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_013418594.1 RVAN_RS04590 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::A6WUV8
         (450 letters)



>NCBI__GCF_000166055.1:WP_013418594.1
          Length = 459

 Score =  471 bits (1212), Expect = e-137
 Identities = 252/445 (56%), Positives = 318/445 (71%), Gaps = 4/445 (0%)

Query: 2   SHSAPPKPATARRSEALTGEIRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGR 61
           +H+A  +P  +R+S  L G + +PGDKSISHR+ + G LA G TRITGLLE ED++ T R
Sbjct: 3   THAADVRPLMSRKSGRLQGAVVVPGDKSISHRALILGALAEGRTRITGLLEAEDILCTAR 62

Query: 62  AMQAMGAKIRKDGD-AWIINGVGNGCLLQPEAALDFGNAGTGARLTMGLVGTYDMRTSFI 120
           A++A+GA + +D D AW + G G G L  P   LDFGN+GTGARL MG+V  + +   F 
Sbjct: 63  ALEALGAGVERDADGAWTVTGRGLGGLAAPAGDLDFGNSGTGARLMMGVVAGHPLAARFT 122

Query: 121 GDASLSKRPMGRVLNPLREMGVQVEAAEGDRMPLTLIGPKTANPITYRVPMASAQVKSAV 180
           GDASL KRPMGRVL PL+ MG+ +E    + +PLTL+G     PI+YR+P+ SAQVKSAV
Sbjct: 123 GDASLQKRPMGRVLAPLQSMGLAIEEEGRNTLPLTLVGTGDLVPISYRLPVPSAQVKSAV 182

Query: 181 LLAGLNTPGVTTVIEPVMTRDHTEKMLQGFGADLSVETDKDGVRHIRITGQGKLIGQTID 240
           LLAGL   G T+VIE   +RDHTEKML+ FGA++SVE  + G+R I + G+  L GQ + 
Sbjct: 183 LLAGLFASGETSVIESEKSRDHTEKMLRYFGAEISVEPFEGGLR-IALEGRRTLQGQPVA 241

Query: 241 VPGDPSSTAFPLVAALLVEGSDVTIRNVLMNPTRTGLILTLQEMGADIEVLNARLAGGED 300
           VPGDPSS AF + AAL+   SD+ ++NVL+NPTRTG   TL EMGADI   N R   GE 
Sbjct: 242 VPGDPSSAAFLVAAALITPASDILVKNVLVNPTRTGFYETLAEMGADISFENEREVSGEP 301

Query: 301 VADLRVKASKLKGVVVPPERAPSMIDEYPVLAIAAAFAEGETVMDGLDELRVKESDRLAA 360
           VAD+R + S+L+GV VP  RAPSMIDEYP+LA  A  AEGET+M+GL ELRVKESDRLAA
Sbjct: 302 VADIRARTSELRGVTVPAARAPSMIDEYPMLAALATLAEGETLMEGLAELRVKESDRLAA 361

Query: 361 VARGLEANGVDCTEGEMSLTVRGRPDGKGLGGGTVATHLDHRIAMSFLVMGLASEKPVTV 420
           +  GL A G        +LTV G P  K  GG T+ TH+DHRIAMSFLV+GLA+E+PVTV
Sbjct: 362 MVDGLVACGAIAHARGDTLTVLGLP--KVRGGATIKTHMDHRIAMSFLVLGLATEEPVTV 419

Query: 421 DDSTMIATSFPEFMDMMPGLGAKIE 445
           DD++MIATSFPEF  +M  +GA ++
Sbjct: 420 DDASMIATSFPEFRTLMQQVGATLD 444


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: 664
Number of extensions: 29
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: 459
Length adjustment: 33
Effective length of query: 417
Effective length of database: 426
Effective search space:   177642
Effective search space used:   177642
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_013418594.1 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.4002.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     8e-128  412.7   0.1     9e-128  412.5   0.1    1.0  1  lcl|NCBI__GCF_000166055.1:WP_013418594.1  RVAN_RS04590 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000166055.1:WP_013418594.1  RVAN_RS04590 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.5   0.1    9e-128    9e-128       1     414 [.      21     441 ..      21     442 .. 0.95

  Alignments for each domain:
  == domain 1  score: 412.5 bits;  conditional E-value: 9e-128
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               g + +pg+KSishRal+l+aLaeg+t++t+lL++eD+l t +al++lGa ve++ ++ ++++g g   l
  lcl|NCBI__GCF_000166055.1:WP_013418594.1  21 GAVVVPGDKSISHRALILGALAEGRTRITGLLEAEDILCTARALEALGAGVERDaDGAWTVTGRGLggL 89 
                                               67889***********************************************666*******988778* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               + p   ld+gnsGt aRl++gv+a ++    +tgd sl+kRP++r++ +L+++g  ie++  +++lPl+
  lcl|NCBI__GCF_000166055.1:WP_013418594.1  90 AAPAGDLDFGNSGTGARLMMGVVAGHPLAARFTGDASLQKRPMGRVLAPLQSMGLAIEEEG-RNTLPLT 157
                                               **********************************************************866.68***** PP

                                 TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               + g+  + +i++  +  S+Q+ksa+lla+   l a++++ v+e+++sr+++e++L  ++++ ++ve  +
  lcl|NCBI__GCF_000166055.1:WP_013418594.1 158 LVGTGDLvPISYRLPVPSAQVKSAVLLAG---LFASGETSVIESEKSRDHTEKMLRYFGAE-ISVEPFE 222
                                               ****7777*********************...66789999999****************99.9999877 PP

                                 TIGR01356 204 e.rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                               +  +i ++g  + + + v+v+gD+SsAaf++aaa+it+  ++ v+n++ n+t+++  + ++L emGad+
  lcl|NCBI__GCF_000166055.1:WP_013418594.1 223 GgLRIALEGRRTLQGQPVAVPGDPSSAAFLVAAALITPAsDILVKNVLVNPTRTG--FYETLAEMGADI 289
                                               75888888888855555**************************************..888********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               ++e++r        d++ + +s+l+gv+v  ++++s+iDe+p+la+la++Aeget +++++elRvkEsd
  lcl|NCBI__GCF_000166055.1:WP_013418594.1 290 SFENERevsgepvaDIRAR-TSELRGVTVpAARAPSMIDEYPMLAALATLAEGETLMEGLAELRVKESD 357
                                               ******9999999999999.789******88************************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkkkelkg.avvdtydDHRiamalavlglaaegeveiedaecv 398
                                               R+aa+++ L + G+ ++ + d l++ G   +++g a+++t+ DHRiam++ vlgla e++v+++da+++
  lcl|NCBI__GCF_000166055.1:WP_013418594.1 358 RLAAMVDGLVACGAIAHARGDTLTVLGLP-KVRGgATIKTHMDHRIAMSFLVLGLATEEPVTVDDASMI 425
                                               ****************************6.66655********************************** PP

                                 TIGR01356 399 aksfPeFfevleqlga 414
                                               a+sfPeF  +++q+ga
  lcl|NCBI__GCF_000166055.1:WP_013418594.1 426 ATSFPEFRTLMQQVGA 441
                                               *************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (459 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: 00:00:00.02
# Mc/sec: 9.06
//
[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