Alignments for a candidate for aroA in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Magnetospirillum magneticum AMB-1

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_043745553.1 AMB_RS21555 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q9R4E4
         (455 letters)



>NCBI__GCF_000009985.1:WP_043745553.1
          Length = 444

 Score =  469 bits (1207), Expect = e-137
 Identities = 256/445 (57%), Positives = 311/445 (69%), Gaps = 11/445 (2%)

Query: 7   SRPATARKSSGLSGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGKAMQAM 66
           ++P ++R+++ L+G+  +PGDKSISHR+ M G LA GE+ +TGLLEG+DV+ T   M+A+
Sbjct: 2   AKPLSSRRAAPLAGSAPVPGDKSISHRALMLGALAVGESVVTGLLEGDDVLRTAACMRAL 61

Query: 67  GARIRKEGD-TWIIDGVGNGGLLAPEAPLDFGNAATGCRLTMGLVGVYDFDSTFIGDASL 125
           GA + +  D +W + G G GGL+ P   LD GN+ TG RL MGLV  + F   F GD SL
Sbjct: 62  GAEVERRDDGSWRLFGRGVGGLMEPADVLDMGNSGTGARLLMGLVATHPFTCFFTGDGSL 121

Query: 126 TKRPMGRVLNPLREMGVQVKSEDGDRLPVTLRGPKTPTPITYRVPMASAQVKSAVLLAGL 185
             RPM RV++PL  MG +  S DG RLP+ + G   PTPITY +P+ASAQVKSA++LAGL
Sbjct: 122 RSRPMRRVIDPLSRMGARFVSRDGGRLPLAVTGTAQPTPITYELPVASAQVKSAIMLAGL 181

Query: 186 NTPGITTVIEPIMTRDHTEKMLQGFGANLTVETDADGVRTIRLEGRGKLTGQVIDVPGDP 245
           NT G TTVIE   TRDHTE ML+ FGA + VE    G R I + G  +LTG+ + VP DP
Sbjct: 182 NTAGETTVIEREATRDHTELMLRNFGATVRVEDAEGGGRAITVVGFPELTGRPVVVPADP 241

Query: 246 SSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGADIEVINPRLAGGEDVADLR 305
           SS AFP+VAALLV GS++ + NV  NP RTGL  TL EMGADI   +PR   GE VADL 
Sbjct: 242 SSAAFPVVAALLVEGSEIRLPNVGTNPLRTGLYQTLLEMGADIRFDHPRDQAGEPVADLV 301

Query: 306 VRSSTLKGVTVPEDRAPSMIDEYPILAVAAAFAEGATVMNGLEELRVKESDRLSAVANGL 365
           VRSS LKGV VP +RAPSMIDEYPILAVAAAFAEG T M GL ELRVKESDRL+A+A GL
Sbjct: 302 VRSSRLKGVDVPAERAPSMIDEYPILAVAAAFAEGTTRMRGLGELRVKESDRLAAMARGL 361

Query: 366 KLNGVDCDEGETSLVVRGR---PDGKGLGNASGAAVATHLDHRIAMSFLVMGLVSENPVT 422
              GV  +E + +L+V G    PDG        A V TH DHRIAMSFLVMG+ S  PV 
Sbjct: 362 AACGVAVEEEKDALIVHGTGRIPDG-------DATVTTHFDHRIAMSFLVMGMASARPVA 414

Query: 423 VDDATMIATSFPEFMDLMAGLGAKI 447
           VDD+  I TSFP F++LM GLGAKI
Sbjct: 415 VDDSEAIDTSFPAFVELMNGLGAKI 439


Lambda     K      H
   0.316    0.135    0.380 

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: 679
Number of extensions: 31
Number of successful extensions: 4
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: 455
Length of database: 444
Length adjustment: 33
Effective length of query: 422
Effective length of database: 411
Effective search space:   173442
Effective search space used:   173442
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_043745553.1 AMB_RS21555 (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.5234.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-129  418.3   0.0   1.7e-129  418.2   0.0    1.0  1  lcl|NCBI__GCF_000009985.1:WP_043745553.1  AMB_RS21555 3-phosphoshikimate 1


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_043745553.1  AMB_RS21555 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.2   0.0  1.7e-129  1.7e-129       3     414 ..      17     437 ..      15     438 .. 0.94

  Alignments for each domain:
  == domain 1  score: 418.2 bits;  conditional E-value: 1.7e-129
                                 TIGR01356   3 ikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..lke 68 
                                                 +pg+KSishRal+l+aLa ge+vvt+lL+++D+l t  ++r+lGa+ve ++++++   g g   l e
  lcl|NCBI__GCF_000009985.1:WP_043745553.1  17 APVPGDKSISHRALMLGALAVGESVVTGLLEGDDVLRTAACMRALGAEVErRDDGSWRLFGRGVggLME 85 
                                               569***********************************************5559999987766566*** PP

                                 TIGR01356  69 peaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlais 137
                                               p ++ld+gnsGt aRll+g++a++++++ +tgd sl+ RP++r++++L+++ga++ s++  g+lPla++
  lcl|NCBI__GCF_000009985.1:WP_043745553.1  86 PADVLDMGNSGTGARLLMGLVATHPFTCFFTGDGSLRSRPMRRVIDPLSRMGARFVSRD-GGRLPLAVT 153
                                               ********************************************************999.59******* PP

                                 TIGR01356 138 gp.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede. 204
                                               g+ ++ +i++  + aS+Q+ksa++la+   l++ ++++v+e++ +r+++e++L  +++  v+ve  ++ 
  lcl|NCBI__GCF_000009985.1:WP_043745553.1 154 GTaQPTPITYELPVASAQVKSAIMLAG---LNTAGETTVIEREATRDHTELMLRNFGAT-VRVEDAEGg 218
                                               **7777*********************...88899999999****************88.999999888 PP

                                 TIGR01356 205 .rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadve 271
                                                r i+v g  + + + v v++D+SsAaf+++aa++ ++ e+++ n+g+n+++++  + ++L emGad++
  lcl|NCBI__GCF_000009985.1:WP_043745553.1 219 gRAITVVGFPELTGRPVVVPADPSSAAFPVVAALLVEGsEIRLPNVGTNPLRTG--LYQTLLEMGADIR 285
                                               9999999999955556*******************9999***************..666********** PP

                                 TIGR01356 272 veeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdR 331
                                               +++ r        d++v+ +s lkgv+v  ++++s+iDe+p+lav+aafAeg+tr++++ elRvkEsdR
  lcl|NCBI__GCF_000009985.1:WP_043745553.1 286 FDHPRdqagepvaDLVVR-SSRLKGVDVpAERAPSMIDEYPILAVAAAFAEGTTRMRGLGELRVKESDR 353
                                               ***9999***********.789******88*************************************** PP

                                 TIGR01356 332 iaaiaeeLeklGveveeledgllieGkkkelkg..avvdtydDHRiamalavlglaaegeveiedaecv 398
                                               +aa+a+ L++ Gv vee +d l+++G+  ++ +  a+v t+ DHRiam++ v+g+a +++v ++d+e++
  lcl|NCBI__GCF_000009985.1:WP_043745553.1 354 LAAMARGLAACGVAVEEEKDALIVHGTG-RIPDgdATVTTHFDHRIAMSFLVMGMASARPVAVDDSEAI 421
                                               ***************************6.5554479********************************* PP

                                 TIGR01356 399 aksfPeFfevleqlga 414
                                               ++sfP F+e+++ lga
  lcl|NCBI__GCF_000009985.1:WP_043745553.1 422 DTSFPAFVELMNGLGA 437
                                               ************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (444 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: 10.90
//
[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