Alignments for a candidate for aroA in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Azospirillum brasilense Sp245

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate AZOBR_RS03090 AZOBR_RS03090 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::A6WUV8
         (450 letters)



>FitnessBrowser__azobra:AZOBR_RS03090
          Length = 445

 Score =  456 bits (1173), Expect = e-133
 Identities = 257/440 (58%), Positives = 305/440 (69%), Gaps = 5/440 (1%)

Query: 8   KPATARRSEALTGEIRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGRAMQAMG 67
           KP  +  + AL G IR+PGDKSISHRS M G +A GET I GLLEGEDV+NT  AM+ +G
Sbjct: 5   KPLRSSSTGALAGTIRVPGDKSISHRSLMLGAVAVGETVIHGLLEGEDVLNTAAAMRLLG 64

Query: 68  AKIRKDGDA-WIINGVGNGCLLQPEAALDFGNAGTGARLTMGLVGTYDMRTSFIGDASLS 126
           A+  + GD  W + GVG G L +P   LD GN+GT ARL MGLV ++ +   F GDASL+
Sbjct: 65  AQAERGGDGVWRVRGVGLGGLGEPAQVLDMGNSGTAARLLMGLVASHPITCVFTGDASLN 124

Query: 127 KRPMGRVLNPLREMGVQVEAAEGDRMPLTLIGPKTANPITYRVPMASAQVKSAVLLAGLN 186
           KRPM RV  PL +MG +     G R+PL ++G     PITYR+P+ASAQVKSAV+L GLN
Sbjct: 125 KRPMARVTGPLEQMGARFVGRSGGRLPLAVVGSDRTVPITYRLPVASAQVKSAVILCGLN 184

Query: 187 TPGVTTVIEPVMTRDHTEKMLQGFGADLSVETDKDGVRHIRITGQGKLIGQTIDVPGDPS 246
           T G TTVIE   TRDHTE ML+ FGA ++ E  +DG   + + GQ +L G+ I VP DPS
Sbjct: 185 TAGTTTVIEAEPTRDHTELMLRHFGATVTTERMEDGALAVSVVGQPELTGREIVVPADPS 244

Query: 247 STAFPLVAALLVEGSDVTIRNVLMNPTRTGLILTLQEMGADIEVLNARLAGGEDVADLRV 306
           S AFP VAALL  GS++ +  V MNP RTGL  TL EMGA+I   N R   GE VADLRV
Sbjct: 245 SAAFPAVAALLRPGSELLLPGVGMNPRRTGLYDTLVEMGANIAFENRRDEAGEPVADLRV 304

Query: 307 KASKLKGVVVPPERAPSMIDEYPVLAIAAAFAEGETVMDGLDELRVKESDRLAAVARGLE 366
           K   LKG+VVP +RAPSMIDEYP+LA AAA AEG TVM GL ELRVKESDRLA VA GL 
Sbjct: 305 KHGPLKGIVVPADRAPSMIDEYPILAAAAACAEGTTVMLGLKELRVKESDRLAMVADGLT 364

Query: 367 ANGVDCTEG-EMSLTVRGRPDGK-GLGGGTVATHLDHRIAMSFLVMGLASEKPVTVDDST 424
             GV    G + SLTV G   GK   GG TVAT +DHRIAMSFLV+G+A+ +PV VDD  
Sbjct: 365 KCGVKVEVGADDSLTVYG--TGKPPQGGATVATAMDHRIAMSFLVLGMATSEPVQVDDGA 422

Query: 425 MIATSFPEFMDMMPGLGAKI 444
            I TSFP F+ +M G+GAKI
Sbjct: 423 FIDTSFPGFVALMNGVGAKI 442


Lambda     K      H
   0.316    0.135    0.381 

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: 650
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: 450
Length of database: 445
Length adjustment: 33
Effective length of query: 417
Effective length of database: 412
Effective search space:   171804
Effective search space used:   171804
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate AZOBR_RS03090 AZOBR_RS03090 (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.5698.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-122  394.2   0.0   3.8e-122  394.0   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS03090  AZOBR_RS03090 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS03090  AZOBR_RS03090 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.0   0.0  3.8e-122  3.8e-122       1     414 [.      17     440 ..      17     441 .. 0.94

  Alignments for each domain:
  == domain 1  score: 394.0 bits;  conditional E-value: 3.8e-122
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               g i++pg+KSishR+l+l+a a getv+++lL++eD+l+t  a+r lGa+ e++ ++++ ++gvg   l
  lcl|FitnessBrowser__azobra:AZOBR_RS03090  17 GTIRVPGDKSISHRSLMLGAVAVGETVIHGLLEGEDVLNTAAAMRLLGAQAERGgDGVWRVRGVGLggL 85 
                                               789*************************************************88799******998889 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                                ep ++ld+gnsGt+aRll+g++a ++ ++v+tgd sl+kRP+ r++ +L+++ga++  ++  g+lPla
  lcl|FitnessBrowser__azobra:AZOBR_RS03090  86 GEPAQVLDMGNSGTAARLLMGLVASHPITCVFTGDASLNKRPMARVTGPLEQMGARFVGRS-GGRLPLA 153
                                               ***********************************************************99.59***** PP

                                 TIGR01356 136 isgp.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               + g   +++i++  + aS+Q+ksa++l++   l++ ++++v+e + +r+++e++L  +++  v+ e+ +
  lcl|FitnessBrowser__azobra:AZOBR_RS03090 154 VVGSdRTVPITYRLPVASAQVKSAVILCG---LNTAGTTTVIEAEPTRDHTELMLRHFGAT-VTTERME 218
                                               ****5555*********************...88899999999****************99.6666666 PP

                                 TIGR01356 204 e..rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGad 269
                                               +    ++v g+ + + +e+ v++D+SsAaf+++aa++ ++ e+ + ++g+n+ +++  + ++L emGa+
  lcl|FitnessBrowser__azobra:AZOBR_RS03090 219 DgaLAVSVVGQPELTGREIVVPADPSSAAFPAVAALLRPGsELLLPGVGMNPRRTG--LYDTLVEMGAN 285
                                               545566677776677778**********************9***************..666******** PP

                                 TIGR01356 270 veveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEs 329
                                               + +e+ r        d++v+ +  lkg+ v   +++s+iDe+p+la++aa+Aeg+t++ +++elRvkEs
  lcl|FitnessBrowser__azobra:AZOBR_RS03090 286 IAFENRRdeagepvaDLRVK-HGPLKGIVVpADRAPSMIDEYPILAAAAACAEGTTVMLGLKELRVKES 353
                                               ********************.678******77999********************************** PP

                                 TIGR01356 330 dRiaaiaeeLeklGveveele.dgllieGkkkelkg.avvdtydDHRiamalavlglaaegeveiedae 396
                                               dR+a +a+ L+k Gv+ve+++ d+l+++G+ k  +g a+v t  DHRiam++ vlg+a +++v+++d +
  lcl|FitnessBrowser__azobra:AZOBR_RS03090 354 DRLAMVADGLTKCGVKVEVGAdDSLTVYGTGKPPQGgATVATAMDHRIAMSFLVLGMATSEPVQVDDGA 422
                                               *******************87369******96666559******************************* PP

                                 TIGR01356 397 cvaksfPeFfevleqlga 414
                                                +++sfP F+ +++ +ga
  lcl|FitnessBrowser__azobra:AZOBR_RS03090 423 FIDTSFPGFVALMNGVGA 440
                                               **************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (445 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.46
//
[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