Alignments for a candidate for aroA in Mycolicibacterium vanbaalenii PYR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Mycolicibacterium vanbaalenii PYR-1

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011779012.1 MVAN_RS08915 3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::P9WPY5
         (450 letters)



>NCBI__GCF_000015305.1:WP_011779012.1
          Length = 446

 Score =  605 bits (1559), Expect = e-177
 Identities = 310/448 (69%), Positives = 357/448 (79%), Gaps = 8/448 (1%)

Query: 1   MKTWPAPTAPTPVRATVTVPGSKSQTNRALVLAALAAAQGRGASTISGALRSRDTELMLD 60
           M TWPAP+  TPV ATVTVPGSKSQTNRALVLAALA  QG  +STISGALRSRDT+LM+ 
Sbjct: 1   MSTWPAPSTATPVHATVTVPGSKSQTNRALVLAALAVPQG--SSTISGALRSRDTDLMIS 58

Query: 61  ALQTLGLRVDGV------GSELTVSGRIEPGPGARVDCGLAGTVLRFVPPLAALGSVPVT 114
           ALQ LG+ V+        G+ELTVSG + P  GAR+DCGLAGTVLRFVPP+AAL +  VT
Sbjct: 59  ALQGLGVVVEAPDTDGSDGTELTVSGALAPKAGARIDCGLAGTVLRFVPPVAALTTETVT 118

Query: 115 FDGDQQARGRPIAPLLDALRELGVAVDGTGLPFRVRGNGSLAGGTVAIDASASSQFVSGL 174
           FDGD+QAR RPIAPLLD LR LGVA+DG GLPF VRG GS+ GGTV IDAS SSQFVSGL
Sbjct: 119 FDGDEQARARPIAPLLDGLRALGVAIDGDGLPFSVRGQGSVRGGTVEIDASGSSQFVSGL 178

Query: 175 LLSAASFTDGLTVQHTGSSLPSAPHIAMTAAMLRQAGVDIDDSTPNRWQVRPGPVAARRW 234
           LLS A+FT+GLTV HTG ++PSAPHIAMT +MLR AGV++DDS  +RW+V PGP+AAR W
Sbjct: 179 LLSGAAFTEGLTVVHTGGAVPSAPHIAMTVSMLRDAGVEVDDSAADRWRVAPGPIAARHW 238

Query: 235 DIEPDLTNAVAFLSAAVVSGGTVRITGWPRVSVQPADHILAILRQLNAVVIHADSSLEVR 294
            +EPDL+NAV FL+AAV+SGGTVR+TGWP VS QPA  IL++L  L + V   +S LEV+
Sbjct: 239 AVEPDLSNAVPFLAAAVISGGTVRVTGWPTVSTQPAATILSLLTSLGSEVRQGNSHLEVQ 298

Query: 295 GPTGYDGFDVDLRAVGELTPSVAALAALASPGSVSRLSGIAHLRGHETDRLAALSTEINR 354
           G T YDG DVDLR VGEL PSVAA+AALASPGSVSRL GIAHLRGHETDRLAALS E+NR
Sbjct: 299 GATSYDGIDVDLRDVGELAPSVAAMAALASPGSVSRLRGIAHLRGHETDRLAALSAELNR 358

Query: 355 LGGTCRETPDGLVITATPLRPGIWRAYADHRMAMAGAIIGLRVAGVEVDDIAATTKTLPE 414
           LGG C ET DGLVITA  +  G+WR+YADHRMA AGAI+GLRV GVEV+DI  T KTLP+
Sbjct: 359 LGGQCEETDDGLVITARQMHGGVWRSYADHRMATAGAIVGLRVPGVEVEDIGTTAKTLPD 418

Query: 415 FPRLWAEMVGPGQGWGYPQPRSGQRARR 442
           FP+LWA+M+          P +G+   R
Sbjct: 419 FPQLWADMLAGQTDLQAGAPHAGRNQGR 446


Lambda     K      H
   0.317    0.134    0.398 

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: 797
Number of extensions: 51
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: 446
Length adjustment: 33
Effective length of query: 417
Effective length of database: 413
Effective search space:   172221
Effective search space used:   172221
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_011779012.1 MVAN_RS08915 (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.24653.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-112  361.7   0.0   2.8e-112  361.5   0.0    1.0  1  lcl|NCBI__GCF_000015305.1:WP_011779012.1  MVAN_RS08915 3-phosphoshikimate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015305.1:WP_011779012.1  MVAN_RS08915 3-phosphoshikimate 1-carboxyvinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  361.5   0.0  2.8e-112  2.8e-112       2     414 ..      16     428 ..      15     429 .. 0.94

  Alignments for each domain:
  == domain 1  score: 361.5 bits;  conditional E-value: 2.8e-112
                                 TIGR01356   2 eikipgsKSishRalllaaLa..egetvvtnlLkseDtlatlealrklGakve..ee....keelvieg 62 
                                                +++pgsKS ++Ral+laaLa  +g++++ + L+s+Dt+ +++al+ lG+ ve  ++    + el++ g
  lcl|NCBI__GCF_000015305.1:WP_011779012.1  16 TVTVPGSKSQTNRALVLAALAvpQGSSTISGALRSRDTDLMISALQGLGVVVEapDTdgsdGTELTVSG 84 
                                               589*****************9778*************************99986432221234677777 PP

                                 TIGR01356  63 vgglkepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegs 131
                                                     + a +d+g +Gt++R++ +v+al+ ++v+++gde+ ++RPi +l++ Lr+lg+ i+       
  lcl|NCBI__GCF_000015305.1:WP_011779012.1  85 AL-APKAGARIDCGLAGTVLRFVPPVAALTTETVTFDGDEQARARPIAPLLDGLRALGVAIDGDG---- 148
                                               44.344459*****************************************************855.... PP

                                 TIGR01356 132 lPlaisgp..lkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgve 198
                                               lP++++g+  ++gg+ve+++s SsQ++s+lll+++  +++ t+ ++g+ + s p+i +t+ +l+++gve
  lcl|NCBI__GCF_000015305.1:WP_011779012.1 149 LPFSVRGQgsVRGGTVEIDASGSSQFVSGLLLSGAAFTEGLTVVHTGGAVPSAPHIAMTVSMLRDAGVE 217
                                               9******998899******************************************************** PP

                                 TIGR01356 199 veeederkivvkggqkykqkevevegDaSsAafflaaaaitgeevtvenlgenstqgdkaiiivLeemG 267
                                               v+ +  ++++v +g  ++ ++++ve D+S+A  flaaa+i+g++v+v+++ + stq+ + i+++L ++G
  lcl|NCBI__GCF_000015305.1:WP_011779012.1 218 VDDSAADRWRVAPGP-IAARHWAVEPDLSNAVPFLAAAVISGGTVRVTGWPTVSTQPAATILSLLTSLG 285
                                               *************97.88889************************************************ PP

                                 TIGR01356 268 adveveeqrdvevegasklkgvkvdidvdsliDelptlavlaafA..egetriknieelRvkEsdRiaa 334
                                                +v++ ++ ++ev+ga ++ g++  +d+ ++ +++p +a++aa+A    ++r+++i++lR +E+dR+aa
  lcl|NCBI__GCF_000015305.1:WP_011779012.1 286 SEVRQGNS-HLEVQGATSYDGID--VDLRDVGELAPSVAAMAALAspGSVSRLRGIAHLRGHETDRLAA 351
                                               ********.8*************..********************4335789***************** PP

                                 TIGR01356 335 iaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksfP 403
                                               + +eL++lG ++ee+ dgl+i+ +  +++g+v+++y DHR+a+a a++gl++  +ve+ed +++ak+ P
  lcl|NCBI__GCF_000015305.1:WP_011779012.1 352 LSAELNRLGGQCEETDDGLVITAR--QMHGGVWRSYADHRMATAGAIVGLRVP-GVEVEDIGTTAKTLP 417
                                               ************************..7*************************9.*************** PP

                                 TIGR01356 404 eFfevleqlga 414
                                               +F ++++ + a
  lcl|NCBI__GCF_000015305.1:WP_011779012.1 418 DFPQLWADMLA 428
                                               ****9998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (446 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: 8.00
//
[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