Alignments for a candidate for aroA in Derxia gummosa DSM 723

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Derxia gummosa DSM 723

Align 3-phosphoshikimate 1-carboxyvinyltransferase; 5-enolpyruvylshikimate-3-phosphate synthase; EPSP synthase; EPSPS; EC 2.5.1.19 (characterized)
to candidate WP_034410976.1 H566_RS0107825 3-phosphoshikimate 1-carboxyvinyltransferase

Query= SwissProt::P24497
         (427 letters)



>NCBI__GCF_000482785.1:WP_034410976.1
          Length = 444

 Score =  422 bits (1086), Expect = e-123
 Identities = 240/434 (55%), Positives = 293/434 (67%), Gaps = 19/434 (4%)

Query: 4   LTLQPIARVDGTVNLPGSKSVSNRALLLAALARGTTVLTNLLDSDDVRHMLNALSALGVH 63
           L +QP   V GT  LPGSKS+SNR LLLAALA G T++ +LLDSDD R M  AL ALGV 
Sbjct: 11  LGVQPA--VAGTYALPGSKSISNRVLLLAALAEGETLVDDLLDSDDTRVMRGALEALGVG 68

Query: 64  YVLSSDRTRCEVTGTGGPLQAGSALELFLGNAGTAMRPLAAALCL------GSNDIV-LT 116
            +   +  R  V G GG      A +LF+GN+G ++R L  A+        G+ D+V L 
Sbjct: 69  LLPEGESLR--VAGCGGRFPTLRA-DLFVGNSGLSIRTLVPAIAAVLGSAGGAGDVVSLA 125

Query: 117 GEPRMKERPIGHLVDALRQGGAQIDYLEQENYPPLRLRGG-FTGGDVEVDGSVSSQFLTA 175
           G  RM ERPIG LVD L Q GA++++L    YPPL L     T   V V G+VSSQFLT 
Sbjct: 126 GIARMHERPIGDLVDGLSQLGAKVEWLGTPGYPPLALHPAPLTADRVSVRGNVSSQFLTG 185

Query: 176 LLMASPLAPQDT--VIAIKGELVSRPYIDITLHLMKTFGVEVENQAYQRFIVRGNQQYQS 233
           LL A+PL  +D   VI ++GEL+S+PY+ IT+ LMK FGVEV    +QRF V   Q Y+S
Sbjct: 186 LLQAAPLVARDKPLVIEVEGELISKPYVHITISLMKRFGVEVAQDGWQRFTVAPGQGYRS 245

Query: 234 PGDYLVEGDASSASYFLAAGAIKGGTVKVTGIGRNSVQGDIRFADVLEKMGATVTWGEDY 293
           PG   VEGDAS+ASYFLAAGA+ GG V+VTG GR+S+QGD+RFAD L  MGA ++WG+D+
Sbjct: 246 PGRISVEGDASTASYFLAAGALGGGPVRVTGAGRDSIQGDVRFADALAAMGARISWGDDW 305

Query: 294 I--ACTRGELNAIDMDMNHIPDAAMTIATAALFARGTTTLRNIYNWRVKETDRLFAMATE 351
           I  A   G L  +D+D NHIPDAAMT+A  AL A G TTLRNI +WRVKETDR+ A+A E
Sbjct: 306 IEAAAPEGGLTGVDLDCNHIPDAAMTLAVCALSAAGPTTLRNIGSWRVKETDRIAAVAAE 365

Query: 352 LRKVGAEVEEGEDYIRITPPLTLQFAEIGTYNDHRMAMCFSLVALS--DTPVTILDPKCT 409
            RK+GA VEEG D+IR+TPP+ L  AEI TY+DHRMAM FSL  L     P+ ILDP C 
Sbjct: 366 CRKLGATVEEGADWIRVTPPVALSTAEIHTYDDHRMAMAFSLATLGARGVPLRILDPDCV 425

Query: 410 AKTFPDYFGQLARI 423
           AKTFP YF    R+
Sbjct: 426 AKTFPGYFDVFTRL 439


Lambda     K      H
   0.319    0.135    0.389 

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: 527
Number of extensions: 27
Number of successful extensions: 9
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: 427
Length of database: 444
Length adjustment: 32
Effective length of query: 395
Effective length of database: 412
Effective search space:   162740
Effective search space used:   162740
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_034410976.1 H566_RS0107825 (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.15564.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.5e-126  406.6   0.0   6.2e-126  406.5   0.0    1.0  1  lcl|NCBI__GCF_000482785.1:WP_034410976.1  H566_RS0107825 3-phosphoshikimat


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000482785.1:WP_034410976.1  H566_RS0107825 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.5   0.0  6.2e-126  6.2e-126       3     414 ..      21     441 ..      19     442 .. 0.93

  Alignments for each domain:
  == domain 1  score: 406.5 bits;  conditional E-value: 6.2e-126
                                 TIGR01356   3 ikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgglkepe. 70 
                                                ++pgsKSis+R+lllaaLaeget v++lL+s+Dt+++  al++lG+    e+e+l + g+gg ++p+ 
  lcl|NCBI__GCF_000482785.1:WP_034410976.1  21 YALPGSKSISNRVLLLAALAEGETLVDDLLDSDDTRVMRGALEALGVGLLPEGESLRVAGCGG-RFPTl 88 
                                               579***********************************************99**********8.67766 PP

                                 TIGR01356  71 .aeldlgnsGttaRlltgvlalas.......gevvltgdeslkkRPierlveaLrelgaeieskeeegs 131
                                                a l +gnsG ++R l++++a++          v l g  ++++RPi++lv+ L++lga++e   + g+
  lcl|NCBI__GCF_000482785.1:WP_034410976.1  89 rADLFVGNSGLSIRTLVPAIAAVLgsaggagDVVSLAGIARMHERPIGDLVDGLSQLGAKVEWLGTPGY 157
                                               6*************998776665436667755688********************************** PP

                                 TIGR01356 132 lPlaisgp.lkggivelsgsaSsQyksalllaap.lalqavtleivgeklisrpyieitLkllksfgve 198
                                               +Pla++   l+++ v ++g++SsQ++++ll aap +a ++  +  v+++lis+py++it+ l+k+fgve
  lcl|NCBI__GCF_000482785.1:WP_034410976.1 158 PPLALHPApLTADRVSVRGNVSSQFLTGLLQAAPlVARDKPLVIEVEGELISKPYVHITISLMKRFGVE 226
                                               ******876888**********************63333444445555********************* PP

                                 TIGR01356 199 veeederkivvkggqkykqk.evevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeem 266
                                               v ++  ++++v +gq y+++ +++vegDaS+A++flaa+a+ g+ v+v++ g +s qgd+++++ L +m
  lcl|NCBI__GCF_000482785.1:WP_034410976.1 227 VAQDGWQRFTVAPGQGYRSPgRISVEGDASTASYFLAAGALGGGPVRVTGAGRDSIQGDVRFADALAAM 295
                                               ***999**********99888************************************************ PP

                                 TIGR01356 267 Gadveveeqrdveveg.asklkgvkvdidvdsliDelptlavlaafAegetriknieelRvkEsdRiaa 334
                                               Ga++++ ++ ++e    + +l gv+   d+++++D+++tlav a+ A g+t+++ni ++RvkE+dRiaa
  lcl|NCBI__GCF_000482785.1:WP_034410976.1 296 GARISWGDD-WIEAAApEGGLTGVD--LDCNHIPDAAMTLAVCALSAAGPTTLRNIGSWRVKETDRIAA 361
                                               *********.9*9998455666666..****************************************** PP

                                 TIGR01356 335 iaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaae.geveiedaecvaksf 402
                                               +a+e +klG++vee++d++ +++    l++a+++tydDHR+ama+++++l a+  +++i d+ cvak+f
  lcl|NCBI__GCF_000482785.1:WP_034410976.1 362 VAAECRKLGATVEEGADWIRVTPP-VALSTAEIHTYDDHRMAMAFSLATLGARgVPLRILDPDCVAKTF 429
                                               ************************.6**************************9779************* PP

                                 TIGR01356 403 PeFfevleqlga 414
                                               P +f+v  +lga
  lcl|NCBI__GCF_000482785.1:WP_034410976.1 430 PGYFDVFTRLGA 441
                                               ********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (444 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: 8.07
//
[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