Alignments for a candidate for aroA in Herbaspirillum seropedicae SmR1

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.8766.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: 00:00:00.01
# Mc/sec: 12.56
//
[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