Alignments for a candidate for aroG in Methylocella silvestris BL2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroG in Methylocella silvestris BL2

Align Phospho-2-dehydro-3-deoxyheptonate aldolase 2, chloroplastic; 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 2; DAHP synthase 2; PhDAHP2; Phospho-2-keto-3-deoxyheptonate aldolase 2; EC 2.5.1.54 (characterized)
to candidate WP_012589176.1 MSIL_RS00640 3-deoxy-7-phosphoheptulonate synthase class II

Query= SwissProt::A0A067XGX8
         (512 letters)



>NCBI__GCF_000021745.1:WP_012589176.1
          Length = 463

 Score =  535 bits (1378), Expect = e-156
 Identities = 264/451 (58%), Positives = 325/451 (72%), Gaps = 1/451 (0%)

Query: 58  STTKWNLESWKTKPAFQLPDYPDKVELESVLKTLSTYPPIVFAGEARNLEEKLGEAALGN 117
           S   W+  SW+ KP  Q P Y D   L  V + L+ +PP+VFAGEAR L+  LG+ A G 
Sbjct: 2   SVESWSPSSWRAKPIEQSPVYSDAAALADVERQLAGFPPLVFAGEARKLKRMLGKVANGE 61

Query: 118 AFLLQGGDCAESFKEFSANNIRDTFRVMLQMGVVLMFGGQMPVIKVGRMAGQFAKPRSDP 177
           AFLLQGGDCAESF E SA+NIRD FRV LQM VV  F   +PV+KVGR+AGQFAKPRS P
Sbjct: 62  AFLLQGGDCAESFAEHSADNIRDFFRVFLQMAVVETFAAALPVVKVGRIAGQFAKPRSAP 121

Query: 178 FEEKDGVKLPSYRGDNVNGDAFDEKSRIPDPHRMVRAYTQSVATLNLLRAFASGGYAAMQ 237
            E   GV LPSYRGD VN  AF+  +R+PDP R + AY Q+ ATLNLLRAFA+GGYA ++
Sbjct: 122 NETVGGVSLPSYRGDIVNDIAFEASARVPDPARQLMAYRQAAATLNLLRAFATGGYANLE 181

Query: 238 RVNQWNLDFTDQSEQGDRYRELAHRVDEAMGFMTAAGLTVD-HTIMTTTDFWTSHECLLL 296
             +QW L F   S Q  RY+ELA  + + +GFM A GL  + H  +  TDF+TSHE LLL
Sbjct: 182 NAHQWMLGFIKDSPQSARYQELADHITQTLGFMRAIGLDPESHQELRQTDFYTSHEALLL 241

Query: 297 PYEQALTREDSTSGLYYDCSAHMIWVGERTRQLDGAHVEFLRGIANPLGIKVSHKMDPDE 356
            +E+ALTR DST+G YY  S HMIW+G+RTRQ   AH+E+ RG+ NP+G+K    ++PDE
Sbjct: 242 GFEEALTRVDSTTGDYYATSGHMIWIGDRTRQPGHAHIEYARGVKNPIGLKCGPTLNPDE 301

Query: 357 LVKLIDILNPQNKPGRITVITRMGADNMRVKLPHLIRAVRGAGQIVTWVSDPMHGNTTKA 416
           L++LIDILNP N+ GR+T+I R GAD +   LP LIRAV+  G+ V W  DPMHGNT KA
Sbjct: 302 LIRLIDILNPDNEAGRLTLICRFGADKVEASLPTLIRAVQQEGRSVVWSCDPMHGNTVKA 361

Query: 417 PCGLKTRSFDSIRAELRAFFDVHEQEGSYPGGVHLEMTGQNVTECVGGSRTITYNDLSSR 476
             G KTR FD I +E+R+FF VH+ EG+YPGGVHLEMTG+NVTEC GG+R I+  DL  R
Sbjct: 362 ASGYKTRPFDKIMSEIRSFFAVHQGEGTYPGGVHLEMTGKNVTECTGGARAISDADLHDR 421

Query: 477 YHTHCDPRLNASQALELAFAIAERLRRRRLG 507
           YHT+CDPRLNA QA+E+AF IAE L+  R+G
Sbjct: 422 YHTYCDPRLNAEQAIEVAFLIAELLKTGRMG 452


Lambda     K      H
   0.319    0.134    0.401 

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: 680
Number of extensions: 26
Number of successful extensions: 2
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: 512
Length of database: 463
Length adjustment: 34
Effective length of query: 478
Effective length of database: 429
Effective search space:   205062
Effective search space used:   205062
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: 52 (24.6 bits)

Align candidate WP_012589176.1 MSIL_RS00640 (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.10185.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.3e-215  699.1   0.0   1.1e-214  698.9   0.0    1.0  1  lcl|NCBI__GCF_000021745.1:WP_012589176.1  MSIL_RS00640 3-deoxy-7-phosphohe


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021745.1:WP_012589176.1  MSIL_RS00640 3-deoxy-7-phosphoheptulonate synthase class II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  698.9   0.0  1.1e-214  1.1e-214       1     441 [.       6     448 ..       6     450 .. 0.99

  Alignments for each domain:
  == domain 1  score: 698.9 bits;  conditional E-value: 1.1e-214
                                 TIGR01358   1 wsleswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesf 69 
                                               ws++swr+kp  q P y da+al  v+ +l+ +PPlv+age++klk+ l++va+GeafllqgGdcaesf
  lcl|NCBI__GCF_000021745.1:WP_012589176.1   6 WSPSSWRAKPIEQSPVYSDAAALADVERQLAGFPPLVFAGEARKLKRMLGKVANGEAFLLQGGDCAESF 74 
                                               89******************************************************************* PP

                                 TIGR01358  70 keveadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaaf 138
                                                e +adnird +rv+lqmavv t++a lPvvkvgriaGq+akPrs+p e+ +gv lpsyrGd++n  af
  lcl|NCBI__GCF_000021745.1:WP_012589176.1  75 AEHSADNIRDFFRVFLQMAVVETFAAALPVVKVGRIAGQFAKPRSAPNETVGGVSLPSYRGDIVNDIAF 143
                                               ********************************************************************* PP

                                 TIGR01358 139 deaarvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealr 207
                                               ++ arvpdp r + ay ++aatlnllra+++gGya+l++ h+W l f+k+sp++ary++la++i+++l 
  lcl|NCBI__GCF_000021745.1:WP_012589176.1 144 EASARVPDPARQLMAYRQAAATLNLLRAFATGGYANLENAHQWMLGFIKDSPQSARYQELADHITQTLG 212
                                               ********************************************************************* PP

                                 TIGR01358 208 fmsavgvaeae..alkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahvef 274
                                               fm+a+g+++++  +l+++++ytshealll +eealtrvds++g+++ +s+h++WiG+rtrq  +ah+e+
  lcl|NCBI__GCF_000021745.1:WP_012589176.1 213 FMRAIGLDPEShqELRQTDFYTSHEALLLGFEEALTRVDSTTGDYYATSGHMIWIGDRTRQPGHAHIEY 281
                                               ********987789******************************************************* PP

                                 TIGR01358 275 lrgvknPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWv 343
                                               +rgvknPig+k+gp++++del++li++l+P+ne Grltli r+Ga+k+   lP l++av+++Gr+vvW 
  lcl|NCBI__GCF_000021745.1:WP_012589176.1 282 ARGVKNPIGLKCGPTLNPDELIRLIDILNPDNEAGRLTLICRFGADKVEASLPTLIRAVQQEGRSVVWS 350
                                               ********************************************************************* PP

                                 TIGR01358 344 tdpmhGntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdla 412
                                               +dpmhGnt++aasGyktr fd+i+se+++ff+vh+ eGt+pGGvhle+tG++vtec+GGar+i++ dl+
  lcl|NCBI__GCF_000021745.1:WP_012589176.1 351 CDPMHGNTVKAASGYKTRPFDKIMSEIRSFFAVHQGEGTYPGGVHLEMTGKNVTECTGGARAISDADLH 419
                                               ********************************************************************* PP

                                 TIGR01358 413 sryetacdPrlnaeqslelaflvaeklre 441
                                               +ry+t cdPrlnaeq++e+afl+ae l+ 
  lcl|NCBI__GCF_000021745.1:WP_012589176.1 420 DRYHTYCDPRLNAEQAIEVAFLIAELLKT 448
                                               *************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (443 nodes)
Target sequences:                          1  (463 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.37
//
[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