Alignments for a candidate for aroA in Azospirillum lipoferum B510

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Azospirillum lipoferum B510

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_012972917.1 AZL_RS01560 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::A6WUV8
         (450 letters)



>NCBI__GCF_000010725.1:WP_012972917.1
          Length = 452

 Score =  460 bits (1183), Expect = e-134
 Identities = 258/446 (57%), Positives = 308/446 (69%), Gaps = 10/446 (2%)

Query: 8   KPATARRSEALTGEIRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGRAMQAMG 67
           +P  +  + A+ G IR+PGDKSISHRS M G +A GET I GLLEGEDV++T  AM+ +G
Sbjct: 5   RPLRSTTTGAIRGSIRVPGDKSISHRSLMLGAIAVGETVIHGLLEGEDVLHTAAAMRLLG 64

Query: 68  AKIRKDGDA-----WIINGVGNGCLLQPEAALDFGNAGTGARLTMGLVGTYDMRTSFIGD 122
           A+  ++ +      W + GVG G L +P   LD GN+GT ARL MGLV  + +   F GD
Sbjct: 65  AEAEREDNGQGPGVWRVRGVGLGALREPAQVLDMGNSGTAARLLMGLVAGHPITCVFTGD 124

Query: 123 ASLSKRPMGRVLNPLREMGVQVEAAEGDRMPLTLIGPKTANPITYRVPMASAQVKSAVLL 182
           ASL+KRPM RV  PL EMG +     G R+PLT++G     PITYR+P+ASAQVKSA+LL
Sbjct: 125 ASLNKRPMARVTKPLEEMGARFVGRSGGRLPLTVVGSGDLVPITYRLPVASAQVKSAILL 184

Query: 183 AGLNTPGVTTVIEPVMTRDHTEKMLQGFGADLSVETDKDGVRHIRITGQGKLIGQTIDVP 242
           AGLNT G TTVIE   TRDHTE ML+ FGA ++ E   DG   + + GQ +L G+TI VP
Sbjct: 185 AGLNTAGATTVIEAEPTRDHTELMLRHFGASVTTERLADGALAVTVIGQPELTGRTIHVP 244

Query: 243 GDPSSTAFPLVAALLVEGSDVTIRNVLMNPTRTGLILTLQEMGADIEVLNARLAGGEDVA 302
            DPSS AFP+VAALL  GS++ + +V MNP RTGL  TL EMGADI   N R   GE VA
Sbjct: 245 ADPSSAAFPVVAALLRPGSELLLNDVGMNPRRTGLYDTLVEMGADIAFENRRDQAGEPVA 304

Query: 303 DLRVKASKLKGVVVPPERAPSMIDEYPVLAIAAAFAEGETVMDGLDELRVKESDRLAAVA 362
           DLRV+   LKGVVVP +RAPSMIDEYPVLA AAA AEG TVM GL ELRVKESDRLA VA
Sbjct: 305 DLRVRHGALKGVVVPADRAPSMIDEYPVLAAAAACAEGTTVMLGLKELRVKESDRLAMVA 364

Query: 363 RGLEANGVDCTEG-EMSLTVRGRPDGKG---LGGGTVATHLDHRIAMSFLVMGLASEKPV 418
            GL   GV    G + SLTV G   G G    GG TV T +DHRIAMSFLV+G+A+E+PV
Sbjct: 365 EGLTRCGVSVEVGADDSLTVHG-TGGTGKAPKGGATVLTAMDHRIAMSFLVLGMATEQPV 423

Query: 419 TVDDSTMIATSFPEFMDMMPGLGAKI 444
           +VDD   I TSFP F+ +M GLGA I
Sbjct: 424 SVDDGAFIDTSFPGFVGLMNGLGAAI 449


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: 662
Number of extensions: 30
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: 452
Length adjustment: 33
Effective length of query: 417
Effective length of database: 419
Effective search space:   174723
Effective search space used:   174723
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 WP_012972917.1 AZL_RS01560 (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.21032.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.6e-120  386.6   0.0   7.5e-120  386.4   0.0    1.0  1  lcl|NCBI__GCF_000010725.1:WP_012972917.1  AZL_RS01560 3-phosphoshikimate 1


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000010725.1:WP_012972917.1  AZL_RS01560 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.4   0.0  7.5e-120  7.5e-120       1     414 [.      17     447 ..      17     448 .. 0.93

  Alignments for each domain:
  == domain 1  score: 386.4 bits;  conditional E-value: 7.5e-120
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.ke....elviegvg 64 
                                               g+i++pg+KSishR+l+l+a+a getv+++lL++eD+l t  a+r lGa+ e+e ++    ++ ++gvg
  lcl|NCBI__GCF_000010725.1:WP_012972917.1  17 GSIRVPGDKSISHRSLMLGAIAVGETVIHGLLEGEDVLHTAAAMRLLGAEAEREdNGqgpgVWRVRGVG 85 
                                               78*************************************************965343233379****99 PP

                                 TIGR01356  65 g..lkepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegs 131
                                                  l+ep ++ld+gnsGt+aRll+g++a ++ ++v+tgd sl+kRP+ r++++L+e+ga++  ++  g+
  lcl|NCBI__GCF_000010725.1:WP_012972917.1  86 LgaLREPAQVLDMGNSGTAARLLMGLVAGHPITCVFTGDASLNKRPMARVTKPLEEMGARFVGRS-GGR 153
                                               8899***********************************************************99.59* PP

                                 TIGR01356 132 lPlaisgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgvev 199
                                               lPl++ g   + +i++  + aS+Q+ksa+lla+   l++ ++++v+e + +r+++e++L  +++  v+ 
  lcl|NCBI__GCF_000010725.1:WP_012972917.1 154 LPLTVVGSGDLvPITYRLPVASAQVKSAILLAG---LNTAGATTVIEAEPTRDHTELMLRHFGAS-VTT 218
                                               ********7777*********************...8999999********************88.777 PP

                                 TIGR01356 200 eeede..rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLee 265
                                               e+  +    ++v g+ + + ++++v++D+SsAaf+++aa++ ++ e+ ++++g+n+ +++  + ++L e
  lcl|NCBI__GCF_000010725.1:WP_012972917.1 219 ERLADgaLAVTVIGQPELTGRTIHVPADPSSAAFPVVAALLRPGsELLLNDVGMNPRRTG--LYDTLVE 285
                                               7766655666777777677778**********************9***************..666**** PP

                                 TIGR01356 266 mGadveveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelR 325
                                               mGad+ +e+ r        d++v+ +  lkgv v   +++s+iDe+p+la++aa+Aeg+t++ +++elR
  lcl|NCBI__GCF_000010725.1:WP_012972917.1 286 MGADIAFENRRdqagepvaDLRVR-HGALKGVVVpADRAPSMIDEYPVLAAAAACAEGTTVMLGLKELR 353
                                               ************************.679******77999****************************** PP

                                 TIGR01356 326 vkEsdRiaaiaeeLeklGveveele.dgllieGkk...kelkg.avvdtydDHRiamalavlglaaege 389
                                               vkEsdR+a +ae L++ Gv+ve+++ d+l+++G+    k  kg a+v t  DHRiam++ vlg+a e++
  lcl|NCBI__GCF_000010725.1:WP_012972917.1 354 VKESDRLAMVAEGLTRCGVSVEVGAdDSLTVHGTGgtgKAPKGgATVLTAMDHRIAMSFLVLGMATEQP 422
                                               ***********************87369*****998887788779************************ PP

                                 TIGR01356 390 veiedaecvaksfPeFfevleqlga 414
                                               v ++d + +++sfP F+ +++ lga
  lcl|NCBI__GCF_000010725.1:WP_012972917.1 423 VSVDDGAFIDTSFPGFVGLMNGLGA 447
                                               ********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (452 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: 10.91
//
[ok]

This GapMind analysis is from Apr 10 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