Alignments for a candidate for aroB in Thiomicrospira cyclica ALM1

GapMind for Amino acid biosynthesis

Alignments for a candidate for aroB in Thiomicrospira cyclica ALM1

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_013834642.1 THICY_RS00400 3-dehydroquinate synthase

Query= SwissProt::Q8RU74
         (442 letters)



>NCBI__GCF_000214825.1:WP_013834642.1
          Length = 359

 Score =  418 bits (1074), Expect = e-121
 Identities = 210/354 (59%), Positives = 267/354 (75%), Gaps = 5/354 (1%)

Query: 83  VDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPNVT 142
           VDL  RSYPI+IG  LL QP L+   + G +V++VTN+TVAPLYLD+  +  TD    + 
Sbjct: 6   VDLAERSYPIFIGQDLLQQPGLVAPFVKGTQVMIVTNSTVAPLYLDRAKALFTD----LQ 61

Query: 143 VESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRGVN 202
           V++V+LPDGE++KN+E L ++FD+ I    DR+ T VALGGGVIGDM G+AAA+Y RGV 
Sbjct: 62  VDAVVLPDGEEYKNLEILNRIFDQLIGGHFDRKSTLVALGGGVIGDMTGFAAAAYQRGVP 121

Query: 203 FIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASGLA 262
           FIQIPTT+++QVDSSVGGKTG+NHP GKNMIGAF+QPQ V+IDT TLNTL DR+L++GLA
Sbjct: 122 FIQIPTTLLSQVDSSVGGKTGVNHPQGKNMIGAFHQPQAVVIDTLTLNTLEDRQLSAGLA 181

Query: 263 EVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRATL 322
           EVIKYGLIRD  FFEW EQN+  L+ARD      AI+RSC+NKAD+V+ DE E G RA L
Sbjct: 182 EVIKYGLIRDLAFFEWLEQNLEGLMARDHALLAQAIERSCQNKADIVAADETEQGQRALL 241

Query: 323 NLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAKLP 382
           NLGHTFGHA+E G+GYG WLHGEA++AG + A  MS+ LG +  + V+R+  I ++AKLP
Sbjct: 242 NLGHTFGHAIEAGMGYGAWLHGEAISAGMMQAAYMSQLLGDLSAADVERIGAIFKRAKLP 301

Query: 383 TSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETL 436
             PP  ++ E F   MA DKKV  GK+RL+LLK S+G    +GDY  + L +TL
Sbjct: 302 IYPPNELSNEQFMHYMAGDKKVQAGKVRLVLLK-SIGQAYISGDYPAELLQKTL 354


Lambda     K      H
   0.318    0.133    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: 406
Number of extensions: 8
Number of successful extensions: 3
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: 442
Length of database: 359
Length adjustment: 31
Effective length of query: 411
Effective length of database: 328
Effective search space:   134808
Effective search space used:   134808
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_013834642.1 THICY_RS00400 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

# 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/TIGR01357.hmm
# target sequence database:        /tmp/gapView.31708.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01357  [M=344]
Accession:   TIGR01357
Description: aroB: 3-dehydroquinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.8e-121  389.1   0.0   1.1e-120  388.9   0.0    1.0  1  lcl|NCBI__GCF_000214825.1:WP_013834642.1  THICY_RS00400 3-dehydroquinate s


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000214825.1:WP_013834642.1  THICY_RS00400 3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.9   0.0  1.1e-120  1.1e-120       1     340 [.      13     351 ..      13     355 .. 0.95

  Alignments for each domain:
  == domain 1  score: 388.9 bits;  conditional E-value: 1.1e-120
                                 TIGR01357   1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletv 68 
                                               y++ +g++ll++        k ++++++t+++v+ l+ ++ +++  +   +v+ +v+pdgee+K+le +
  lcl|NCBI__GCF_000214825.1:WP_013834642.1  13 YPIFIGQDLLQQPGLVAPFvKGTQVMIVTNSTVAPLYLDRAKALFTD--LQVDAVVLPDGEEYKNLEIL 79 
                                               578899999996544433345699***************99999976..9******************* PP

                                 TIGR01357  69 aklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplg 137
                                               +++ dql+  +++rks+lva+GGGv+gD++GF+Aa+y+RG++++q+PTtll++vDssvGGKtg+n+p+g
  lcl|NCBI__GCF_000214825.1:WP_013834642.1  80 NRIFDQLIGGHFDRKSTLVALGGGVIGDMTGFAAAAYQRGVPFIQIPTTLLSQVDSSVGGKTGVNHPQG 148
                                               ********************************************************************* PP

                                 TIGR01357 138 kNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeel 206
                                               kN+iGaf+qP+aV+id+ +l+tl +r+l++G+aEviK+gli d ++fe+le+n + l  + +++ l+++
  lcl|NCBI__GCF_000214825.1:WP_013834642.1 149 KNMIGAFHQPQAVVIDTLTLNTLEDRQLSAGLAEVIKYGLIRDLAFFEWLEQNLEGLMAR-DHALLAQA 216
                                               *****************************************************9987765.559***** PP

                                 TIGR01357 207 ikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllka 274
                                               i+rs++ Ka++V++De+e+g RalLN+GHt+gHaiEa ++y+ + HGea++ Gm+++a++s+ lg l+a
  lcl|NCBI__GCF_000214825.1:WP_013834642.1 217 IERSCQNKADIVAADETEQGQRALLNLGHTFGHAIEAGMGYGaWLHGEAISAGMMQAAYMSQLLGDLSA 285
                                               ********************************************************************* PP

                                 TIGR01357 275 ellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeell 340
                                                ++er+ a++k+++lp+  +++ls e++++++  DKK +++k++lvll++iG+a+++ ++++e l+
  lcl|NCBI__GCF_000214825.1:WP_013834642.1 286 ADVERIGAIFKRAKLPIYPPNELSNEQFMHYMAGDKKVQAGKVRLVLLKSIGQAYISGDYPAELLQ 351
                                               *******************************************************99888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (344 nodes)
Target sequences:                          1  (359 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: 00:00:00.01
# Mc/sec: 11.47
//
[ok]

This GapMind analysis is from Apr 10 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