Alignments for a candidate for aroA in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Dyella japonica UNC79MFTsu3.2

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate N515DRAFT_1432 N515DRAFT_1432 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1432
          Length = 434

 Score =  461 bits (1185), Expect = e-134
 Identities = 227/429 (52%), Positives = 313/429 (72%), Gaps = 1/429 (0%)

Query: 1   MDYQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMG 60
           +D+ + P++ L G + VPGDKS+SHR+++L+A+AEG++ + GFL G D  A  + LQ++G
Sbjct: 4   LDWLSQPARALHGNVRVPGDKSVSHRSMMLSALAEGRSHIRGFLEGEDTRATAAVLQKLG 63

Query: 61  ASIQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSL 120
             I+    E   +V+GVG+ GL+   +ALDCGN+GT +RLL+GLLAGQ F++ L GD SL
Sbjct: 64  VRIET-PSEGERIVDGVGLHGLRGTAQALDCGNAGTGMRLLAGLLAGQAFDSTLVGDESL 122

Query: 121 QRRPMKRIIDPLTLMGAKIDSTGNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLY 180
            +RPM+R+ +PL  MGA+ID+   +PPL+++G   L GI Y LP+ASAQVKS LLLAGLY
Sbjct: 123 SKRPMRRVTEPLAAMGARIDTQDGLPPLRVHGGQPLKGIRYTLPVASAQVKSALLLAGLY 182

Query: 181 ARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFF 240
           A+G+T + EP P+RD+TER+L  F + ++ +     +SGG +L+A D+ +P D SSAAFF
Sbjct: 183 AQGETEVIEPHPTRDYTERMLAAFGWPIEFEPGRARLSGGHRLRATDVEVPADFSSAAFF 242

Query: 241 IVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARL 300
           +VA +I PG+ +RL  VG+NP R G++  L++MGADI V +  E   EP  D+ VRHA L
Sbjct: 243 LVAGSIVPGAELRLPAVGLNPRRTGLLQALRLMGADIAVENQRESGGEPVGDLIVRHAPL 302

Query: 301 KGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIA 360
            G+++P   VP  IDEFP L IAAAVAQG+TV+R AAELRVKE+DRIA M  G++ +G  
Sbjct: 303 HGVELPEALVPDMIDEFPALFIAAAVAQGRTVVRGAAELRVKESDRIATMAAGMKAIGAR 362

Query: 361 AESLPDGVIIQGGTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFVE 420
            E  PDG II+GG L GGEV+S+ DHRIAM+FAVAG +A+ P+RI +C NV TSFP F+E
Sbjct: 363 IEETPDGAIIEGGALRGGEVDSHGDHRIAMSFAVAGLVAQEPIRIADCANVATSFPGFME 422

Query: 421 LANEVGMNV 429
           LAN  G ++
Sbjct: 423 LANGCGFDL 431


Lambda     K      H
   0.318    0.137    0.392 

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: 625
Number of extensions: 31
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: 438
Length of database: 434
Length adjustment: 32
Effective length of query: 406
Effective length of database: 402
Effective search space:   163212
Effective search space used:   163212
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: 51 (24.3 bits)

Align candidate N515DRAFT_1432 N515DRAFT_1432 (3-phosphoshikimate 1-carboxyvinyltransferase)
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

# 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/TIGR01356.hmm
# target sequence database:        /tmp/gapView.2048470.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01356  [M=415]
Accession:   TIGR01356
Description: aroA: 3-phosphoshikimate 1-carboxyvinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   4.8e-128  413.4   0.0   5.9e-128  413.1   0.0    1.0  1  FitnessBrowser__Dyella79:N515DRAFT_1432  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Dyella79:N515DRAFT_1432  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.1   0.0  5.9e-128  5.9e-128       1     411 [.      16     426 ..      16     429 .. 0.95

  Alignments for each domain:
  == domain 1  score: 413.1 bits;  conditional E-value: 5.9e-128
                                TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..lk 67 
                                              g++++pg+KS+shR+++l+aLaeg++ ++++L++eDt+at  +l+klG+++e   ++e +++gvg   l+
  FitnessBrowser__Dyella79:N515DRAFT_1432  16 GNVRVPGDKSVSHRSMMLSALAEGRSHIRGFLEGEDTRATAAVLQKLGVRIETPsEGERIVDGVGLhgLR 85 
                                              789*************************************************5549999****9986677 PP

                                TIGR01356  68 epeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlais 137
                                                 ++ld+gn+Gt +Rll g+la ++++++l gdesl+kRP++r++e+L ++ga+i+ ++  g +Pl+++
  FitnessBrowser__Dyella79:N515DRAFT_1432  86 GTAQALDCGNAGTGMRLLAGLLAGQAFDSTLVGDESLSKRPMRRVTEPLAAMGARIDTQD--GLPPLRVH 153
                                              777******************************************************876..89****** PP

                                TIGR01356 138 gplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederk 206
                                              g++++ gi +  + aS+Q+ksallla+   l a++++ v+e+  +r+y+e++L+ ++     +e e + +
  FitnessBrowser__Dyella79:N515DRAFT_1432 154 GGQPLkGIRYTLPVASAQVKSALLLAG---LYAQGETEVIEPHPTRDYTERMLAAFGWP---IEFEPG-R 216
                                              **9999*********************...77789999999***********9988766...888877.8 PP

                                TIGR01356 207 ivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeq 275
                                               ++ gg+  + ++vev++D+SsAaffl+a+ i ++ e+++  +g n+ +++  +++ L+ mGad+ ve+q
  FitnessBrowser__Dyella79:N515DRAFT_1432 217 ARLSGGHRLRATDVEVPADFSSAAFFLVAGSIVPGaELRLPAVGLNPRRTG--LLQALRLMGADIAVENQ 284
                                              8999999988889**********************9***************..888************** PP

                                TIGR01356 276 r........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaia 336
                                              r        d++v++   l+gv+  ++ v+++iDe+p+l ++aa+A+g t++++++elRvkEsdRia +a
  FitnessBrowser__Dyella79:N515DRAFT_1432 285 ResggepvgDLIVRH-APLHGVELpEALVPDMIDEFPALFIAAAVAQGRTVVRGAAELRVKESDRIATMA 353
                                              **************5.68******99******************************************** PP

                                TIGR01356 337 eeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFf 406
                                              + ++++G+++ee++dg +ieG+   l+g++vd+++DHRiam++av+gl+a+++++i d + va+sfP F+
  FitnessBrowser__Dyella79:N515DRAFT_1432 354 AGMKAIGARIEETPDGAIIEGG--ALRGGEVDSHGDHRIAMSFAVAGLVAQEPIRIADCANVATSFPGFM 421
                                              **********************..6********************************************* PP

                                TIGR01356 407 evleq 411
                                              e+++ 
  FitnessBrowser__Dyella79:N515DRAFT_1432 422 ELANG 426
                                              99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (434 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: 15.76
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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