Alignments for a candidate for aroA in Rhodopseudomonas palustris CGA009

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Rhodopseudomonas palustris CGA009

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011155632.1 TX73_RS00320 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::C3MC80
         (448 letters)



>NCBI__GCF_000195775.1:WP_011155632.1
          Length = 445

 Score =  491 bits (1263), Expect = e-143
 Identities = 267/447 (59%), Positives = 319/447 (71%), Gaps = 7/447 (1%)

Query: 1   MSHGLSPRPATAKKSADLKGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTG 60
           M+    P P  A+KS  L GT R+PGDKSISHR+ + G LA GETRI+GLLEGEDVINT 
Sbjct: 1   MTDSNQPMPLQARKSGALHGTARVPGDKSISHRALILGALAVGETRISGLLEGEDVINTA 60

Query: 61  KAMQAMGAKIRKEGDT-WIINGVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTF 119
           KAM+A+GAK+ + GD  W ++GVG      PEAPLDFGN+GTGCRL MG V      +TF
Sbjct: 61  KAMRALGAKVERTGDCEWRVHGVGVAGFATPEAPLDFGNSGTGCRLAMGAVAGSPIVATF 120

Query: 120 IGDASLTKRPMGRVLDPLREMGVQV-KSAEGDRLPVTLRGPKTPNPITYRVPMASAQVKS 178
            GDASL  RPM R++DPL  MG +V  S+EG RLP+ L+G + P PI YR P+ SAQ+KS
Sbjct: 121 DGDASLRSRPMRRIVDPLELMGAKVVSSSEGGRLPLALQGARDPLPILYRTPVPSAQIKS 180

Query: 179 AVLLAGLNTPGITTVIEPVMTRDHTEKMLQGFGANLSVETDTAGVRTIRLEGRGKLTGQV 238
           AVLLAGL+ PGITTVIE   +RDHTE MLQ FGA +  E + A  R I L G+ +L G  
Sbjct: 181 AVLLAGLSAPGITTVIEAEASRDHTELMLQHFGATIVTEAEGAHGRKISLTGQPELRGAP 240

Query: 239 IDVPGDPSSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGANIEVMNPRLAGG 298
           + VP DPSS AFP+VAAL+VPGSD+ + +V+ NP RTGLI TL+EMGA+IE  + R   G
Sbjct: 241 VVVPADPSSAAFPMVAALVVPGSDIELTDVMTNPLRTGLITTLREMGASIEDSDVRGDAG 300

Query: 299 EDVADLRVRYSELKGVTVPEERAPSMIDEYPVLAVAAAFAEGATVMNGLDELRVKESDRL 358
           E +A  RVR S+LKGV VP ERAPSMIDEY VLAVAAAFAEG TVM GL ELRVKESDRL
Sbjct: 301 EPMARFRVRGSKLKGVEVPPERAPSMIDEYLVLAVAAAFAEGTTVMRGLHELRVKESDRL 360

Query: 359 SAVADGLKLNGVDCDEGEASLVVRGRPGGKGLGNAAGGQVKTHLDHRIAMSFLVLGLASE 418
            A A  L++NGV  +     L+V G+    G     GG V TH+DHRIAMS L +GLAS+
Sbjct: 361 EATAAMLRVNGVAVEIAGDDLIVEGKGHVPG-----GGVVATHMDHRIAMSALAMGLASD 415

Query: 419 HPVTVDDATMIATSFPEFMDLMTGLGA 445
            PVTVDD   IATSFP+F+ +M  LGA
Sbjct: 416 KPVTVDDTAFIATSFPDFVPMMQRLGA 442


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: 683
Number of extensions: 39
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: 448
Length of database: 445
Length adjustment: 33
Effective length of query: 415
Effective length of database: 412
Effective search space:   170980
Effective search space used:   170980
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_011155632.1 TX73_RS00320 (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.13113.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-126  407.2   0.1   4.2e-126  407.0   0.1    1.0  1  lcl|NCBI__GCF_000195775.1:WP_011155632.1  TX73_RS00320 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195775.1:WP_011155632.1  TX73_RS00320 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.0   0.1  4.2e-126  4.2e-126       1     414 [.      20     442 ..      20     443 .. 0.95

  Alignments for each domain:
  == domain 1  score: 407.0 bits;  conditional E-value: 4.2e-126
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               g  ++pg+KSishRal+l+aLa get++ +lL++eD+++t +a+r+lGakve++ + e+ ++gvg   +
  lcl|NCBI__GCF_000195775.1:WP_011155632.1  20 GTARVPGDKSISHRALILGALAVGETRISGLLEGEDVINTAKAMRALGAKVERTgDCEWRVHGVGVagF 88 
                                               5679************************************************876889*****998889 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               ++pea ld+gnsGt  Rl +g++a ++   +++gd sl+ RP++r+v++L+ +ga++ s++e g+lPla
  lcl|NCBI__GCF_000195775.1:WP_011155632.1  89 ATPEAPLDFGNSGTGCRLAMGAVAGSPIVATFDGDASLRSRPMRRIVDPLELMGAKVVSSSEGGRLPLA 157
                                               ********************************************************************* PP

                                 TIGR01356 136 isgp.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               ++g   +++i + ++  S+Q ksa+lla+   l+a ++++v+e + sr+++e++L+ +++  v  e e 
  lcl|NCBI__GCF_000195775.1:WP_011155632.1 158 LQGArDPLPILYRTPVPSAQIKSAVLLAG---LSAPGITTVIEAEASRDHTELMLQHFGATIV-TEAEG 222
                                               ***97777*********************...8899***********************9944.44444 PP

                                 TIGR01356 204 e..rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGad 269
                                                  rki+++g+ + +   v v++D+SsAaf+++aa++ ++ +++++++++n+++++  +i++L+emGa+
  lcl|NCBI__GCF_000195775.1:WP_011155632.1 223 AhgRKISLTGQPELRGAPVVVPADPSSAAFPMVAALVVPGsDIELTDVMTNPLRTG--LITTLREMGAS 289
                                               457999999999966666*********************99***************..888******** PP

                                 TIGR01356 270 veveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEs 329
                                               +e  + r          +v+g sklkgv+v +++++s+iDe+++lav+aafAeg+t++++++elRvkEs
  lcl|NCBI__GCF_000195775.1:WP_011155632.1 290 IEDSDVRgdagepmaRFRVRG-SKLKGVEVpPERAPSMIDEYLVLAVAAAFAEGTTVMRGLHELRVKES 357
                                               **99999999****999***6.78******99************************************* PP

                                 TIGR01356 330 dRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecv 398
                                               dR++a+a+ L+  Gv ve   d l++eGk +   g+vv t+ DHRiam+   +gla +++v+++d++ +
  lcl|NCBI__GCF_000195775.1:WP_011155632.1 358 DRLEATAAMLRVNGVAVEIAGDDLIVEGKGHVPGGGVVATHMDHRIAMSALAMGLASDKPVTVDDTAFI 426
                                               *****************************766666********************************** PP

                                 TIGR01356 399 aksfPeFfevleqlga 414
                                               a+sfP+F+ ++++lga
  lcl|NCBI__GCF_000195775.1:WP_011155632.1 427 ATSFPDFVPMMQRLGA 442
                                               *************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (445 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: 00:00:00.01
# Mc/sec: 9.83
//
[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