Alignments for a candidate for aroA in Hydrogenovibrio marinus DSM 11271

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Hydrogenovibrio marinus DSM 11271

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_029908949.1 P166_RS0103900 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_000711315.1:WP_029908949.1
          Length = 448

 Score =  432 bits (1111), Expect = e-125
 Identities = 233/444 (52%), Positives = 305/444 (68%), Gaps = 14/444 (3%)

Query: 1   MDYQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMG 60
           + +   P   L G I VPGDKS+SHR+++L +IAEG T+V GFL G D+LA + A + MG
Sbjct: 5   VQFHVKPGGVLKGRIRVPGDKSVSHRSIMLGSIAEGTTRVTGFLEGEDSLATLQAFKDMG 64

Query: 61  ASIQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSL 120
             I+  +  N+  + GVG+ GL+ P   LD GNSGTA+RL++G+LAGQ F   L GD+SL
Sbjct: 65  VQIEGPDQGNV-TIHGVGLRGLKKPSNPLDMGNSGTAMRLMAGILAGQDFECTLIGDASL 123

Query: 121 QRRPMKRIIDPLTLMGAKIDST-GNVPPLKIYGNPRLTGIH---YQLPMASAQVKSCLLL 176
            +RPMKR+  PL+ MGA ID+  G +PPL +   P  TG++   Y LPMASAQVKSC+LL
Sbjct: 124 SKRPMKRVTQPLSEMGADIDTAEGGMPPLHL--KPTKTGLNAIDYTLPMASAQVKSCVLL 181

Query: 177 AGLYARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQS-----ICVSGGGKLKANDISIP 231
           AGLYA G T + EPAP+RDHTER+LK F Y ++ +K       + + GGG LKA DI +P
Sbjct: 182 AGLYANGTTSVVEPAPTRDHTERMLKGFGYDVKTEKLDSMQTRVELKGGGVLKAMDIDVP 241

Query: 232 GDISSAAFFIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTA 291
            DISSAAFF+VAA I P + + +  VG+NPTR GVI++LK+MGADI + + +    EP A
Sbjct: 242 SDISSAAFFMVAAAIAPEADLVIEHVGINPTRTGVIDILKLMGADITLENESTVGGEPVA 301

Query: 292 DITVRHARLKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMV 351
           DI V+ ++LKGI IP   VPL IDEFPVL +AAA A+G+TVL  A ELRVKE+DRI  M 
Sbjct: 302 DIHVKSSKLKGIKIPEALVPLAIDEFPVLFVAAAAAEGQTVLTGAEELRVKESDRIQVMA 361

Query: 352 DGLQKLGIAAESLPDGVIIQGGTLEG--GEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCD 409
           D L  +GI A+  PDG++I GG  +   G +NS+ DHRI+MA  VAG  A   + I +C 
Sbjct: 362 DALIAVGIDAQPTPDGMVINGGQQKSQVGGINSHHDHRISMAMTVAGLNAVDDIVIDDCA 421

Query: 410 NVKTSFPNFVELANEVGMNVKGVR 433
           NV TSFP FV+L N++GM V  V+
Sbjct: 422 NVNTSFPTFVQLVNQIGMTVNVVK 445


Lambda     K      H
   0.318    0.137    0.392 

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: 640
Number of extensions: 43
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: 438
Length of database: 448
Length adjustment: 32
Effective length of query: 406
Effective length of database: 416
Effective search space:   168896
Effective search space used:   168896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_029908949.1 P166_RS0103900 (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.2705836.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     4e-131  423.6   0.6   4.5e-131  423.4   0.6    1.0  1  NCBI__GCF_000711315.1:WP_029908949.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000711315.1:WP_029908949.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.4   0.6  4.5e-131  4.5e-131       1     414 [.      17     439 ..      17     440 .. 0.95

  Alignments for each domain:
  == domain 1  score: 423.4 bits;  conditional E-value: 4.5e-131
                             TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..lkepe 70 
                                           g+i++pg+KS+shR+++l+++aeg+t+vt++L++eD latl+a++++G+++e  ++++++i+gvg   lk p+
  NCBI__GCF_000711315.1:WP_029908949.1  17 GRIRVPGDKSVSHRSIMLGSIAEGTTRVTGFLEGEDSLATLQAFKDMGVQIEgPDQGNVTIHGVGLrgLKKPS 89 
                                           79**************************************************76799******99888***** PP

                             TIGR01356  71 aeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkg. 142
                                           + ld+gnsGt++Rl+ g+la +++e++l gd sl+kRP++r++++L+e+ga+i+ +e  g +Pl+++ +++g 
  NCBI__GCF_000711315.1:WP_029908949.1  90 NPLDMGNSGTAMRLMAGILAGQDFECTLIGDASLSKRPMKRVTQPLSEMGADIDTAE-GGMPPLHLKPTKTGl 161
                                           ******************************************************988.69********96666 PP

                             TIGR01356 143 .givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeede..rkivvkgg 212
                                            +i +  ++aS+Q+ks++lla+   l a++++ v e+  +r+++e++Lk ++ + v+ e+ d+  +++ +kgg
  NCBI__GCF_000711315.1:WP_029908949.1 162 nAIDYTLPMASAQVKSCVLLAG---LYANGTTSVVEPAPTRDHTERMLKGFGYD-VKTEKLDSmqTRVELKGG 230
                                           8999******************...55667777777****************88.999998885566677777 PP

                             TIGR01356 213 qkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........ 276
                                           +  k  +++v++D+SsAaff++aaai++e ++++e++g+n+t+++  +i++L+ mGad+++e+++        
  NCBI__GCF_000711315.1:WP_029908949.1 231 GVLKAMDIDVPSDISSAAFFMVAAAIAPEaDLVIEHVGINPTRTG--VIDILKLMGADITLENEStvggepva 301
                                           7777779**************************************..788*********************** PP

                             TIGR01356 277 dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGvevee 348
                                           d+ v+ +sklkg+k+ ++ v+ +iDe+p+l v+aa Aeg+t+++++eelRvkEsdRi+++a++L ++G+++++
  NCBI__GCF_000711315.1:WP_029908949.1 302 DIHVK-SSKLKGIKIpEALVPLAIDEFPVLFVAAAAAEGQTVLTGAEELRVKESDRIQVMADALIAVGIDAQP 373
                                           *****.799******99******************************************************** PP

                             TIGR01356 349 ledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlga 414
                                           ++dg++i+G++++ + + +++++DHRi ma++v+gl a + + i+d + v++sfP F+++++q+g+
  NCBI__GCF_000711315.1:WP_029908949.1 374 TPDGMVINGGQQKSQVGGINSHHDHRISMAMTVAGLNAVDDIVIDDCANVNTSFPTFVQLVNQIGM 439
                                           **********999999**********************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (448 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: 00:00:00.00
# Mc/sec: 18.89
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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