Alignments for a candidate for aroA in Allochromatium vinosum DSM 180

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Allochromatium vinosum DSM 180

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_012970853.1 ALVIN_RS08160 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_000025485.1:WP_012970853.1
          Length = 488

 Score =  477 bits (1228), Expect = e-139
 Identities = 253/436 (58%), Positives = 314/436 (72%), Gaps = 6/436 (1%)

Query: 3   YQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGAS 62
           Y   P   L G + VPGDKSISHR+++L+AIAEG+TQV GFL GAD LA ++A + MG S
Sbjct: 53  YLISPGGSLRGRLRVPGDKSISHRSIMLSAIAEGRTQVSGFLEGADALATLAAFRAMGVS 112

Query: 63  IQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQR 122
           I+   D   LV+EGVGM GL+AP   LD GNSGTA+RLL GLLAGQ F   L GD SL R
Sbjct: 113 IEGPSDGE-LVIEGVGMRGLRAPDTTLDMGNSGTAMRLLVGLLAGQGFTATLVGDDSLTR 171

Query: 123 RPMKRIIDPLTLMGAKI-DSTGNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLYA 181
           RPM+R+ +PL LMGA+I  S     PL I     L G+ Y+LPMASAQVKSCL+LAGLYA
Sbjct: 172 RPMRRVTEPLALMGAQIRTSPTGTAPLTIEPVDHLNGLEYRLPMASAQVKSCLMLAGLYA 231

Query: 182 RGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFI 241
            G+TCI EP P+RDHTER+L  F Y++++    +C++GGG+L A  + IP DISSAAFF+
Sbjct: 232 EGETCIVEPEPTRDHTERMLTAFGYSVRRQGLRVCLTGGGRLTACRLRIPADISSAAFFL 291

Query: 242 VAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLK 301
           V A+I PGS + L  VG+NPTR+GVIN+++ MGADIE+        EP ADI V+ ARL+
Sbjct: 292 VGASIAPGSDLLLEAVGINPTRVGVINIMRAMGADIELLDKRTAGGEPVADIRVKSARLR 351

Query: 302 GIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAA 361
           GI IP DQVPL IDEFP L IAAA A+G+TVL  A ELRVKE+DRI  M DGL KLGI A
Sbjct: 352 GIRIPVDQVPLAIDEFPALFIAAACAEGETVLTGAEELRVKESDRIQVMADGLTKLGIQA 411

Query: 362 ESLPDGVIIQGGTLEG--GE--VNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPN 417
           E  PDG+ IQGGTL    GE  + ++ DHRIAM+FA+AG  A GP+ +R+C NV+TSFP 
Sbjct: 412 EPTPDGIRIQGGTLGSATGENAIEAHGDHRIAMSFAIAGLRASGPIEVRDCANVETSFPG 471

Query: 418 FVELANEVGMNVKGVR 433
           F +LA+  G+ ++  R
Sbjct: 472 FPQLASNAGLTIEEQR 487


Lambda     K      H
   0.318    0.137    0.392 

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: 747
Number of extensions: 33
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: 438
Length of database: 488
Length adjustment: 33
Effective length of query: 405
Effective length of database: 455
Effective search space:   184275
Effective search space used:   184275
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_012970853.1 ALVIN_RS08160 (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.5958.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   7.4e-123  396.3   0.0   9.2e-123  396.0   0.0    1.0  1  lcl|NCBI__GCF_000025485.1:WP_012970853.1  ALVIN_RS08160 3-phosphoshikimate


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025485.1:WP_012970853.1  ALVIN_RS08160 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.0   0.0  9.2e-123  9.2e-123       1     410 [.      63     477 ..      63     481 .. 0.94

  Alignments for each domain:
  == domain 1  score: 396.0 bits;  conditional E-value: 9.2e-123
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 
                                               g++++pg+KSishR+++l+a+aeg+t+v ++L+++D latl a+r++G+++e  +++elviegvg+  l
  lcl|NCBI__GCF_000025485.1:WP_012970853.1  63 GRLRVPGDKSISHRSIMLSAIAEGRTQVSGFLEGADALATLAAFRAMGVSIEgPSDGELVIEGVGMrgL 131
                                               789*************************************************6669********9999* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               + p+ +ld+gnsGt++Rll+g+la ++++ +l gd+sl +RP++r++e+L  +ga+i+ +  +g++Pl+
  lcl|NCBI__GCF_000025485.1:WP_012970853.1 132 RAPDTTLDMGNSGTAMRLLVGLLAGQGFTATLVGDDSLTRRPMRRVTEPLALMGAQIRTSP-TGTAPLT 199
                                               **********************************************************877.69***** PP

                                 TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               i+   ++ g  +  ++aS+Q+ks+l+la+   l a++++ + e++ +r+++e++L  ++    +v+++ 
  lcl|NCBI__GCF_000025485.1:WP_012970853.1 200 IEPVDHLnGLEYRLPMASAQVKSCLMLAG---LYAEGETCIVEPEPTRDHTERMLTAFGY---SVRRQG 262
                                               ***97778*********************...66778888888***********987765...599998 PP

                                 TIGR01356 204 erkivvkggqk.ykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                                 ++ ++gg+  ++++ +++++D+SsAaffl+ a i+++ ++ +e +g+n+t+ +  +i+++++mGad+
  lcl|NCBI__GCF_000025485.1:WP_012970853.1 263 L-RVCLTGGGRlTACR-LRIPADISSAAFFLVGASIAPGsDLLLEAVGINPTRVG--VINIMRAMGADI 327
                                               7.88899988856666.**********************9***************..888********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               e+ ++r        d++v+ +  l+g+++   +v+ +iDe+p+l ++aa+Aeget+++++eelRvkEsd
  lcl|NCBI__GCF_000025485.1:WP_012970853.1 328 ELLDKRtaggepvaDIRVK-SARLRGIRIpVDQVPLAIDEFPALFIAAACAEGETVLTGAEELRVKESD 395
                                               *****9*************.568******55889*********************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkk..kelkgavvdtydDHRiamalavlglaaegeveiedaec 397
                                               Ri+++a+ L+klG+++e+++dg+ i+G++  +   +  ++ ++DHRiam++a++gl+a+g++e+ d + 
  lcl|NCBI__GCF_000025485.1:WP_012970853.1 396 RIQVMADGLTKLGIQAEPTPDGIRIQGGTlgSATGENAIEAHGDHRIAMSFAIAGLRASGPIEVRDCAN 464
                                               *****************************966666699******************************* PP

                                 TIGR01356 398 vaksfPeFfevle 410
                                               v++sfP F +++ 
  lcl|NCBI__GCF_000025485.1:WP_012970853.1 465 VETSFPGFPQLAS 477
                                               ********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (488 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: 00:00:00.02
# Mc/sec: 9.77
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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