GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroA in Ruegeria conchae TW15

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_010438017.1 G7G_RS0102615 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::C3MC80
         (448 letters)



>NCBI__GCF_000192475.1:WP_010438017.1
          Length = 452

 Score =  450 bits (1158), Expect = e-131
 Identities = 248/448 (55%), Positives = 305/448 (68%), Gaps = 9/448 (2%)

Query: 3   HGLSPRPATAKKSADLKGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGKA 62
           HG +P P T+     L GT  +PGDKSISHRS + G +A GETRI+GLLEGEDV++T KA
Sbjct: 4   HG-TPIPMTSHPCGPLTGTAEVPGDKSISHRSLILGAMAVGETRISGLLEGEDVLDTAKA 62

Query: 63  MQAMGAKIRKEGD-TWIINGVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTFIG 121
           M+A GA++   G   W ++GVG G    P+  +D GN+GTG RL MG +      +TF G
Sbjct: 63  MRAFGAEVTDHGGGEWSVHGVGVGGFAEPDQVIDCGNSGTGVRLIMGAMATSPITATFTG 122

Query: 122 DASLTKRPMGRVLDPLREMGVQVKSAEGDRLPVTLRGPKTPNPITYRVPMASAQVKSAVL 181
           DASL KRPM RV DPL   G Q     G RLP+T+ G   P P+ Y VP+ SAQVKSAVL
Sbjct: 123 DASLNKRPMARVTDPLALFGTQSVGRNGGRLPMTIVGAADPIPVRYEVPVPSAQVKSAVL 182

Query: 182 LAGLNTPGITTVIEPVMTRDHTEKMLQGFGANLSVETDTAGVRTIRLEGRGKLTGQVIDV 241
           LAGLN PG T VIE   TRDH+E+ML GFGA ++VE DT   R I L GR +L  QVI V
Sbjct: 183 LAGLNAPGKTVVIEKEATRDHSERMLAGFGAEITVE-DTDEGRVITLTGRPELKPQVIAV 241

Query: 242 PGDPSSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGANIEVMNPRLAGGEDV 301
           P DPSS AFP+ AAL+ PGSDV +  + +NPTR GL  TL+EMGA++   N R  GGE V
Sbjct: 242 PRDPSSAAFPVCAALITPGSDVLVPGIGLNPTRAGLFTTLREMGADLTYENEREEGGEPV 301

Query: 302 ADLRVRYS-ELKGVTVPEERAPSMIDEYPVLAVAAAFAEGATVMNGLDELRVKESDRLSA 360
           ADLR +YS  +KG++VP ERA SMIDEYPVL+V AA A G  +M G+ ELRVKESDR+ A
Sbjct: 302 ADLRAKYSPNMKGISVPPERAASMIDEYPVLSVVAANATGTMMMGGVKELRVKESDRIDA 361

Query: 361 VADGLKLNGVDCDEGEASLVVRGRPGGKGLGNAAGGQV-KTHLDHRIAMSFLVLGLASEH 419
           +A GL+ NGV  DEG+    V     G G+G   GG + ++ LDHRIAMSF+V+G+ ++ 
Sbjct: 362 MARGLRANGVTVDEGDDWWSVE----GLGIGGVPGGGICESFLDHRIAMSFMVMGMGAKK 417

Query: 420 PVTVDDATMIATSFPEFMDLMTGLGATI 447
            V+VDD   IATSFP F  LMTGLGA +
Sbjct: 418 AVSVDDGGPIATSFPIFEPLMTGLGAKL 445


Lambda     K      H
   0.316    0.135    0.385 

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: 728
Number of extensions: 53
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 448
Length of database: 452
Length adjustment: 33
Effective length of query: 415
Effective length of database: 419
Effective search space:   173885
Effective search space used:   173885
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_010438017.1 G7G_RS0102615 (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.1873256.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-118  382.7   0.0   1.1e-118  382.6   0.0    1.0  1  NCBI__GCF_000192475.1:WP_010438017.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_010438017.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.6   0.0  1.1e-118  1.1e-118       2     414 ..      21     443 ..      20     444 .. 0.96

  Alignments for each domain:
  == domain 1  score: 382.6 bits;  conditional E-value: 1.1e-118
                             TIGR01356   2 eikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..lkepea 71 
                                             ++pg+KSishR+l+l+a+a get++ +lL++eD+l t +a+r++Ga+v+++ ++e+ ++gvg   ++ep++
  NCBI__GCF_000192475.1:WP_010438017.1  21 TAEVPGDKSISHRSLILGAMAVGETRISGLLEGEDVLDTAKAMRAFGAEVTDHgGGEWSVHGVGVggFAEPDQ 93 
                                           6789***********************************************666********99888****** PP

                             TIGR01356  72 eldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkgg 143
                                           ++d+gnsGt +Rl++g++a+++ + ++tgd sl+kRP+ r++++L  +g +   ++  g+lP++i g   + +
  NCBI__GCF_000192475.1:WP_010438017.1  94 VIDCGNSGTGVRLIMGAMATSPITATFTGDASLNKRPMARVTDPLALFGTQSVGRN-GGRLPMTIVGAaDPIP 165
                                           ***************************************************99988.69********96666* PP

                             TIGR01356 144 ivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede.rkivvkggqky 215
                                           + +  +  S+Q+ksa+lla+   l+a + ++v+ek+ +r++ e++L+ ++++ ++ve +de r i+++g  + 
  NCBI__GCF_000192475.1:WP_010438017.1 166 VRYEVPVPSAQVKSAVLLAG---LNAPGKTVVIEKEATRDHSERMLAGFGAE-ITVEDTDEgRVITLTGRPEL 234
                                           ********************...8999***********************99.****9999888999999889 PP

                             TIGR01356 216 kqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dve 279
                                           k++ ++v+ D+SsAaf++ aa+it++ +v v ++g n+t+++  ++++L+emGad+++e++r        d++
  NCBI__GCF_000192475.1:WP_010438017.1 235 KPQVIAVPRDPSSAAFPVCAALITPGsDVLVPGIGLNPTRAG--LFTTLREMGADLTYENEReeggepvaDLR 305
                                           9999**************************************..888************************** PP

                             TIGR01356 280 vegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeled 351
                                            + + ++kg+ v +++++s+iDe+p+l+v+aa A g+ ++ +++elRvkEsdRi a+a+ L++ Gv+v+e+ d
  NCBI__GCF_000192475.1:WP_010438017.1 306 AKYSPNMKGISVpPERAASMIDEYPVLSVVAANATGTMMMGGVKELRVKESDRIDAMARGLRANGVTVDEGDD 378
                                           ************99*********************************************************** PP

                             TIGR01356 352 gllieGkk..kelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                           + ++eG        g+  +++ DHRiam++ v+g+ a++ v ++d + +a+sfP F  ++  lga
  NCBI__GCF_000192475.1:WP_010438017.1 379 WWSVEGLGigGVPGGGICESFLDHRIAMSFMVMGMGAKKAVSVDDGGPIATSFPIFEPLMTGLGA 443
                                           *******99455555899***************************************99999987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 25.67
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

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:

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:

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:

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:

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