Alignments for a candidate for aroA in Methylocapsa acidiphila B2

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Methylocapsa acidiphila B2

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_026606222.1 METAC_RS0105305 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::C3MC80
         (448 letters)



>NCBI__GCF_000427445.1:WP_026606222.1
          Length = 445

 Score =  468 bits (1205), Expect = e-136
 Identities = 257/442 (58%), Positives = 315/442 (71%), Gaps = 6/442 (1%)

Query: 6   SPRPATAKKSADLKGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGKAMQA 65
           +P    A+ S  L+G ++ PGDKSISHR+ + G L+ GET I GLLEG+DV+ T  A +A
Sbjct: 5   APNRLAAQASGPLRGRLKPPGDKSISHRALILGLLSVGETLIDGLLEGDDVLRTAAACRA 64

Query: 66  MGAKIRKEGD-TWIINGVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTFIGDAS 124
           +GA++ + G+  W ++G G G+LLAP  PLDFGN+GTG RL MG+VG +   + F GDAS
Sbjct: 65  LGAEVVRLGEGRWRVSGCGIGSLLAPREPLDFGNSGTGARLMMGVVGGHAITACFDGDAS 124

Query: 125 LTKRPMGRVLDPLREMGVQVKS-AEGDRLPVTLRGPKTPNPITYRVPMASAQVKSAVLLA 183
           L KRPM R+LDPL +MG +V S AEG R P+ L+G   P PI Y  P+ASAQ+KSAVLLA
Sbjct: 125 LRKRPMRRILDPLVQMGAEVLSEAEGGRCPILLKGASEPVPILYETPVASAQIKSAVLLA 184

Query: 184 GLNTPGITTVIEPVMTRDHTEKMLQGFGANLSVETDTAGVRTIRLEGRGKLTGQVIDVPG 243
           GLN+PG TTV+E   +RDHTEKML  FGA +SVE      R I LEGR +L    + VP 
Sbjct: 185 GLNSPGRTTVVETEASRDHTEKMLAHFGATISVEPFGTHGRKISLEGRPELRPAPLSVPA 244

Query: 244 DPSSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGANIEVMNPRLAGGEDVAD 303
           DPSS AFP+VAA + PGSD+ I  V+ NP R GL+ TL EMGA+IE+++ R+ GGE+VAD
Sbjct: 245 DPSSAAFPMVAATIAPGSDIVIEGVMTNPLRAGLLATLLEMGADIEILDRRIEGGEEVAD 304

Query: 304 LRVRYSELKGVTVPEERAPSMIDEYPVLAVAAAFAEGATVMNGLDELRVKESDRLSAVAD 363
           LRVR + LKGV VP  RAPSMIDEYP+LAVAAAFA G T + GL ELRVKESDRL+AVA 
Sbjct: 305 LRVRAAALKGVDVPAARAPSMIDEYPILAVAAAFASGLTRLRGLHELRVKESDRLAAVAA 364

Query: 364 GLKLNGVDCDEGEASLVVRGRPGGKGLGNAAGGQVKTHLDHRIAMSFLVLGLASEHPVTV 423
           GL+  GV        L+V GR GG+  G   GG V+THLDHRIAMSFL LGLAS  P+ +
Sbjct: 365 GLREAGVATQIIGDDLIVEGR-GGEVEG---GGSVETHLDHRIAMSFLCLGLASRQPMAI 420

Query: 424 DDATMIATSFPEFMDLMTGLGA 445
           DD+ MIATSFP F   M  LGA
Sbjct: 421 DDSRMIATSFPTFKADMERLGA 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: 644
Number of extensions: 30
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_026606222.1 METAC_RS0105305 (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.8774.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-123  398.7   0.0   1.6e-123  398.5   0.0    1.0  1  lcl|NCBI__GCF_000427445.1:WP_026606222.1  METAC_RS0105305 3-phosphoshikima


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000427445.1:WP_026606222.1  METAC_RS0105305 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  398.5   0.0  1.6e-123  1.6e-123       1     414 [.      19     442 ..      19     443 .. 0.96

  Alignments for each domain:
  == domain 1  score: 398.5 bits;  conditional E-value: 1.6e-123
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               g++k pg+KSishRal+l++L+ get +++lL+++D+l t  a+r+lGa+v +  ++++ + g+g   l
  lcl|NCBI__GCF_000427445.1:WP_026606222.1  19 GRLKPPGDKSISHRALILGLLSVGETLIDGLLEGDDVLRTAAACRALGAEVVRLgEGRWRVSGCGIgsL 87 
                                               7899**********************************************9955499*******98999 PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                                 p + ld+gnsGt aRl++gv+  ++ +  ++gd sl+kRP++r++++L ++gae+ s+ e g+ P+ 
  lcl|NCBI__GCF_000427445.1:WP_026606222.1  88 LAPREPLDFGNSGTGARLMMGVVGGHAITACFDGDASLRKRPMRRILDPLVQMGAEVLSEAEGGRCPIL 156
                                               ********************************************************************* PP

                                 TIGR01356 136 isgp.lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               ++g   +++i + ++ aS+Q ksa+lla+   l+  + ++v e + sr+++e++L+ +++  ++ve   
  lcl|NCBI__GCF_000427445.1:WP_026606222.1 157 LKGAsEPVPILYETPVASAQIKSAVLLAG---LNSPGRTTVVETEASRDHTEKMLAHFGAT-ISVEPFG 221
                                               ****6666*********************...77778888888****************88.9999877 PP

                                 TIGR01356 204 e..rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGad 269
                                               +  rki+++g  + ++  ++v++D+SsAaf+++aa+i+++ ++++e++++n+++++  ++++L emGad
  lcl|NCBI__GCF_000427445.1:WP_026606222.1 222 ThgRKISLEGRPELRPAPLSVPADPSSAAFPMVAATIAPGsDIVIEGVMTNPLRAG--LLATLLEMGAD 288
                                               767999999998888889**************************************..888******** PP

                                 TIGR01356 270 veveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEs 329
                                               +e+ + r        d++v+ a  lkgv+v  ++++s+iDe+p+lav+aafA+g tr+++++elRvkEs
  lcl|NCBI__GCF_000427445.1:WP_026606222.1 289 IEILDRRieggeevaDLRVR-AAALKGVDVpAARAPSMIDEYPILAVAAAFASGLTRLRGLHELRVKES 356
                                               ********************.789******88************************************* PP

                                 TIGR01356 330 dRiaaiaeeLeklGveveeledgllieGkkkelkg.avvdtydDHRiamalavlglaaegeveiedaec 397
                                               dR+aa+a+ L++ Gv ++   d l++eG+  e++g ++v+t+ DHRiam++  lgla ++++ i+d+ +
  lcl|NCBI__GCF_000427445.1:WP_026606222.1 357 DRLAAVAAGLREAGVATQIIGDDLIVEGRGGEVEGgGSVETHLDHRIAMSFLCLGLASRQPMAIDDSRM 425
                                               ******************************9999879******************************** PP

                                 TIGR01356 398 vaksfPeFfevleqlga 414
                                               +a+sfP F  ++e+lga
  lcl|NCBI__GCF_000427445.1:WP_026606222.1 426 IATSFPTFKADMERLGA 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: 10.97
//
[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