Alignments for a candidate for aroA in Geobacter uraniireducens Rf4

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Geobacter uraniireducens Rf4

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011938379.1 GURA_RS07445 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::A6TL04
         (425 letters)



>NCBI__GCF_000016745.1:WP_011938379.1
          Length = 428

 Score =  452 bits (1163), Expect = e-132
 Identities = 227/417 (54%), Positives = 307/417 (73%)

Query: 8   EKLEGKMTVPGDKSISHRAIMLSSISKGTSRVKGFLRGEDCLSTISCFRDLGIDIEDRGT 67
           + + G++ VPGDKSISHR+IML SI++GT+ V GFLRGED ++T++ FR +G+D+ D G 
Sbjct: 10  QSVRGEIAVPGDKSISHRSIMLGSIARGTTTVCGFLRGEDNMATLNAFRAMGVDVRDDGE 69

Query: 68  EIIIQGKGLHGLSEPLNVLDAGNSGTTIRLISGILAGQKFLTIVTGDASLRKRPMERIAT 127
            + I+GKGL GLSEP +VLD GNSGT++RL++G+LAGQ+F +++TGD  LR RPM+R+  
Sbjct: 70  TLRIEGKGLAGLSEPTDVLDCGNSGTSMRLMTGLLAGQRFFSVLTGDQYLRNRPMKRVLE 129

Query: 128 PLRKMGAFIEGRDYGNLAPLVIRGGNLKGMDYASPVSSAQVKSAILLAGLYGEGDTIVRE 187
           PL +MGA I GR  G+ APL + G  L G+ YASPVSSAQVKSAILLAGLY +G+T V E
Sbjct: 130 PLSRMGATIFGRAGGDKAPLAVVGRGLTGVTYASPVSSAQVKSAILLAGLYADGETEVTE 189

Query: 188 KITSRDHTEKMLKGLGANISTDQGVTRLGKSELYGQSIEVPGDISSAAFFMAGAAALPGS 247
              SRDH+E+ML+  GA+I T  G  ++   EL G+ I VPGDISSAAFF+  A  +PGS
Sbjct: 190 PHLSRDHSERMLRYFGADIETFAGGVKVRGRELTGRDITVPGDISSAAFFIVAALIVPGS 249

Query: 248 FLITEGVGLNPTRTGIIDVLRDMGGDIEIHNLRQSGGEEIGDIMIRGKKLYGTEIGKEII 307
            L+ +GVG+NPTRTGIID+L  MGG IE+ N R+  GE + D+++R  +L G EIG +++
Sbjct: 250 ELLIKGVGVNPTRTGIIDILTAMGGSIELLNCREISGEPVADLLVRASELKGIEIGGDLV 309

Query: 308 PRLIDEIPVLAIIAATAEGKTIITGAEELKVKESNRITAMVTEMQKVGIKVTELPDGMEI 367
           PR IDE PV+ + A+ AEG+T+I  A EL+VKE++RI AM   ++K G+ V E  +GME+
Sbjct: 310 PRAIDEFPVICVAASCAEGRTVIRDARELRVKETDRIAAMAVNLRKAGVDVVETENGMEL 369

Query: 368 EGGQVITGGRVESYGDHRIAMAMAICGLFAQEPIKINDSQCIDISFPNFEEKLKAVV 424
            G + + G   ES+GDHRIAM+M I GL A+  I +ND++CI  SFPNF   L+ VV
Sbjct: 370 IGVERLEGCTAESFGDHRIAMSMLIAGLAARGEITVNDTECIATSFPNFIALLEKVV 426


Lambda     K      H
   0.317    0.138    0.383 

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: 592
Number of extensions: 24
Number of successful extensions: 1
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: 425
Length of database: 428
Length adjustment: 32
Effective length of query: 393
Effective length of database: 396
Effective search space:   155628
Effective search space used:   155628
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_011938379.1 GURA_RS07445 (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.6292.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.3e-133  429.1   0.1     1e-132  428.8   0.0    1.0  1  lcl|NCBI__GCF_000016745.1:WP_011938379.1  GURA_RS07445 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016745.1:WP_011938379.1  GURA_RS07445 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.8   0.0    1e-132    1e-132       1     413 [.      14     426 ..      14     427 .. 0.96

  Alignments for each domain:
  == domain 1  score: 428.8 bits;  conditional E-value: 1e-132
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg..lk 67 
                                               gei++pg+KSishR+++l+++a+g+t+v ++L++eD  atl+a+r++G++v++++e+l ieg+g   l 
  lcl|NCBI__GCF_000016745.1:WP_011938379.1  14 GEIAVPGDKSISHRSIMLGSIARGTTTVCGFLRGEDNMATLNAFRAMGVDVRDDGETLRIEGKGLagLS 82 
                                               89************************************************************987889* PP

                                 TIGR01356  68 epeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlai 136
                                               ep+++ld+gnsGt++Rl+tg+la +++ +vltgd+ l++RP++r++e+L+++ga+i  + + +++Pla+
  lcl|NCBI__GCF_000016745.1:WP_011938379.1  83 EPTDVLDCGNSGTSMRLMTGLLAGQRFFSVLTGDQYLRNRPMKRVLEPLSRMGATIFGRAGGDKAPLAV 151
                                               ********************************************************************* PP

                                 TIGR01356 137 sgplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeeder 205
                                                g    g+++ s+  S+Q+ksa+lla+   l a++++ v+e+ +sr++ e++L  ++++   +e   + 
  lcl|NCBI__GCF_000016745.1:WP_011938379.1 152 VGRGLTGVTYASPVSSAQVKSAILLAG---LYADGETEVTEPHLSRDHSERMLRYFGAD---IETFAG- 213
                                               **7666*********************...67789999999**************9988...888877. PP

                                 TIGR01356 206 kivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveve 273
                                                ++v+g +  + ++++v+gD+SsAaff++aa+i ++ e+ ++++g n+t+++  ii++L +mG+++e+ 
  lcl|NCBI__GCF_000016745.1:WP_011938379.1 214 GVKVRGRE-LTGRDITVPGDISSAAFFIVAALIVPGsELLIKGVGVNPTRTG--IIDILTAMGGSIELL 279
                                               9****987.55556**********************9***************..888************ PP

                                 TIGR01356 274 eqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRia 333
                                               + r        d+ v+ as+lkg+++    v+++iDe+p++ v+a++Aeg t+i++++elRvkE+dRia
  lcl|NCBI__GCF_000016745.1:WP_011938379.1 280 NCReisgepvaDLLVR-ASELKGIEIgGDLVPRAIDEFPVICVAASCAEGRTVIRDARELRVKETDRIA 347
                                               *999999*99999999.899******99***************************************** PP

                                 TIGR01356 334 aiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksf 402
                                               a+a +L+k Gv+v e+e+g++  G  ++l+g ++++++DHRiam++ ++glaa+ge++++d+ec+a+sf
  lcl|NCBI__GCF_000016745.1:WP_011938379.1 348 AMAVNLRKAGVDVVETENGMELIGV-ERLEGCTAESFGDHRIAMSMLIAGLAARGEITVNDTECIATSF 415
                                               *************************.6****************************************** PP

                                 TIGR01356 403 PeFfevleqlg 413
                                               P+F+ +le+++
  lcl|NCBI__GCF_000016745.1:WP_011938379.1 416 PNFIALLEKVV 426
                                               *******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (428 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: 7.90
//
[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