Alignments for a candidate for aroA in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Rhodomicrobium vannielii ATCC 17100

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_245258033.1 RVAN_RS04590 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::A6WUV8
         (450 letters)



>NCBI__GCF_000166055.1:WP_245258033.1
          Length = 448

 Score =  464 bits (1194), Expect = e-135
 Identities = 249/435 (57%), Positives = 312/435 (71%), Gaps = 4/435 (0%)

Query: 12  ARRSEALTGEIRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGRAMQAMGAKIR 71
           +R+S  L G + +PGDKSISHR+ + G LA G TRITGLLE ED++ T RA++A+GA + 
Sbjct: 2   SRKSGRLQGAVVVPGDKSISHRALILGALAEGRTRITGLLEAEDILCTARALEALGAGVE 61

Query: 72  KDGD-AWIINGVGNGCLLQPEAALDFGNAGTGARLTMGLVGTYDMRTSFIGDASLSKRPM 130
           +D D AW + G G G L  P   LDFGN+GTGARL MG+V  + +   F GDASL KRPM
Sbjct: 62  RDADGAWTVTGRGLGGLAAPAGDLDFGNSGTGARLMMGVVAGHPLAARFTGDASLQKRPM 121

Query: 131 GRVLNPLREMGVQVEAAEGDRMPLTLIGPKTANPITYRVPMASAQVKSAVLLAGLNTPGV 190
           GRVL PL+ MG+ +E    + +PLTL+G     PI+YR+P+ SAQVKSAVLLAGL   G 
Sbjct: 122 GRVLAPLQSMGLAIEEEGRNTLPLTLVGTGDLVPISYRLPVPSAQVKSAVLLAGLFASGE 181

Query: 191 TTVIEPVMTRDHTEKMLQGFGADLSVETDKDGVRHIRITGQGKLIGQTIDVPGDPSSTAF 250
           T+VIE   +RDHTEKML+ FGA++SVE  + G+R I + G+  L GQ + VPGDPSS AF
Sbjct: 182 TSVIESEKSRDHTEKMLRYFGAEISVEPFEGGLR-IALEGRRTLQGQPVAVPGDPSSAAF 240

Query: 251 PLVAALLVEGSDVTIRNVLMNPTRTGLILTLQEMGADIEVLNARLAGGEDVADLRVKASK 310
            + AAL+   SD+ ++NVL+NPTRTG   TL EMGADI   N R   GE VAD+R + S+
Sbjct: 241 LVAAALITPASDILVKNVLVNPTRTGFYETLAEMGADISFENEREVSGEPVADIRARTSE 300

Query: 311 LKGVVVPPERAPSMIDEYPVLAIAAAFAEGETVMDGLDELRVKESDRLAAVARGLEANGV 370
           L+GV VP  RAPSMIDEYP+LA  A  AEGET+M+GL ELRVKESDRLAA+  GL A G 
Sbjct: 301 LRGVTVPAARAPSMIDEYPMLAALATLAEGETLMEGLAELRVKESDRLAAMVDGLVACGA 360

Query: 371 DCTEGEMSLTVRGRPDGKGLGGGTVATHLDHRIAMSFLVMGLASEKPVTVDDSTMIATSF 430
                  +LTV G P  K  GG T+ TH+DHRIAMSFLV+GLA+E+PVTVDD++MIATSF
Sbjct: 361 IAHARGDTLTVLGLP--KVRGGATIKTHMDHRIAMSFLVLGLATEEPVTVDDASMIATSF 418

Query: 431 PEFMDMMPGLGAKIE 445
           PEF  +M  +GA ++
Sbjct: 419 PEFRTLMQQVGATLD 433


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: 27
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: 450
Length of database: 448
Length adjustment: 33
Effective length of query: 417
Effective length of database: 415
Effective search space:   173055
Effective search space used:   173055
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_245258033.1 RVAN_RS04590 (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.2719890.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.3e-128  412.8   0.1   8.2e-128  412.6   0.1    1.0  1  NCBI__GCF_000166055.1:WP_245258033.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166055.1:WP_245258033.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.6   0.1  8.2e-128  8.2e-128       1     414 [.      10     430 ..      10     431 .. 0.95

  Alignments for each domain:
  == domain 1  score: 412.6 bits;  conditional E-value: 8.2e-128
                             TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..lkepe 70 
                                           g + +pg+KSishRal+l+aLaeg+t++t+lL++eD+l t +al++lGa ve++ ++ ++++g g   l+ p 
  NCBI__GCF_000166055.1:WP_245258033.1  10 GAVVVPGDKSISHRALILGALAEGRTRITGLLEAEDILCTARALEALGAGVERDaDGAWTVTGRGLggLAAPA 82 
                                           67889***********************************************666*******988778***** PP

                             TIGR01356  71 aeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkg. 142
                                             ld+gnsGt aRl++gv+a ++    +tgd sl+kRP++r++ +L+++g  ie++  +++lPl++ g+  + 
  NCBI__GCF_000166055.1:WP_245258033.1  83 GDLDFGNSGTGARLMMGVVAGHPLAARFTGDASLQKRPMGRVLAPLQSMGLAIEEEG-RNTLPLTLVGTGDLv 154
                                           ******************************************************866.68*********7777 PP

                             TIGR01356 143 givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede.rkivvkggqk 214
                                           +i++  +  S+Q+ksa+lla+   l a++++ v+e+++sr+++e++L  ++++ ++ve  ++  +i ++g  +
  NCBI__GCF_000166055.1:WP_245258033.1 155 PISYRLPVPSAQVKSAVLLAG---LFASGETSVIESEKSRDHTEKMLRYFGAE-ISVEPFEGgLRIALEGRRT 223
                                           *********************...66789999999****************99.9999877758888888888 PP

                             TIGR01356 215 ykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dv 278
                                            + + v+v+gD+SsAaf++aaa+it+  ++ v+n++ n+t+++  + ++L emGad+++e++r        d+
  NCBI__GCF_000166055.1:WP_245258033.1 224 LQGQPVAVPGDPSSAAFLVAAALITPAsDILVKNVLVNPTRTG--FYETLAEMGADISFENERevsgepvaDI 294
                                           55555**************************************..888***************9999999999 PP

                             TIGR01356 279 evegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveele 350
                                           + + +s+l+gv+v  ++++s+iDe+p+la+la++Aeget +++++elRvkEsdR+aa+++ L + G+ ++ + 
  NCBI__GCF_000166055.1:WP_245258033.1 295 RAR-TSELRGVTVpAARAPSMIDEYPMLAALATLAEGETLMEGLAELRVKESDRLAAMVDGLVACGAIAHARG 366
                                           999.789******88********************************************************** PP

                             TIGR01356 351 dgllieGkkkelkg.avvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                           d l++ G   +++g a+++t+ DHRiam++ vlgla e++v+++da+++a+sfPeF  +++q+ga
  NCBI__GCF_000166055.1:WP_245258033.1 367 DTLTVLGLP-KVRGgATIKTHMDHRIAMSFLVLGLATEEPVTVDDASMIATSFPEFRTLMQQVGA 430
                                           ********6.66655***********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (448 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 26.15
//
[ok]

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