Alignments for a candidate for aroA in Xanthobacter autotrophicus Py2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Xanthobacter autotrophicus Py2

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_012113130.1 XAUT_RS05570 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::C3MC80
         (448 letters)



>NCBI__GCF_000017645.1:WP_012113130.1
          Length = 456

 Score =  506 bits (1302), Expect = e-148
 Identities = 282/448 (62%), Positives = 321/448 (71%), Gaps = 8/448 (1%)

Query: 3   HGLSP-RPATAKKSADLKGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGK 61
           HG  P +PATA +S  L G VR+PGDKS+SHR+ +FG  A G TRITGLLEGEDV+NT K
Sbjct: 13  HGDGPAQPATALRSPALTGRVRVPGDKSVSHRALIFGLFAEGITRITGLLEGEDVLNTAK 72

Query: 62  AMQAMGAKIRKEGD-TWIINGVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTFI 120
           A  A+GA++ + G   W + G G   L +P APLDFGN+GTG RL MG V   D  +TF 
Sbjct: 73  ACAALGARVTRRGPGEWEVEGAGADGLSSPAAPLDFGNSGTGVRLMMGAVAGQDVTATFD 132

Query: 121 GDASLTKRPMGRVLDPLREMGVQ-VKSAEGDRLPVTLRGPKTPNPITYRVPMASAQVKSA 179
           GDASL +RPM RVLDPL  MGV+ V SAEG RLP+TL+G      ITY  PM SAQVKSA
Sbjct: 133 GDASLRRRPMKRVLDPLTAMGVEIVDSAEGGRLPLTLKGSDRTKAITYETPMPSAQVKSA 192

Query: 180 VLLAGLNTPGITTVIEPVMTRDHTEKMLQGFGANLSVETDTAGVRTIRLEGRGKLTGQVI 239
           VLLAGL   G T VIE   TRDHTE+ML  FGA++ VE   A  R I L+GR  L    +
Sbjct: 193 VLLAGLGAAGETVVIEREATRDHTERMLAHFGADVRVEPHGAHGRRIALKGRPTLVAAPV 252

Query: 240 DVPGDPSSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGANIEVMNPRLAGGE 299
           DVP DPSS AFPLVAAL+VPGSDVT+ +V+MNP RTGLI TL EMGA+IEV+  R  GGE
Sbjct: 253 DVPADPSSAAFPLVAALIVPGSDVTLTDVMMNPLRTGLITTLLEMGASIEVVAERTEGGE 312

Query: 300 DVADLRVRYSELKGVTVPEERAPSMIDEYPVLAVAAAFAEGATVMNGLDELRVKESDRLS 359
            VADLRVR+S LKGV VP ERAP+MIDEYP+LAVAAAFAEG T M GL ELRVKESDRL+
Sbjct: 313 RVADLRVRHSRLKGVEVPPERAPAMIDEYPILAVAAAFAEGVTAMRGLSELRVKESDRLA 372

Query: 360 AVADGLKLNGVDCDEGEASLVVRGRPGGKGLGNAAGGQVKTHLDHRIAMSFLVLGLASEH 419
           AVADGL   GV  +     L+V G    KG     GG V TH+DHRIAMSFLVLGLASE 
Sbjct: 373 AVADGLAACGVAHEVVGDDLLVTGATTVKG-----GGPVATHMDHRIAMSFLVLGLASEQ 427

Query: 420 PVTVDDATMIATSFPEFMDLMTGLGATI 447
            V+VDD   IATSFP FM +M GLGA I
Sbjct: 428 GVSVDDVAFIATSFPTFMPMMRGLGAVI 455


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: 685
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: 448
Length of database: 456
Length adjustment: 33
Effective length of query: 415
Effective length of database: 423
Effective search space:   175545
Effective search space used:   175545
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_012113130.1 XAUT_RS05570 (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.16675.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-129  418.3   0.1   1.8e-129  418.1   0.1    1.0  1  lcl|NCBI__GCF_000017645.1:WP_012113130.1  XAUT_RS05570 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000017645.1:WP_012113130.1  XAUT_RS05570 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.1   0.1  1.8e-129  1.8e-129       1     414 [.      31     453 ..      31     454 .. 0.96

  Alignments for each domain:
  == domain 1  score: 418.1 bits;  conditional E-value: 1.8e-129
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               g++++pg+KS+shRal+++++aeg t++t+lL++eD+l+t +a+ +lGa+v++   +e+ +eg g   l
  lcl|NCBI__GCF_000017645.1:WP_012113130.1  31 GRVRVPGDKSVSHRALIFGLFAEGITRITGLLEGEDVLNTAKACAALGARVTRRgPGEWEVEGAGAdgL 99 
                                               789*************************************************5559*******998899 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                                 p a ld+gnsGt +Rl++g++a ++ + +++gd sl++RP++r++++L ++g+ei ++ e g+lPl+
  lcl|NCBI__GCF_000017645.1:WP_012113130.1 100 SSPAAPLDFGNSGTGVRLMMGAVAGQDVTATFDGDASLRRRPMKRVLDPLTAMGVEIVDSAEGGRLPLT 168
                                               ********************************************************************* PP

                                 TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               ++g  +  +i++ +++ S+Q+ksa+lla+   l a ++++v+e++ +r+++e++L+ ++++ v+ve + 
  lcl|NCBI__GCF_000017645.1:WP_012113130.1 169 LKGSDRTkAITYETPMPSAQVKSAVLLAG---LGAAGETVVIEREATRDHTERMLAHFGAD-VRVEPHG 233
                                               ****5555*********************...8999***********************99.9999998 PP

                                 TIGR01356 204 e..rkivvkggqk.ykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGa 268
                                                  r+i +kg  +  + + v+v++D+SsAaf+l+aa+i ++ +vt++++++n+++++  +i++L emGa
  lcl|NCBI__GCF_000017645.1:WP_012113130.1 234 AhgRRIALKGRPTlVAAP-VDVPADPSSAAFPLVAALIVPGsDVTLTDVMMNPLRTG--LITTLLEMGA 299
                                               877899999998866666.**********************9***************..888******* PP

                                 TIGR01356 269 dveveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkE 328
                                               ++ev ++r        d++v+ +s lkgv+v +++++ +iDe+p+lav+aafAeg+t +++++elRvkE
  lcl|NCBI__GCF_000017645.1:WP_012113130.1 300 SIEVVAERteggervaDLRVR-HSRLKGVEVpPERAPAMIDEYPILAVAAAFAEGVTAMRGLSELRVKE 367
                                               ******999************.689******99************************************ PP

                                 TIGR01356 329 sdRiaaiaeeLeklGveveeledgllieGkkkelkg.avvdtydDHRiamalavlglaaegeveiedae 396
                                               sdR+aa+a+ L++ Gv  e+  d ll++G++ ++kg + v t+ DHRiam++ vlgla e++v ++d +
  lcl|NCBI__GCF_000017645.1:WP_012113130.1 368 SDRLAAVADGLAACGVAHEVVGDDLLVTGAT-TVKGgGPVATHMDHRIAMSFLVLGLASEQGVSVDDVA 435
                                               ******************************5.8887699****************************** PP

                                 TIGR01356 397 cvaksfPeFfevleqlga 414
                                                +a+sfP F+ +++ lga
  lcl|NCBI__GCF_000017645.1:WP_012113130.1 436 FIATSFPTFMPMMRGLGA 453
                                               *************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (456 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.13
//
[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