Alignments for a candidate for aroA in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Phaeobacter inhibens BS107

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate GFF470 PGA1_c04810 3-phosphoshikimate 1-carboxyvinyltransferase AroA

Query= BRENDA::A6WUV8
         (450 letters)



>FitnessBrowser__Phaeo:GFF470
          Length = 449

 Score =  471 bits (1213), Expect = e-137
 Identities = 253/447 (56%), Positives = 315/447 (70%), Gaps = 3/447 (0%)

Query: 1   MSHSAPPKPATARRSEALTGEIRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTG 60
           MS    P P T+ R++ LTG   +PGDKSISHRS + G LA GET+I+GLLEGEDV++T 
Sbjct: 1   MSGHGTPIPMTSHRADPLTGIAEVPGDKSISHRSLILGALAVGETKISGLLEGEDVLDTA 60

Query: 61  RAMQAMGAK-IRKDGDAWIINGVGNGCLLQPEAALDFGNAGTGARLTMGLVGTYDMRTSF 119
           +AMQAMGA+ I   G  W ++GVG G L +PE  +D GN+GTG RL MG++ T  +  +F
Sbjct: 61  KAMQAMGAEVINHGGGNWSVHGVGVGGLAEPEQVIDCGNSGTGVRLIMGVMATSPITVTF 120

Query: 120 IGDASLSKRPMGRVLNPLREMGVQVEAAEGDRMPLTLIGPKTANPITYRVPMASAQVKSA 179
            GDASL+KRPM RV +PL   G Q     G R+P+T++G     P+ Y VP+ SAQVKSA
Sbjct: 121 TGDASLNKRPMARVTDPLALFGTQSVGRSGGRLPMTIVGAAEPTPVRYTVPVPSAQVKSA 180

Query: 180 VLLAGLNTPGVTTVIEPVMTRDHTEKMLQGFGADLSVETDKDGVRHIRITGQGKLIGQTI 239
           VLLAGLN PG T VIE   TRDH+E+ML GFGA+++VE D D  R I +TGQ +L  Q I
Sbjct: 181 VLLAGLNAPGQTVVIEKEATRDHSERMLAGFGAEITVE-DTDEGRVITLTGQPELKPQVI 239

Query: 240 DVPGDPSSTAFPLVAALLVEGSDVTIRNVLMNPTRTGLILTLQEMGADIEVLNARLAGGE 299
            VP DPSS AFP+ AAL+  GSDV +  + +NPTR GL  TLQ+MGAD+   N R  GGE
Sbjct: 240 AVPRDPSSAAFPVCAALITPGSDVLVPGIGLNPTRAGLFYTLQDMGADLTFENMREEGGE 299

Query: 300 DVADLRVKAS-KLKGVVVPPERAPSMIDEYPVLAIAAAFAEGETVMDGLDELRVKESDRL 358
            VADLR + S  +KG+ VPPERA SMIDEYPVL++ A+FA G+T+M G+ ELRVKESDR+
Sbjct: 300 PVADLRARYSPDMKGIDVPPERAASMIDEYPVLSVVASFATGKTMMTGVKELRVKESDRI 359

Query: 359 AAVARGLEANGVDCTEGEMSLTVRGRPDGKGLGGGTVATHLDHRIAMSFLVMGLASEKPV 418
            A+ARGL ANGV   EG+    V G       GGGT  + LDHRIAMSF+VMG+ ++KPV
Sbjct: 360 DAMARGLRANGVMVEEGDDWWAVTGLGPEGVPGGGTCESFLDHRIAMSFMVMGMGAQKPV 419

Query: 419 TVDDSTMIATSFPEFMDMMPGLGAKIE 445
           TVDD T IATSFP F  +M  LGA++E
Sbjct: 420 TVDDGTPIATSFPIFTPLMTTLGARLE 446


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: 704
Number of extensions: 41
Number of successful extensions: 5
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: 449
Length adjustment: 33
Effective length of query: 417
Effective length of database: 416
Effective search space:   173472
Effective search space used:   173472
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 GFF470 PGA1_c04810 (3-phosphoshikimate 1-carboxyvinyltransferase AroA)
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.17507.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.4e-122  392.7   0.0   1.1e-121  392.5   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF470  PGA1_c04810 3-phosphoshikimate 1


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF470  PGA1_c04810 3-phosphoshikimate 1-carboxyvinyltransferase AroA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.5   0.0  1.1e-121  1.1e-121       1     414 [.      20     443 ..      20     444 .. 0.96

  Alignments for each domain:
  == domain 1  score: 392.5 bits;  conditional E-value: 1.1e-121
                         TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..lkepeaeld 74 
                                       g+ ++pg+KSishR+l+l+aLa get++ +lL++eD+l t +a++++Ga+v ++ ++++ ++gvg   l+epe+++d
  lcl|FitnessBrowser__Phaeo:GFF470  20 GIAEVPGDKSISHRSLILGALAVGETKISGLLEGEDVLDTAKAMQAMGAEVINHgGGNWSVHGVGVggLAEPEQVID 96 
                                       56789*********************************************99666********99888********* PP

                         TIGR01356  75 lgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkggivelsgs 150
                                       +gnsGt +Rl++gv+a+++ +v++tgd sl+kRP+ r++++L  +g +   ++  g+lP++i g   + ++ +  + 
  lcl|FitnessBrowser__Phaeo:GFF470  97 CGNSGTGVRLIMGVMATSPITVTFTGDASLNKRPMARVTDPLALFGTQSVGRS-GGRLPMTIVGAaEPTPVRYTVPV 172
                                       *************************************************9988.59********96666******** PP

                         TIGR01356 151 aSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede.rkivvkggqkykqkevevegDa 226
                                        S+Q+ksa+lla+   l+a + ++v+ek+ +r++ e++L+ ++++ ++ve +de r i+++g+ + k++ ++v+ D+
  lcl|FitnessBrowser__Phaeo:GFF470 173 PSAQVKSAVLLAG---LNAPGQTVVIEKEATRDHSERMLAGFGAE-ITVEDTDEgRVITLTGQPELKPQVIAVPRDP 245
                                       *************...8999***********************99.****99997888888888899999******* PP

                         TIGR01356 227 SsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dvevegasklkgvkv.di 293
                                       SsAaf++ aa+it++ +v v ++g n+t+++  ++++L+ mGad+++e+ r        d++ + + ++kg++v ++
  lcl|FitnessBrowser__Phaeo:GFF470 246 SSAAFPVCAALITPGsDVLVPGIGLNPTRAG--LFYTLQDMGADLTFENMReeggepvaDLRARYSPDMKGIDVpPE 320
                                       *******************************..888**************99**********************99* PP

                         TIGR01356 294 dvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkk..kelkgavvd 368
                                       +++s+iDe+p+l+v+a+fA g+t++++++elRvkEsdRi a+a+ L++ Gv vee+ d+  ++G        g++ +
  lcl|FitnessBrowser__Phaeo:GFF470 321 RAASMIDEYPVLSVVASFATGKTMMTGVKELRVKESDRIDAMARGLRANGVMVEEGDDWWAVTGLGpeGVPGGGTCE 397
                                       ****************************************************************9984455569*** PP

                         TIGR01356 369 tydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                       ++ DHRiam++ v+g+ a+++v+++d   +a+sfP F  ++ +lga
  lcl|FitnessBrowser__Phaeo:GFF470 398 SFLDHRIAMSFMVMGMGAQKPVTVDDGTPIATSFPIFTPLMTTLGA 443
                                       ****************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (449 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: 9.25
//
[ok]

This GapMind analysis is from Apr 09 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