Alignments for a candidate for aroG in Frankia alni ACN14A

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Frankia alni ACN14A

Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011606192.1 FRAAL_RS22165 3-deoxy-7-phosphoheptulonate synthase class II

Query= BRENDA::O68903
         (455 letters)



>NCBI__GCF_000058485.1:WP_011606192.1
          Length = 465

 Score =  524 bits (1349), Expect = e-153
 Identities = 267/450 (59%), Positives = 325/450 (72%), Gaps = 7/450 (1%)

Query: 9   VDTLPE-LRSRLDDALGRPAAQQPEWPDADLARRVRAVLESVPPITVPAEIDRLRENLAA 67
           V T+P  L S LD     PA QQP WPD +  +     L ++PP+    E+  L E LA 
Sbjct: 3   VGTVPWCLVSALDVWRTLPAKQQPSWPDLEELQSAYNQLAALPPLVTAPEVRSLTERLAM 62

Query: 68  VARGEAFMLQGGDCAETFADNTEPHIRANVRTLLQMAVVLTYGASLPVVKIGRIAGQYAK 127
           VARGEAF+LQGGDCAETFA NT   IR  V+TLLQMAVVLTYGAS PVVK+ RIAGQY+K
Sbjct: 63  VARGEAFLLQGGDCAETFAANTANKIRDKVKTLLQMAVVLTYGASTPVVKVARIAGQYSK 122

Query: 128 PRSSGTDA-LGLPSYRGDIVNSLVPTPEARVADPGRMIRAYANAGAAMNLLRAMTTAGMA 186
           PRS+  ++  GLPSYRGD VN +  T  AR  DP RM+ +Y  +   +NL+RA  T G A
Sbjct: 123 PRSADIESSTGLPSYRGDAVNDIAATAAARRPDPMRMVASYHQSAITLNLVRAFATGGFA 182

Query: 187 DLHRLHDWNKDFVRTSPAGERYEALAAEIDRGLRFMSACGVN--DSSLHTTEIFASHEAL 244
           DL ++H+WNK FVR S AG RYE +A  I+R L FM+ACG++   ++L   E+F SHE L
Sbjct: 183 DLSKVHEWNKAFVRDSAAGRRYEVMATNIERALAFMAACGIDLGSAALTGVELFTSHEGL 242

Query: 245 LLDYERALLRLDTRGDEPKLYDLSSHFLWIGERTKQLDGAHIAFAELLANPIGLKIGPST 304
           LL+YERAL R++     P  YDLS+H +WIGERT+ L GAH+     + NPIG KIGP  
Sbjct: 243 LLEYERALTRVEDATGNP--YDLSAHMIWIGERTRDLGGAHVDLLSRVGNPIGCKIGPKA 300

Query: 305 TPEMAVEYVERLDPHNQPGRLTLIIRMGNGKVRDVLPAIVEKVTASGHKVIWQCDPMHGN 364
           +P+  +E  ERL+P + PGRLTLI RMG GK+RD LP I+EKV A+G  V+W CDPMHGN
Sbjct: 301 SPDEVLELAERLNPQHVPGRLTLITRMGAGKIRDALPPIIEKVNAAGPPVVWSCDPMHGN 360

Query: 365 THESSTGYKTRHFDRIVDEVQGFFEVHRRLGTHPGGIHIELTGEDVTECLGGAQEISDTD 424
           T + S G KTRHFD ++DEV GFFEVH+ LGTHPGG+HIELTGE+VTECLGGA+ I + D
Sbjct: 361 TRDVS-GIKTRHFDDVLDEVFGFFEVHKALGTHPGGLHIELTGENVTECLGGAELIGEED 419

Query: 425 LAGRYETACDPRLNTQQSLELAFLVAEMLR 454
           L GRYETACDPRLNT Q+LELAFLVAEML+
Sbjct: 420 LGGRYETACDPRLNTGQALELAFLVAEMLQ 449


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: 589
Number of extensions: 22
Number of successful extensions: 5
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: 465
Length adjustment: 33
Effective length of query: 422
Effective length of database: 432
Effective search space:   182304
Effective search space used:   182304
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_011606192.1 FRAAL_RS22165 (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.10273.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-206  671.6   0.0   2.3e-206  671.4   0.0    1.0  1  lcl|NCBI__GCF_000058485.1:WP_011606192.1  FRAAL_RS22165 3-deoxy-7-phosphoh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000058485.1:WP_011606192.1  FRAAL_RS22165 3-deoxy-7-phosphoheptulonate synthase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  671.4   0.0  2.3e-206  2.3e-206       2     443 .]      13     452 ..      12     452 .. 0.99

  Alignments for each domain:
  == domain 1  score: 671.4 bits;  conditional E-value: 2.3e-206
                                 TIGR01358   2 sleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfk 70 
                                               +l+ wr+ pa+q+P +Pd e+l++  ++l+ lPPlv+a e+++l e+la va+GeafllqgGdcae+f 
  lcl|NCBI__GCF_000058485.1:WP_011606192.1  13 ALDVWRTLPAKQQPSWPDLEELQSAYNQLAALPPLVTAPEVRSLTERLAMVARGEAFLLQGGDCAETFA 81 
                                               5789***************************************************************** PP

                                 TIGR01358  71 eveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafd 139
                                               +++a++irdk+++llqmavvltygas Pvvkv+riaGqy+kPrs++ie+     lpsyrGd +n  a +
  lcl|NCBI__GCF_000058485.1:WP_011606192.1  82 ANTANKIRDKVKTLLQMAVVLTYGASTPVVKVARIAGQYSKPRSADIESST--GLPSYRGDAVNDIAAT 148
                                               ************************************************998..59************** PP

                                 TIGR01358 140 eaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrf 208
                                               +aar+pdp r+v  y++sa tlnl+ra+++gG+adl+kvheWn+ fv++s ag rye +a++i++al f
  lcl|NCBI__GCF_000058485.1:WP_011606192.1 149 AAARRPDPMRMVASYHQSAITLNLVRAFATGGFADLSKVHEWNKAFVRDSAAGRRYEVMATNIERALAF 217
                                               ********************************************************************* PP

                                 TIGR01358 209 msavgvaeae.alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflr 276
                                               m a+g++  + al+ vel+tshe lll+ye+altrv++ +g+ +dlsah++WiGertr l gahv++l+
  lcl|NCBI__GCF_000058485.1:WP_011606192.1 218 MAACGIDLGSaALTGVELFTSHEGLLLEYERALTRVEDATGNPYDLSAHMIWIGERTRDLGGAHVDLLS 286
                                               *******98879********************************************************* PP

                                 TIGR01358 277 gvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtd 345
                                               +v nPig k+gp+ ++de+l+l e+l+P++ PGrltli+r+Ga ki++ lP+++e+v+aaG  vvW +d
  lcl|NCBI__GCF_000058485.1:WP_011606192.1 287 RVGNPIGCKIGPKASPDEVLELAERLNPQHVPGRLTLITRMGAGKIRDALPPIIEKVNAAGPPVVWSCD 355
                                               ********************************************************************* PP

                                 TIGR01358 346 pmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasr 414
                                               pmhGnt    sG ktr+fdd+l+ev +ffevhka+GthpGG+h+eltGe+vteclGGa+ i e+dl  r
  lcl|NCBI__GCF_000058485.1:WP_011606192.1 356 PMHGNTRD-VSGIKTRHFDDVLDEVFGFFEVHKALGTHPGGLHIELTGENVTECLGGAELIGEEDLGGR 423
                                               ******87.57********************************************************** PP

                                 TIGR01358 415 yetacdPrlnaeqslelaflvaeklrear 443
                                               yetacdPrln+ q+lelaflvae+l++ar
  lcl|NCBI__GCF_000058485.1:WP_011606192.1 424 YETACDPRLNTGQALELAFLVAEMLQQAR 452
                                               *************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (465 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: 00:00:00.02
# Mc/sec: 9.21
//
[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