GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroE in Pseudomonas fluorescens GW456-L13

Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate PfGW456L13_644 Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)

Query= BRENDA::Q88RQ5
         (274 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_644
          Length = 273

 Score =  434 bits (1117), Expect = e-127
 Identities = 215/272 (79%), Positives = 242/272 (88%)

Query: 1   MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVT 60
           MD+YVVFGNPIGHSKSPLIHRLFAEQTGQ L+Y TLLAPLD+FS CAR FF +G G NVT
Sbjct: 1   MDRYVVFGNPIGHSKSPLIHRLFAEQTGQKLDYNTLLAPLDDFSTCARRFFLEGRGANVT 60

Query: 61  VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120
           VPFKEEA+RL +SLT RA+RAGAVNTLSKLADG+L GDNTDGAGLVRDLTVNAG  L GK
Sbjct: 61  VPFKEEAYRLANSLTARAQRAGAVNTLSKLADGSLLGDNTDGAGLVRDLTVNAGFSLKGK 120

Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEP 180
           RIL+LGAGGAVRG LEP+LA +P S++IANRTV+KAE LA  F +LGP+ ASG+ WLQE 
Sbjct: 121 RILLLGAGGAVRGALEPLLAEQPASVIIANRTVDKAELLAELFCDLGPISASGYDWLQES 180

Query: 181 VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLG 240
           VD+IINATSASL G++PPIA SL+E G+TVCYDMMYGKEPT FC+WA++ GAA  +DGLG
Sbjct: 181 VDLIINATSASLTGDVPPIAPSLIEPGKTVCYDMMYGKEPTSFCRWASEHGAAVSMDGLG 240

Query: 241 MLAEQAAEAFFIWRGVRPDTAPVLAELRRQLA 272
           MLAEQAAEAFF+WRGVRPDTAPVLAELRRQLA
Sbjct: 241 MLAEQAAEAFFLWRGVRPDTAPVLAELRRQLA 272


Lambda     K      H
   0.319    0.137    0.405 

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: 328
Number of extensions: 10
Number of successful extensions: 1
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: 274
Length of database: 273
Length adjustment: 25
Effective length of query: 249
Effective length of database: 248
Effective search space:    61752
Effective search space used:    61752
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: 47 (22.7 bits)

Align candidate PfGW456L13_644 (Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25))
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))

# 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/TIGR00507.hmm
# target sequence database:        /tmp/gapView.137750.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00507  [M=270]
Accession:   TIGR00507
Description: aroE: shikimate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
    1.2e-78  250.0   0.0    1.3e-78  249.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_644  Shikimate 5-dehydrogenase I alph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_644  Shikimate 5-dehydrogenase I alpha (EC 1.1.1.25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.8   0.0   1.3e-78   1.3e-78       3     269 ..       4     271 ..       2     272 .. 0.94

  Alignments for each domain:
  == domain 1  score: 249.8 bits;  conditional E-value: 1.3e-78
                                              TIGR00507   3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvn 58 
                                                            + v+Gnpi hSksplih  +++q+g++l Y  + +++++++     ++ +g +G+n
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_644   4 YVVFGNPIGHSKSPLIHRLFAEQTGQKLDYNTLLAPLDDFSTCARRFFLEG-RGAN 58 
                                                            78*********************************************9988.8*** PP

                                              TIGR00507  59 vTvPfKeevlellDeieesakligavNTlk.ledgklvgynTDgiGlvssLek.ls 112
                                                            vTvPfKee+++l+  ++ +a+ +gavNTl  l dg l+g+nTDg Glv +L     
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_644  59 VTVPFKEEAYRLANSLTARAQRAGAVNTLSkLADGSLLGDNTDGAGLVRDLTVnAG 114
                                                            *****************************99********************99766 PP

                                              TIGR00507 113 klksekrvliiGAGGaakavaleLlka.dkeviiaNRtvekaeelaerlqelgeil 167
                                                            +  ++kr+l++GAGGa ++++ +Ll + + +viiaNRtv+kae lae +  lg i 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_644 115 FSLKGKRILLLGAGGAVRGALEPLLAEqPASVIIANRTVDKAELLAELFCDLGPIS 170
                                                            6666******************98866489***********************988 PP

                                              TIGR00507 168 alsleevelkkvdliinatsaglsgeideaevkaellkegk.lvvDlvynpletpl 222
                                                            a    +  +++vdliinatsa+l+g++  +++ ++l++ gk +++D++y +  t +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_644 171 ASG-YDWLQESVDLIINATSASLTGDV--PPIAPSLIEPGKtVCYDMMYGKEPTSF 223
                                                            766.6666789****************..********98763789*********** PP

                                              TIGR00507 223 lkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269
                                                             ++a+++g +  +dGlgMl +Qaa +F lw+gv pd   v   l+++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_644 224 CRWASEHGaAVSMDGLGMLAEQAAEAFFLWRGVRPDTAPVLAELRRQL 271
                                                            ********66678**************************999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (273 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.75
//
[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