Alignments for a candidate for aroA in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroA in Halomonas desiderata SP1

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_086508940.1 BZY95_RS05305 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase

Query= BRENDA::Q83E11
         (438 letters)



>NCBI__GCF_002151265.1:WP_086508940.1
          Length = 760

 Score =  454 bits (1169), Expect = e-132
 Identities = 242/435 (55%), Positives = 305/435 (70%), Gaps = 7/435 (1%)

Query: 1   MDYQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMG 60
           + ++  P   ++G I VPGDKSISHR+++L A+AEG T+V GFL G D+LA + A ++MG
Sbjct: 315 LTFRAAPGGRVAGRIRVPGDKSISHRSIMLGALAEGVTEVKGFLEGEDSLATLQAFREMG 374

Query: 61  ASIQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSL 120
            +I+      +  V GVGM GL+AP   L  GN+GTA+RL +GLLAGQ F+T L GD+SL
Sbjct: 375 VAIEGPHQGRV-TVHGVGMHGLKAPAGPLYVGNAGTAMRLFAGLLAGQAFDTELIGDASL 433

Query: 121 QRRPMKRIIDPLTLMGAKIDST-GNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGL 179
            +RPM R+ DPL LMGA+ID+  G  PPLKI+G  +L GI Y +PMASAQVKSCLLLAGL
Sbjct: 434 TKRPMGRVADPLRLMGARIDTAEGGRPPLKIHGGQKLEGITYDMPMASAQVKSCLLLAGL 493

Query: 180 YARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAF 239
           YA G+T + EPAP+RDHTER+L  F Y + ++  +  ++GGGKL A  I +P DISSA F
Sbjct: 494 YAEGETRVREPAPTRDHTERMLAGFGYEVHREGDTCWLNGGGKLSAAPIDVPSDISSATF 553

Query: 240 FIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHAR 299
           F+VAA ITPGS + L  VG+NPTR+GVIN+LK+MGAD+ +T+  E   EP AD+ +R+A 
Sbjct: 554 FLVAAAITPGSNLLLEHVGINPTRIGVINILKLMGADLHLTNEREVGGEPVADLHIRYAP 613

Query: 300 LKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGI 359
           LKGIDIP DQVPL IDEFP L +AAA A G T LR A ELRVKE+DRI AM DGL  LG+
Sbjct: 614 LKGIDIPLDQVPLAIDEFPALFVAAACATGTTRLRGAEELRVKESDRIQAMADGLATLGV 673

Query: 360 AAESLPDGVIIQGG-----TLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTS 414
               L DG+ I G         GG ++S  DHRIAM+F VA   A   + I +C NV TS
Sbjct: 674 EHTVLEDGIDIVGAGDREVAYGGGRIDSLGDHRIAMSFVVASLRAGEEIVIDDCANVATS 733

Query: 415 FPNFVELANEVGMNV 429
           FP F ELA  VG+ V
Sbjct: 734 FPGFTELARTVGLRV 748


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: 954
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: 438
Length of database: 760
Length adjustment: 36
Effective length of query: 402
Effective length of database: 724
Effective search space:   291048
Effective search space used:   291048
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: 53 (25.0 bits)

Align candidate WP_086508940.1 BZY95_RS05305 (bifunctional prephenate dehydrogenase/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.12874.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-126  407.5   0.0   3.7e-126  407.2   0.0    1.1  1  lcl|NCBI__GCF_002151265.1:WP_086508940.1  BZY95_RS05305 bifunctional preph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508940.1  BZY95_RS05305 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-ca
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.2   0.0  3.7e-126  3.7e-126       1     413 [.     327     745 ..     327     747 .. 0.95

  Alignments for each domain:
  == domain 1  score: 407.2 bits;  conditional E-value: 3.7e-126
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 
                                               g+i++pg+KSishR+++l+aLaeg t+v+++L++eD latl+a+r++G+ +e  ++++++++gvg+  l
  lcl|NCBI__GCF_002151265.1:WP_086508940.1 327 GRIRVPGDKSISHRSIMLGALAEGVTEVKGFLEGEDSLATLQAFREMGVAIEgPHQGRVTVHGVGMhgL 395
                                               79**************************************************666*********9999* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                               k p   l++gn+Gt++Rl  g+la ++++++l gd sl kRP++r+ ++Lr +ga+i+ +e  g++Pl+
  lcl|NCBI__GCF_002151265.1:WP_086508940.1 396 KAPAGPLYVGNAGTAMRLFAGLLAGQAFDTELIGDASLTKRPMGRVADPLRLMGARIDTAE-GGRPPLK 463
                                               **********************************************************988.69***** PP

                                 TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               i+g++k+ gi++  ++aS+Q+ks+llla+   l a++++ v e+  +r+++e++L+ ++ +   v++e 
  lcl|NCBI__GCF_002151265.1:WP_086508940.1 464 IHGGQKLeGITYDMPMASAQVKSCLLLAG---LYAEGETRVREPAPTRDHTERMLAGFGYE---VHREG 526
                                               ****8888*********************...778899****************9887766...***99 PP

                                 TIGR01356 204 erkivvkggqk.ykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                               + ++ ++gg+k  + + ++v++D+SsA+ffl+aaait++ ++ +e++g+n+t+ +  +i++L+ mGad+
  lcl|NCBI__GCF_002151265.1:WP_086508940.1 527 D-TCWLNGGGKlSAAP-IDVPSDISSATFFLVAAAITPGsNLLLEHVGINPTRIG--VINILKLMGADL 591
                                               8.99999999955555.**************************************..888********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               +++++r        d+ ++    lkg+++   +v+ +iDe+p+l v+aa+A g+tr++++eelRvkEsd
  lcl|NCBI__GCF_002151265.1:WP_086508940.1 592 HLTNERevggepvaDLHIR-YAPLKGIDIpLDQVPLAIDEFPALFVAAACATGTTRLRGAEELRVKESD 659
                                               **************99**9.568******5599************************************ PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkk...kelkgavvdtydDHRiamalavlglaaegeveiedae 396
                                               Ri+a+a+ L++lGve ++ledg+ i G+        g+++d+ +DHRiam++ v++l+a +e+ i+d +
  lcl|NCBI__GCF_002151265.1:WP_086508940.1 660 RIQAMADGLATLGVEHTVLEDGIDIVGAGdreVAYGGGRIDSLGDHRIAMSFVVASLRAGEEIVIDDCA 728
                                               ***************************9986556677******************************** PP

                                 TIGR01356 397 cvaksfPeFfevleqlg 413
                                                va+sfP F e+++++g
  lcl|NCBI__GCF_002151265.1:WP_086508940.1 729 NVATSFPGFTELARTVG 745
                                               ***********998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (760 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 19.80
//
[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