Alignments for a candidate for aroA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Paraburkholderia bryophila 376MFSha3.1

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate H281DRAFT_03922 H281DRAFT_03922 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q9KRB0
         (426 letters)



>FitnessBrowser__Burk376:H281DRAFT_03922
          Length = 434

 Score =  507 bits (1306), Expect = e-148
 Identities = 267/436 (61%), Positives = 326/436 (74%), Gaps = 13/436 (2%)

Query: 1   MESLTLQPIELISGEVNLPGSKSVSNRALLLAALASGTTRLTNLLDSDDIRHMLNALTKL 60
           ME L L P    SG V LPGSKS+SNR LLLAALA G T +TNLLDSDD R ML+AL KL
Sbjct: 1   MEFLDLGPFSRASGTVRLPGSKSISNRVLLLAALAEGETTITNLLDSDDTRVMLDALEKL 60

Query: 61  GVNYRLSADKTTCEVEGLGQAFHTTQPLELFLGNAGTAMRPLAAALCLGQGDYVLTGEPR 120
           GV  RL  D  TC V G   AF T +  +LFLGNAGTA+RPL AAL +  GDY + G PR
Sbjct: 61  GV--RLKRDGDTCVVTGTRGAF-TARTADLFLGNAGTAVRPLTAALAVNGGDYRIHGVPR 117

Query: 121 MKERPIGHLVDALRQAGAQIEYLEQENFPPLRIQGTGLQA-GTVTIDGSISSQFLTAFLM 179
           M ERPIG LVD LRQ GA+I+Y E E FPPLRI+   + A   + + G +SSQFLT+ LM
Sbjct: 118 MHERPIGDLVDGLRQIGAKIDYEENEGFPPLRIRPAQISAEAPIRVRGDVSSQFLTSLLM 177

Query: 180 SAPLAQ---GKVTIKIVGELVSKPYIDITLHIMEQFGVQVINHDYQEFVIPAGQSYVSPG 236
           + PL +   G  T+++ GEL+SKPYIDIT+ +M +FG++V  + + +FV+PAGQ Y SPG
Sbjct: 178 TLPLLRTESGVSTVQVDGELISKPYIDITIKLMARFGIEVERNGWHQFVVPAGQRYQSPG 237

Query: 237 QFLVEGDASSASYFLAAAAIKGGEVKVTGIGKNSIQGDIQFADALEKMGAQIEWGDDYVI 296
             +VEGDASSASYFLAA A+ GG +KV G+G++SIQGD+ FADAL KMGA ++ G+D++ 
Sbjct: 238 TIMVEGDASSASYFLAAGALGGGPLKVEGVGRSSIQGDVGFADALIKMGANLQMGEDWIE 297

Query: 297 AR-----RGELNAVDLDFNHIPDAAMTIATTALFAKGTTAIRNVYNWRVKETDRLAAMAT 351
            R      G+L  +D DFN IPDAAMTIA  ALFA GTT +RN+ +WRVKETDR+AAMAT
Sbjct: 298 VRGVGHDSGKLEPIDTDFNLIPDAAMTIAVAALFADGTTTLRNIASWRVKETDRIAAMAT 357

Query: 352 ELRKVGATVEEGEDFIVITPPTKLI-HAAIDTYDDHRMAMCFSLVALSDTPVTINDPKCT 410
           ELRKVGA V+EGEDF+V+TPP KLI +A+IDTYDDHRMAMCFSLV+L   PV INDPKC 
Sbjct: 358 ELRKVGAKVQEGEDFLVVTPPEKLIPNASIDTYDDHRMAMCFSLVSLGGVPVRINDPKCV 417

Query: 411 SKTFPDYFDKFAQLSR 426
            KTFPDYF++F  L++
Sbjct: 418 GKTFPDYFERFTALAQ 433


Lambda     K      H
   0.318    0.135    0.384 

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: 528
Number of extensions: 23
Number of successful extensions: 9
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: 426
Length of database: 434
Length adjustment: 32
Effective length of query: 394
Effective length of database: 402
Effective search space:   158388
Effective search space used:   158388
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 H281DRAFT_03922 H281DRAFT_03922 (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.16487.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   4.2e-144  466.3   0.0   5.1e-144  466.0   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_03922  H281DRAFT_03922 3-phosphoshikima


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_03922  H281DRAFT_03922 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  466.0   0.0  5.1e-144  5.1e-144       1     412 [.      14     431 ..      14     433 .. 0.95

  Alignments for each domain:
  == domain 1  score: 466.0 bits;  conditional E-value: 5.1e-144
                                    TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg. 65 
                                                  g +++pgsKSis+R+lllaaLaeget++tnlL+s+Dt+++l+al+klG++ +++++++v++g +g 
  lcl|FitnessBrowser__Burk376:H281DRAFT_03922  14 GTVRLPGSKSISNRVLLLAALAEGETTITNLLDSDDTRVMLDALEKLGVRLKRDGDTCVVTGTRGa 79 
                                                  789************************************************************997 PP

                                    TIGR01356  66 lkepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegs 131
                                                  +   +a l lgn+Gt++R+lt++la+ +g++ + g +++++RPi++lv+ Lr++ga+i+++e+eg+
  lcl|FitnessBrowser__Burk376:H281DRAFT_03922  80 FTARTADLFLGNAGTAVRPLTAALAVNGGDYRIHGVPRMHERPIGDLVDGLRQIGAKIDYEENEGF 145
                                                  88888************************************************************* PP

                                    TIGR01356 132 lPlaisgp.lkg.givelsgsaSsQyksalllaap..lalqavtleivgeklisrpyieitLkllk 193
                                                  +Pl+i+   +++ + ++++g++SsQ++++ll++ p  +++++v++  v+++lis+pyi+it+kl++
  lcl|FitnessBrowser__Burk376:H281DRAFT_03922 146 PPLRIRPAqISAeAPIRVRGDVSSQFLTSLLMTLPllRTESGVSTVQVDGELISKPYIDITIKLMA 211
                                                  ******98877779*********************554455555556778**************** PP

                                    TIGR01356 194 sfgveveeederkivvkggqkykqk.evevegDaSsAafflaaaaitgeevtvenlgenstqgdka 258
                                                  +fg+eve++  +++vv+ gq y+++ ++ vegDaSsA++flaa+a+ g+ ++ve++g +s qgd+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_03922 212 RFGIEVERNGWHQFVVPAGQRYQSPgTIMVEGDASSASYFLAAGALGGGPLKVEGVGRSSIQGDVG 277
                                                  *********99**********88888**************************************** PP

                                    TIGR01356 259 iiivLeemGadveveeqrdveveg....asklkgvkvdidvdsliDelptlavlaafAegetrikn 320
                                                  +++ L +mGa++++ e+ ++ev+g    + kl++++   d++ ++D+++t+av+a+fA+g+t+++n
  lcl|FitnessBrowser__Burk376:H281DRAFT_03922 278 FADALIKMGANLQMGED-WIEVRGvghdSGKLEPID--TDFNLIPDAAMTIAVAALFADGTTTLRN 340
                                                  *****************.9*****985555566666..**************************** PP

                                    TIGR01356 321 ieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaa 386
                                                  i+++RvkE+dRiaa+a+eL+k+G++v+e+ed+l++++ +k + +a++dtydDHR+am++++++l  
  lcl|FitnessBrowser__Burk376:H281DRAFT_03922 341 IASWRVKETDRIAAMATELRKVGAKVQEGEDFLVVTPPEKLIPNASIDTYDDHRMAMCFSLVSLGG 406
                                                  **************************************999999********************** PP

                                    TIGR01356 387 egeveiedaecvaksfPeFfevleql 412
                                                    +v+i+d++cv k+fP++fe   +l
  lcl|FitnessBrowser__Burk376:H281DRAFT_03922 407 V-PVRINDPKCVGKTFPDYFERFTAL 431
                                                  8.******************988766 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: 00:00:00.02
# Mc/sec: 7.95
//
[ok]

This GapMind analysis is from Apr 09 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