GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroA in Herbaspirillum seropedicae SmR1

Align 3-phosphoshikimate 1-carboxyvinyltransferase; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS; EC 2.5.1.19 (characterized)
to candidate HSERO_RS18420 HSERO_RS18420 3-phosphoshikimate 1-carboxyvinyltransferase

Query= SwissProt::P24497
         (427 letters)



>FitnessBrowser__HerbieS:HSERO_RS18420
          Length = 443

 Score =  454 bits (1167), Expect = e-132
 Identities = 248/430 (57%), Positives = 302/430 (70%), Gaps = 10/430 (2%)

Query: 4   LTLQPIARVDGTVNLPGSKSVSNRALLLAALARGTTVLTNLLDSDDVRHMLNALSALGVH 63
           + L P+  V GTV LPGSKS+SNR LLLAAL+ GTT + +LL SDD   ML AL  LGV 
Sbjct: 10  IDLAPVHHVQGTVKLPGSKSISNRILLLAALSGGTTRIFDLLASDDTLVMLMALQTLGVK 69

Query: 64  YVLSSDRTRCEVTGTGGPLQAGSALELFLGNAGTAMRPLAAALCLGSNDIVLTGEPRMKE 123
           +          V G  G L    A +LF+GNAGTA+RPL AAL +   D  L G PRM E
Sbjct: 70  WEQIEGTQDYIVHGVNGVLPVHQA-DLFMGNAGTAIRPLTAALAVLGGDYTLHGVPRMHE 128

Query: 124 RPIGHLVDALRQGGAQIDYLEQENYPPLRLRGG-FTGGDVEVDGSVSSQFLTALLMASPL 182
           RPIG LVDAL   G +IDY     YPPL +R G  T   ++V G+VSSQFLTALLMA+PL
Sbjct: 129 RPIGDLVDALNAVGMRIDYTGNPGYPPLHIRRGQLTSSRMKVRGNVSSQFLTALLMAAPL 188

Query: 183 APQDTVIAIK--GELVSRPYIDITLHLMKTFGVEVENQAYQRFIVRGNQQYQSPGDYLVE 240
             ++  + I   GEL+S+PYI+ITL+LM+ F VEVE   +Q+FI++  Q Y+SPG   VE
Sbjct: 189 MAREEAMQIDVVGELISKPYIEITLNLMRRFSVEVERDGWQQFIIKPGQHYRSPGSIHVE 248

Query: 241 GDASSASYFLAAGAIKGGTVKVTGIGRNSVQGDIRFADVLEKMGATVTWGEDYI-ACTRG 299
           GDASSASYFLAAGAI GG ++V G+GR+S+QGD+RF + LE MGAT+T GE++I A + G
Sbjct: 249 GDASSASYFLAAGAITGGPIRVEGVGRDSIQGDVRFVEALELMGATITMGENWIEASSNG 308

Query: 300 ELNAIDMDMNHIPDAAMTIATAALFARGTTTLRNIYNWRVKETDRLFAMATELRKVGAEV 359
            L A+D D NHIPDAAMTIA AAL+A G +TLRNI +WRVKETDRL AMATELRK+GA+V
Sbjct: 309 PLKAVDADFNHIPDAAMTIAVAALYADGPSTLRNIASWRVKETDRLAAMATELRKLGAQV 368

Query: 360 EEGEDYIRITPPLTLQFAEIGTYNDHRMAMCFSLVALS-----DTPVTILDPKCTAKTFP 414
           EEG DY+ +TPP  +  A I TY+DHRMAMCFSL +L         V I DPKC AKTFP
Sbjct: 369 EEGADYLTVTPPAEIGTATIDTYDDHRMAMCFSLASLDGALRRGNRVRINDPKCVAKTFP 428

Query: 415 DYFGQLARIS 424
           DYF    +I+
Sbjct: 429 DYFDVFKKIA 438


Lambda     K      H
   0.319    0.135    0.389 

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: 598
Number of extensions: 21
Number of successful extensions: 7
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: 427
Length of database: 443
Length adjustment: 32
Effective length of query: 395
Effective length of database: 411
Effective search space:   162345
Effective search space used:   162345
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 HSERO_RS18420 HSERO_RS18420 (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.6412.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.1e-143  465.0   0.0   1.2e-143  464.8   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS18420  HSERO_RS18420 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS18420  HSERO_RS18420 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.8   0.0  1.2e-143  1.2e-143       1     413 [.      20     438 ..      20     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: 464.8 bits;  conditional E-value: 1.2e-143
                                  TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve..eekeelviegvgg. 65 
                                                g +k+pgsKSis+R+lllaaL+ g+t++ +lL s+Dtl++l al+ lG+k e  e+ ++ +++gv+g 
  lcl|FitnessBrowser__HerbieS:HSERO_RS18420  20 GTVKLPGSKSISNRILLLAALSGGTTRIFDLLASDDTLVMLMALQTLGVKWEqiEGTQDYIVHGVNGv 87 
                                                789************************************************97444999*******98 PP

                                  TIGR01356  66 lkepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslP 133
                                                l   +a l +gn+Gt++R+lt++la+++g+++l g +++++RPi++lv+aL+++g++i+++ + g++P
  lcl|FitnessBrowser__HerbieS:HSERO_RS18420  88 LPVHQADLFMGNAGTAIRPLTAALAVLGGDYTLHGVPRMHERPIGDLVDALNAVGMRIDYTGNPGYPP 155
                                                88888*************************************************************** PP

                                  TIGR01356 134 laisgp.lkggivelsgsaSsQyksalllaap..lalqavtleivgeklisrpyieitLkllksfgve 198
                                                l+i+ + l++  ++++g++SsQ+++all+aap   +++a ++ +vg +lis+pyieitL+l+++f ve
  lcl|FitnessBrowser__HerbieS:HSERO_RS18420 156 LHIRRGqLTSSRMKVRGNVSSQFLTALLMAAPlmAREEAMQIDVVG-ELISKPYIEITLNLMRRFSVE 222
                                                ***8665888**********************65455667777777.********************* PP

                                  TIGR01356 199 veeederkivvkggqkykqk.evevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLee 265
                                                ve++  +++++k+gq+y+++ +++vegDaSsA++flaa+aitg+ ++ve++g +s qgd+++++ Le 
  lcl|FitnessBrowser__HerbieS:HSERO_RS18420 223 VERDGWQQFIIKPGQHYRSPgSIHVEGDASSASYFLAAGAITGGPIRVEGVGRDSIQGDVRFVEALEL 290
                                                ***999**********99888*********************************************** PP

                                  TIGR01356 266 mGadveveeqrdvevegasklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRia 333
                                                mGa++++ e+ ++e  ++  lk+v+  +d+++++D+++t+av+a++A+g+++++ni+++RvkE+dR+a
  lcl|FitnessBrowser__HerbieS:HSERO_RS18420 291 MGATITMGEN-WIEASSNGPLKAVD--ADFNHIPDAAMTIAVAALYADGPSTLRNIASWRVKETDRLA 355
                                                **********.9****999999999..***************************************** PP

                                  TIGR01356 334 aiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaae....geveiedaec 397
                                                a+a+eL+klG++vee++d+l++++  +e+ +a++dtydDHR+am++++++l  +    ++v+i+d++c
  lcl|FitnessBrowser__HerbieS:HSERO_RS18420 356 AMATELRKLGAQVEEGADYLTVTPP-AEIGTATIDTYDDHRMAMCFSLASLDGAlrrgNRVRINDPKC 422
                                                *************************.6**********************87533223389******** PP

                                  TIGR01356 398 vaksfPeFfevleqlg 413
                                                vak+fP++f+v +++ 
  lcl|FitnessBrowser__HerbieS:HSERO_RS18420 423 VAKTFPDYFDVFKKIA 438
                                                ***********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (443 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: 00:00:00.02
# Mc/sec: 7.43
//
[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:

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:

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:

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:

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