Alignments for a candidate for aroE in Rhodomicrobium vannielii ATCC 17100

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroE in Rhodomicrobium vannielii ATCC 17100

Align Shikimate dehydrogenase (NADP(+)); Short=SDH; EC 1.1.1.25 (characterized, see rationale)
to candidate WP_013420275.1 RVAN_RS13550 shikimate dehydrogenase

Query= uniprot:A0A2M8WD96
         (270 letters)



>NCBI__GCF_000166055.1:WP_013420275.1
          Length = 278

 Score =  176 bits (447), Expect = 4e-49
 Identities = 118/259 (45%), Positives = 148/259 (57%), Gaps = 17/259 (6%)

Query: 8   VIGDPIAQSKSPVIHGFWLDKLGLSASYRKTHVTAEGLAGF---FASRRDDPNWRGCNIT 64
           VIG PI+ S SPVIHGFWL + G++  Y K  V  +  A F   FA+        G N+T
Sbjct: 6   VIGWPISHSLSPVIHGFWLREHGIAGEYGKAAVEPKDFADFVRGFAAA----GLAGGNVT 61

Query: 65  APHKIASLDHVPDPGGVRDTIGAINTVFRSAEGTLIGTNTDAAGFYAPLAE----FDLEG 120
            PHK+ +           + IGA+NT++    G L G NTDA GF A L E    +D  G
Sbjct: 62  VPHKLEAFRLADMRDAAAEAIGAVNTLWLDG-GKLHGANTDAFGFLANLDEQAPDWDKSG 120

Query: 121 APVAMVGAGGAARAILFALARAGVGHVTILNRSPLKAMGLLATFGLKGDVVALN---API 177
           A V ++GAGGAARAI++AL   G   + I+NR+   A  L A F       ALN   A +
Sbjct: 121 AAV-VIGAGGAARAIVWALIERGFAEIRIVNRTKATADALAAEFP-PATSFALNDLPAAL 178

Query: 178 PPVALLVNASSLGMTGQPPLELDLGNLPDDAVVYDAVYAPLETGLLAAARARDLDTVDGL 237
                +VN S+LGM GQPPL++DL  +  +A V D VY PLET LLA ARAR L  VDGL
Sbjct: 179 DGAHFIVNTSTLGMKGQPPLDIDLSPVAANATVNDIVYTPLETPLLAQARARGLHAVDGL 238

Query: 238 EMLIGQAALAFELFFGNAP 256
            ML+ QAA  FEL+FG  P
Sbjct: 239 GMLLHQAAPGFELWFGVRP 257


Lambda     K      H
   0.319    0.137    0.407 

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: 206
Number of extensions: 12
Number of successful extensions: 4
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: 270
Length of database: 278
Length adjustment: 25
Effective length of query: 245
Effective length of database: 253
Effective search space:    61985
Effective search space used:    61985
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 WP_013420275.1 RVAN_RS13550 (shikimate dehydrogenase)
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.1940567.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-72  230.3   0.0    1.4e-72  230.1   0.0    1.0  1  NCBI__GCF_000166055.1:WP_013420275.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166055.1:WP_013420275.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.1   0.0   1.4e-72   1.4e-72       4     260 ..       5     261 ..       2     271 .. 0.92

  Alignments for each domain:
  == domain 1  score: 230.1 bits;  conditional E-value: 1.4e-72
                             TIGR00507   4 gviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDeiee 76 
                                            viG pi hS+sp+ih   l++ g+++eY +  ve++++ +++ g+ a+gl G nvTvP+K e+++l+D  + 
  NCBI__GCF_000166055.1:WP_013420275.1   5 CVIGWPISHSLSPVIHGFWLREHGIAGEYGKAAVEPKDFADFVRGFAAAGLAGGNVTVPHKLEAFRLADMRDA 77 
                                           79*********************************************************************** PP

                             TIGR00507  77 sakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.dkeviiaN 147
                                            a++igavNTl l++gkl g nTD+ G++++L +      +   +++iGAGGaa+a++ +L +    e+ i+N
  NCBI__GCF_000166055.1:WP_013420275.1  78 AAEAIGAVNTLWLDGGKLHGANTDAFGFLANLDEqAPDWDKSGAAVVIGAGGAARAIVWALIERgFAEIRIVN 150
                                           ********************************99544455577899****************995589***** PP

                             TIGR00507 148 RtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDlvynplet 220
                                           Rt++ a +la +++   +  al+     l+    i+n+  +g++g+     ++ + +++++ v D+vy plet
  NCBI__GCF_000166055.1:WP_013420275.1 151 RTKATADALAAEFPP-ATSFALNDLPAALDGAHFIVNTSTLGMKGQP-PLDIDLSPVAANATVNDIVYTPLET 221
                                           **************9.445555555566788**************98.67788888889999*********** PP

                             TIGR00507 221 pllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvek 260
                                           pll+ a+ +g + +dGlgMl +Qaa  Felw+gv p v  
  NCBI__GCF_000166055.1:WP_013420275.1 222 PLLAQARARGLHAVDGLGMLLHQAAPGFELWFGVRPRVTP 261
                                           ***********************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (278 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 12.27
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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