GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroA in Sphingomonas koreensis DSMZ 15582

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate Ga0059261_0167 Ga0059261_0167 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19)

Query= BRENDA::C3MC80
         (448 letters)



>FitnessBrowser__Korea:Ga0059261_0167
          Length = 443

 Score =  469 bits (1208), Expect = e-137
 Identities = 253/440 (57%), Positives = 309/440 (70%), Gaps = 8/440 (1%)

Query: 7   PRPATAKKSADLKGTVRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTGKAMQAM 66
           P P        L+GT+ +PGDKSISHRS MF GLA GE+RI GLLEGEDV+ T  AM+AM
Sbjct: 6   PLPLAISARGPLRGTLTVPGDKSISHRSLMFAGLAVGESRIEGLLEGEDVLATAAAMRAM 65

Query: 67  GAKIRKEGD-TWIINGVGNGALLAPEAPLDFGNAGTGCRLTMGLVGVYDFDSTFIGDASL 125
           GAKI ++GD  W + GVG G LL PE  L+ GN+GT  RL MGLV  +   +TF GDASL
Sbjct: 66  GAKIERDGDGVWHVWGVGVGGLLQPETALEMGNSGTSTRLLMGLVASHPITATFTGDASL 125

Query: 126 TKRPMGRVLDPLREMGVQVKSAEGDRLPVTLRGPKTPNPITYRVPMASAQVKSAVLLAGL 185
           +KRPMGRV+DPL  MG    S+ G RLP+T+RG     PI Y +P+ASAQVKSAVLLAGL
Sbjct: 126 SKRPMGRVIDPLSRMGADFTSSPGGRLPLTMRGLCPAVPIEYTLPVASAQVKSAVLLAGL 185

Query: 186 NTPGITTVIEPVMTRDHTEKMLQGFGANLSVETDTAGVRTIRLEGRGKLTGQVIDVPGDP 245
           NTPGIT VIEPV+TRDH+E+ML GFGANL+VE    G R I + G  +   Q I VPGDP
Sbjct: 186 NTPGITRVIEPVLTRDHSERMLAGFGANLTVEETPQG-RIISIHGEAEFKPQQITVPGDP 244

Query: 246 SSTAFPLVAALLVPGSDVTILNVLMNPTRTGLILTLQEMGANIEVMNPRLAGGEDVADLR 305
           SS AF +VAA +VPGSD+T+ NV +NPTR GLI  L+ MGA+I  +NPR+ GGE VADLR
Sbjct: 245 SSAAFWMVAASIVPGSDITVANVGLNPTRIGLITALRMMGADITEVNPRIVGGEPVADLR 304

Query: 306 VRYSELKGVTVPEERAPSMIDEYPVLAVAAAFAEGATVMNGLDELRVKESDRLSAVADGL 365
           VR++ L  + VP + APSMIDEYPVL VAAAFA G T+  G +ELRVKESDR++A+   L
Sbjct: 305 VRHAPLSAIEVPHDLAPSMIDEYPVLFVAAAFAVGRTIARGAEELRVKESDRIAAMVAAL 364

Query: 366 KLNGVDCDEGEASLVVRGRPGGKGLGNAAGGQVKTHLDHRIAMSFLVLGLASEHPVTVDD 425
             NGV  +E E  L + G  GG     A G  V + LDHRIAMS  V GL ++  V++DD
Sbjct: 365 APNGVPLEEFEDGLAITGTGGGP---IAGGAPVASKLDHRIAMSMAVAGLGAKADVSIDD 421

Query: 426 ATMIATSFPEF---MDLMTG 442
            + +ATS+P F   +D +TG
Sbjct: 422 VSPVATSYPGFFSTLDSLTG 441


Lambda     K      H
   0.316    0.135    0.385 

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: 668
Number of extensions: 39
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 448
Length of database: 443
Length adjustment: 32
Effective length of query: 416
Effective length of database: 411
Effective search space:   170976
Effective search space used:   170976
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 Ga0059261_0167 Ga0059261_0167 (3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))
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.19973.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-126  409.1   0.0   1.1e-126  408.9   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_0167  Ga0059261_0167 3-phosphoshikimat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0167  Ga0059261_0167 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.9   0.0  1.1e-126  1.1e-126       1     413 [.      19     440 ..      19     442 .. 0.95

  Alignments for each domain:
  == domain 1  score: 408.9 bits;  conditional E-value: 1.1e-126
                                 TIGR01356   1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 
                                               g +++pg+KSishR+l++a+La ge+++++lL++eD+lat  a+r++Gak+e++ ++++++ gvg   l
  lcl|FitnessBrowser__Korea:Ga0059261_0167  19 GTLTVPGDKSISHRSLMFAGLAVGESRIEGLLEGEDVLATAAAMRAMGAKIERDgDGVWHVWGVGVggL 87 
                                               6799************************************************66699*****998888* PP

                                 TIGR01356  67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135
                                                +pe +l++gnsGt++Rll+g++a ++ + ++tgd sl+kRP++r++++L+++ga++ s+   g+lPl+
  lcl|FitnessBrowser__Korea:Ga0059261_0167  88 LQPETALEMGNSGTSTRLLMGLVASHPITATFTGDASLSKRPMGRVIDPLSRMGADFTSSP-GGRLPLT 155
                                               **********************************************************988.69***** PP

                                 TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203
                                               ++g  ++ +i +  + aS+Q+ksa+lla+   l++ +++ v+e++++r++ e++L+ +++   +vee+ 
  lcl|FitnessBrowser__Korea:Ga0059261_0167 156 MRGLCPAvPIEYTLPVASAQVKSAVLLAG---LNTPGITRVIEPVLTRDHSERMLAGFGAN-LTVEETP 220
                                               ****6666*********************...8999***********************77.9999988 PP

                                 TIGR01356 204 e.rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270
                                               + r i+++g+++ k+++++v+gD+SsAaf+++aa i ++ ++tv n+g n+t+ +  +i+ L+ mGad+
  lcl|FitnessBrowser__Korea:Ga0059261_0167 221 QgRIISIHGEAEFKPQQITVPGDPSSAAFWMVAASIVPGsDITVANVGLNPTRIG--LITALRMMGADI 287
                                               88999*****9999999********************999***************..888********* PP

                                 TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330
                                               +  + r        d++v++   l++++v +  ++s+iDe+p+l v+aafA g t  +++eelRvkEsd
  lcl|FitnessBrowser__Korea:Ga0059261_0167 288 TEVNPRivggepvaDLRVRH-APLSAIEVpHDLAPSMIDEYPVLFVAAAFAVGRTIARGAEELRVKESD 355
                                               9999999************5.68******667789********************************** PP

                                 TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkk.kelkg.avvdtydDHRiamalavlglaaegeveiedaec 397
                                               Riaa++++L+  Gv  ee+edgl i+G+    + g a v +  DHRiam++av+gl a++ v i+d + 
  lcl|FitnessBrowser__Korea:Ga0059261_0167 356 RIAAMVAALAPNGVPLEEFEDGLAITGTGgGPIAGgAPVASKLDHRIAMSMAVAGLGAKADVSIDDVSP 424
                                               ****************************985555549******************************** PP

                                 TIGR01356 398 vaksfPeFfevleqlg 413
                                               va+s+P Ff  l +l+
  lcl|FitnessBrowser__Korea:Ga0059261_0167 425 VATSYPGFFSTLDSLT 440
                                               ************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (415 nodes)
Target sequences:                          1  (443 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: 9.38
//
[ok]

This GapMind analysis is from Apr 09 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:

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:

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:

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:

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