Alignments for a candidate for aroA in Sphingomonas koreensis DSMZ 15582

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.3699.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.60
//
[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:

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