

  Alignments for each domain:
  == domain 1  score: 711.3 bits;  conditional E-value: 1.8e-218
                                 TIGR01358   4 eswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkev 72 
                                               + + s+paaq+Pe+Pd e +++v++ les+PP++++ e+++l+e+la va+GeafllqgGdcae+f+++
  lcl|NCBI__GCF_000244975.1:WP_005458359.1  31 DDALSRPAAQQPEWPDPEVVSRVRTVLESVPPITVPAEVDRLRERLAMVARGEAFLLQGGDCAETFESN 99 
                                               66789**************************************************************** PP

                                 TIGR01358  73 eadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdea 141
                                               ++++ir +lr+llqmavvltygaslPvvkvgriaGqyakPrs+ ++a +   lp+yrGd++n+ a+d +
  lcl|NCBI__GCF_000244975.1:WP_005458359.1 100 TEPHIRANLRTLLQMAVVLTYGASLPVVKVGRIAGQYAKPRSNSTDALG---LPVYRGDIVNSLAPDPE 165
                                               *********************************************9999...***************** PP

                                 TIGR01358 142 arvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfms 210
                                                rvpdp r++raya++ a++nl+ralt +G+adl +vh+Wn++fv++spag+rye+la+eid++lrfm 
  lcl|NCBI__GCF_000244975.1:WP_005458359.1 166 LRVPDPGRMIRAYANAGAAMNLVRALTGAGMADLAQVHAWNKDFVRTSPAGERYEALASEIDRGLRFMA 234
                                               ********************************************************************* PP

                                 TIGR01358 211 avgvaeaealkrvelytsheallldyeealtrvds...kegqlfdlsahllWiGertrqldgahveflr 276
                                               a+gv++++ l+ +e+++sheallldye+a++r d+    + +l++ls+h+lWiGertrqldgah++f++
  lcl|NCBI__GCF_000244975.1:WP_005458359.1 235 ACGVTDTS-LHSTEIFASHEALLLDYERAMLRLDDpsaDNPSLYNLSSHFLWIGERTRQLDGAHIAFAE 302
                                               ******99.*************************96666789*************************** PP

                                 TIGR01358 277 gvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtd 345
                                                ++nPigik+gp+++++++++++e+ldP nePGrltlisr+G+ k++e lP ++e+v+a+G++v+W++d
  lcl|NCBI__GCF_000244975.1:WP_005458359.1 303 LLANPIGIKIGPTTTPEQAVEYVERLDPRNEPGRLTLISRMGNGKVREVLPAIVEKVEASGHKVIWQCD 371
                                               ********************************************************************* PP

                                 TIGR01358 346 pmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasr 414
                                               pmhGnt+e+++Gyktr+fd+i++ev++ffevh+ +G++pGG+h+eltGedvteclGGa++i++ dl+ r
  lcl|NCBI__GCF_000244975.1:WP_005458359.1 372 PMHGNTHESSNGYKTRHFDRIVDEVQGFFEVHRRLGSYPGGIHVELTGEDVTECLGGAQDISDLDLSGR 440
                                               ********************************************************************* PP

                                 TIGR01358 415 yetacdPrlnaeqslelaflvaeklr 440
                                               yetacdPrln++qslelaflvae+lr
  lcl|NCBI__GCF_000244975.1:WP_005458359.1 441 YETACDPRLNTQQSLELAFLVAEMLR 466
                                               ************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (467 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: 12.43
//
[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