Alignments for a candidate for aroE in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Paraburkholderia bryophila 376MFSha3.1

Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate H281DRAFT_06291 H281DRAFT_06291 shikimate dehydrogenase (EC 1.1.1.25)

Query= BRENDA::Q88RQ5
         (274 letters)



>FitnessBrowser__Burk376:H281DRAFT_06291
          Length = 287

 Score =  267 bits (683), Expect = 2e-76
 Identities = 153/277 (55%), Positives = 181/277 (65%), Gaps = 10/277 (3%)

Query: 2   DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGG-NVT 60
           D+Y V GNP+GHSKSP IH  FA QTG+ +EY+ LLAP+D F    R F + G  G NVT
Sbjct: 8   DRYAVIGNPVGHSKSPFIHSRFAAQTGEPVEYSALLAPVDAFVPHVRAFIEAGGRGLNVT 67

Query: 61  VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120
           VPFK +A     SL+PRA  AGAVNTL ++    + GDNTDG GLVRD+ VN GV L G 
Sbjct: 68  VPFKLDAHAFASSLSPRAAAAGAVNTL-RIDPNGVYGDNTDGFGLVRDIEVNLGVSLKGA 126

Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVA----SGFAW 176
           RIL+LGAGGA RGV+ P+L   P +L I NRT  KAE L  +F +    VA     G A 
Sbjct: 127 RILLLGAGGAARGVVLPMLERAPHTLTIVNRTAAKAEALVDQFAQAASGVACRLSGGNAR 186

Query: 177 LQEP--VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAK 234
             EP   DVI+NAT+ SL   LP   D     G T+ YDMMYG  PT F + A KLG A+
Sbjct: 187 AIEPGAYDVIVNATAGSLEASLPECDDGAFGNG-TLAYDMMYGAHPTVFMEHAQKLG-AR 244

Query: 235 VLDGLGMLAEQAAEAFFIWRGVRPDTAPVLAELRRQL 271
             DGLGML EQAAE+F++WRGVRPD+ PVLAELR  L
Sbjct: 245 GADGLGMLVEQAAESFYVWRGVRPDSVPVLAELRALL 281


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: 260
Number of extensions: 12
Number of successful extensions: 6
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: 287
Length adjustment: 26
Effective length of query: 248
Effective length of database: 261
Effective search space:    64728
Effective search space used:    64728
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 H281DRAFT_06291 H281DRAFT_06291 (shikimate dehydrogenase (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.18190.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
      7e-78  247.5   0.0    7.9e-78  247.3   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06291  H281DRAFT_06291 shikimate dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06291  H281DRAFT_06291 shikimate dehydrogenase (EC 1.1.1.25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.3   0.0   7.9e-78   7.9e-78       3     267 ..      10     279 ..       8     282 .. 0.93

  Alignments for each domain:
  == domain 1  score: 247.3 bits;  conditional E-value: 7.9e-78
                                    TIGR00507   3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevl 68 
                                                  ++viGnp+ hSksp+ih ++++q+g  +eY a+ ++++++   + ++ ++g +G+nvTvPfK  + 
  lcl|FitnessBrowser__Burk376:H281DRAFT_06291  10 YAVIGNPVGHSKSPFIHSRFAAQTGEPVEYSALLAPVDAFVPHVRAFIEAGGRGLNVTVPFKLDAH 75 
                                                  9***************************************************************** PP

                                    TIGR00507  69 ellDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakava 133
                                                  +++  ++++a+++gavNTl+++ + ++g+nTDg Glv ++e  l    ++ r+l++GAGGaa++v+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06291  76 AFASSLSPRAAAAGAVNTLRIDPNGVYGDNTDGFGLVRDIEVnLGVSLKGARILLLGAGGAARGVV 141
                                                  *****************************************98887666***************** PP

                                    TIGR00507 134 leLlka.dkeviiaNRtvekaeelaerlqe..lgeilalsl...eevelkkvdliinatsaglsge 193
                                                  l++l+  +++++i+NRt +kae+l++++++   g  + ls      +e+  +d+i+nat+ +l+  
  lcl|FitnessBrowser__Burk376:H281DRAFT_06291 142 LPMLERaPHTLTIVNRTAAKAEALVDQFAQaaSGVACRLSGgnaRAIEPGAYDVIVNATAGSLEAS 207
                                                  *977654*********************99666777777751114566777*************** PP

                                    TIGR00507 194 ideaevkaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdve 259
                                                  +  +e + + + +g+l++D++y    t++++ a+k+g++ +dGlgMlv+Qaa sF +w+gv pd  
  lcl|FitnessBrowser__Burk376:H281DRAFT_06291 208 L--PECDDGAFGNGTLAYDMMYGAHPTVFMEHAQKLGARGADGLGMLVEQAAESFYVWRGVRPDSV 271
                                                  *..99***********************************************************99 PP

                                    TIGR00507 260 kvfealke 267
                                                   v   l++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06291 272 PVLAELRA 279
                                                  99887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (287 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: 00:00:00.00
# Mc/sec: 8.24
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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