Alignments for a candidate for aroA in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Dinoroseobacter shibae DFL-12

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate 3607613 Dshi_1022 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq)

Query= BRENDA::A6WUV8
         (450 letters)



>FitnessBrowser__Dino:3607613
          Length = 450

 Score =  461 bits (1186), Expect = e-134
 Identities = 248/446 (55%), Positives = 308/446 (69%), Gaps = 3/446 (0%)

Query: 1   MSHSAPPKPATARRSEALTGEIRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTG 60
           MS    P P TA  S  L+G  ++PGDKSISHRS + G LA GET++TGLLEG+DV++T 
Sbjct: 1   MSAHGDPIPMTAHPSGPLSGTAQVPGDKSISHRSLILGALAVGETKVTGLLEGQDVLDTA 60

Query: 61  RAMQAMGAKIRKDGD-AWIINGVGNGCLLQPEAALDFGNAGTGARLTMGLVGTYDMRTSF 119
           RAMQA GA++ +    AW ++GVG G   +PE  +D GN+GTG RL MG + T  +  +F
Sbjct: 61  RAMQAFGAEVIQHAPGAWSVHGVGTGGFAEPEDVIDCGNSGTGVRLIMGAMATTPITATF 120

Query: 120 IGDASLSKRPMGRVLNPLREMGVQVEAAEGDRMPLTLIGPKTANPITYRVPMASAQVKSA 179
            GDASL  RPMGR+ +PL   G       G R+P+TL G     P+ Y VP+ SAQVKSA
Sbjct: 121 TGDASLRSRPMGRITDPLAGFGTTAVGRRGGRLPMTLTGAADPVPVRYTVPVPSAQVKSA 180

Query: 180 VLLAGLNTPGVTTVIEPVMTRDHTEKMLQGFGADLSVETDKDGVRHIRITGQGKLIGQTI 239
           VLLAGLN PG T VIE   TRDH+E+ML+GFGA++SVE+  +G   I +TGQ +L  QTI
Sbjct: 181 VLLAGLNAPGQTVVIEAEATRDHSERMLRGFGAEISVESAPEG-NVITLTGQPELRPQTI 239

Query: 240 DVPGDPSSTAFPLVAALLVEGSDVTIRNVLMNPTRTGLILTLQEMGADIEVLNARLAGGE 299
            VP DPSS AFP+   L+V GSDV +  + +NPTR GL  TLQEMGA++   N R  GGE
Sbjct: 240 VVPRDPSSAAFPVAVGLIVPGSDVLVPGIGLNPTRAGLYTTLQEMGAELSFENMREEGGE 299

Query: 300 DVADLRVKAS-KLKGVVVPPERAPSMIDEYPVLAIAAAFAEGETVMDGLDELRVKESDRL 358
            VADLR + S  ++G+ VPPERAPSMIDEYP+L++ AA+A G TVM G+ ELRVKESDR+
Sbjct: 300 PVADLRARFSDAMQGIEVPPERAPSMIDEYPILSVIAAYATGRTVMRGVKELRVKESDRI 359

Query: 359 AAVARGLEANGVDCTEGEMSLTVRGRPDGKGLGGGTVATHLDHRIAMSFLVMGLASEKPV 418
            A+ARGLEA GV   E E +L V G   G   GG T A+HLDHRIAMSFL  GLA++ PV
Sbjct: 360 DAMARGLEACGVRVEEDEDTLIVHGMGPGGVPGGATCASHLDHRIAMSFLCCGLAAQTPV 419

Query: 419 TVDDSTMIATSFPEFMDMMPGLGAKI 444
           +VDD   IATSFP F  +M  LGA +
Sbjct: 420 SVDDGGPIATSFPIFEPLMTALGATL 445


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: 670
Number of extensions: 44
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: 450
Length adjustment: 33
Effective length of query: 417
Effective length of database: 417
Effective search space:   173889
Effective search space used:   173889
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 3607613 Dshi_1022 (3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq))
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.15404.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   3.8e-118  380.8   0.0   4.3e-118  380.6   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607613  Dshi_1022 3-phosphoshikimate 1-c


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607613  Dshi_1022 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  380.6   0.0  4.3e-118  4.3e-118       2     414 ..      21     443 ..      20     444 .. 0.96

  Alignments for each domain:
  == domain 1  score: 380.6 bits;  conditional E-value: 4.3e-118
                         TIGR01356   2 eikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..lkepeaeldl 75 
                                         ++pg+KSishR+l+l+aLa get+vt+lL+++D+l t +a++++Ga+v ++  + + ++gvg+  ++epe+++d+
  lcl|FitnessBrowser__Dino:3607613  21 TAQVPGDKSISHRSLILGALAVGETKVTGLLEGQDVLDTARAMQAFGAEVIQHaPGAWSVHGVGTggFAEPEDVIDC 97 
                                       6789*********************************************996669********9999********** PP

                         TIGR01356  76 gnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgp.lkggivelsgsa 151
                                       gnsGt +Rl++g++a+++ + ++tgd sl+ RP++r++++L  +g +   ++  g+lP++++g   ++++ +  +  
  lcl|FitnessBrowser__Dino:3607613  98 GNSGTGVRLIMGAMATTPITATFTGDASLRSRPMGRITDPLAGFGTTAVGRR-GGRLPMTLTGAaDPVPVRYTVPVP 173
                                       *************************************************999.59********96777********* PP

                         TIGR01356 152 SsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede.rkivvkggqkykqkevevegDaS 227
                                       S+Q+ksa+lla+   l+a + ++v+e + +r++ e++L  ++++ ++ve   e + i+++g+ + +++++ v+ D+S
  lcl|FitnessBrowser__Dino:3607613 174 SAQVKSAVLLAG---LNAPGQTVVIEAEATRDHSERMLRGFGAE-ISVESAPEgNVITLTGQPELRPQTIVVPRDPS 246
                                       ************...8999***********************99.999999887889999888899999******** PP

                         TIGR01356 228 sAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dvevegasklkgvkv.did 294
                                       sAaf++a+++i ++ +v v ++g n+t+++  + ++L+emGa++++e+ r        d++ + ++ ++g++v +++
  lcl|FitnessBrowser__Dino:3607613 247 SAAFPVAVGLIVPGsDVLVPGIGLNPTRAG--LYTTLQEMGAELSFENMReeggepvaDLRARFSDAMQGIEVpPER 321
                                       **************9***************..666**************99**********************99** PP

                         TIGR01356 295 vdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkk..kelkgavvdt 369
                                       ++s+iDe+p+l+v+aa+A g t++++++elRvkEsdRi a+a+ Le+ Gv+vee ed l+++G        ga+  +
  lcl|FitnessBrowser__Dino:3607613 322 APSMIDEYPILSVIAAYATGRTVMRGVKELRVKESDRIDAMARGLEACGVRVEEDEDTLIVHGMGpgGVPGGATCAS 398
                                       ***************************************************************999556666***** PP

                         TIGR01356 370 ydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                       + DHRiam++   glaa+ +v ++d + +a+sfP F  ++ +lga
  lcl|FitnessBrowser__Dino:3607613 399 HLDHRIAMSFLCCGLAAQTPVSVDDGGPIATSFPIFEPLMTALGA 443
                                       *************************************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (450 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: 12.66
//
[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