Aligments for a candidate for leuC in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Aligments for a candidate for leuC in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate Echvi_2059 Echvi_2059 3-isopropylmalate dehydratase, large subunit

Query= SwissProt::Q7TXH6
         (473 letters)



>FitnessBrowser__Cola:Echvi_2059
          Length = 465

 Score =  513 bits (1321), Expect = e-150
 Identities = 254/466 (54%), Positives = 326/466 (69%), Gaps = 2/466 (0%)

Query: 7   EPRTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELTLA 66
           E +TL +K+WD+H+V S  G  PD+ +ID H +HEVTSP AF  L   G  V  PE T+A
Sbjct: 2   EKKTLFDKVWDEHVVKSVPG-GPDVFFIDKHFIHEVTSPVAFLNLENRGNNVLFPERTVA 60

Query: 67  TEDHNVPTVDIDQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGPQLGLTQ 126
           T DHNVPT+D D+ I D +SR QVE LR NC+++GI LH +G    GIVHV+GP+LG+TQ
Sbjct: 61  TPDHNVPTIDQDKTIKDKLSRMQVEKLRDNCSKYGIELHDLGTDHHGIVHVIGPELGITQ 120

Query: 127 PGMTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGRLPDGVS 186
           PGMTIVCGDSHTSTHGAFGA+A GIGTSEVE V A+Q +     K M + V+G L  GV+
Sbjct: 121 PGMTIVCGDSHTSTHGAFGAIAFGIGTSEVEMVFASQCIMQSKPKRMRITVNGELGKGVT 180

Query: 187 AKDIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMVAPDETT 246
           +KDIIL +I+KI   GG G+ IEY GSAI+SLSME RMTICNMSIE GAR G++APDE T
Sbjct: 181 SKDIILYIISKISASGGTGYFIEYAGSAIQSLSMEARMTICNMSIEMGARGGLIAPDEVT 240

Query: 247 YAFLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTNPGQGVP 306
           + +L+G+ HAP G  WD A+ YW+ LRTD GA FD E   DA  + P +T+GTNPG G+ 
Sbjct: 241 FDYLKGKEHAPKGEDWDKAVEYWKSLRTDEGAEFDLEYTYDAEDIEPMITYGTNPGMGIK 300

Query: 307 LAAAVPDPQLMTDDAERQAAEKALAYMDLRPGTAMREIAVDAVFVGSCTNGRIEDLRVVA 366
           +   +P  + M + + ++   K+L YM  +PG  ++   +D VFVGSCTNGRIED+R VA
Sbjct: 301 IKDIIPTTEGM-EGSNKKTYLKSLDYMGFQPGEPIKGKKIDYVFVGSCTNGRIEDIRAVA 359

Query: 367 EVLRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGMNPDQLA 426
           E ++G+K AD +   IVPGS  V +QA  EGL  I  +AG + RQ GCS CL MN D++ 
Sbjct: 360 EFVKGKKKADNITAWIVPGSREVESQAIEEGLVSILEEAGFKLRQPGCSACLAMNDDKIP 419

Query: 427 SGERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLSSPADL 472
           +G+   +TSNRNFEGRQG G RT L SP   AA A+ G ++ P ++
Sbjct: 420 AGKYAVSTSNRNFEGRQGPGARTLLASPLTVAAVAITGEVADPREV 465


Lambda     K      H
   0.319    0.135    0.402 

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: 637
Number of extensions: 22
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: 473
Length of database: 465
Length adjustment: 33
Effective length of query: 440
Effective length of database: 432
Effective search space:   190080
Effective search space used:   190080
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: 51 (24.3 bits)

Align candidate Echvi_2059 Echvi_2059 (3-isopropylmalate dehydratase, large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

# 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.5800.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.4e-203  661.8   0.1   2.9e-203  661.6   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2059  Echvi_2059 3-isopropylmalate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2059  Echvi_2059 3-isopropylmalate dehydratase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  661.6   0.1  2.9e-203  2.9e-203       2     466 .]       3     465 .]       2     465 .] 0.99

  Alignments for each domain:
  == domain 1  score: 661.6 bits;  conditional E-value: 2.9e-203
                            TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveik 75 
                                           ktl++k++d+hvvk   +++d+++id+h++hevtsp af  l+++g +v  +++t+at dhn++t  +d +ik
  lcl|FitnessBrowser__Cola:Echvi_2059   3 KKTLFDKVWDEHVVKSVPGGPDVFFIDKHFIHEVTSPVAFLNLENRGNNVLFPERTVATPDHNVPTIDQDKTIK 76 
                                          59************************************************************************ PP

                            TIGR00170  76 eekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsev 149
                                          ++ +++qv++l  n+ ++g++l+dl + + givhv+gpe g+t pg+tivcgdsht+thgafga+afgigtsev
  lcl|FitnessBrowser__Cola:Echvi_2059  77 DKLSRMQVEKLRDNCSKYGIELHDLGTDHHGIVHVIGPELGITQPGMTIVCGDSHTSTHGAFGAIAFGIGTSEV 150
                                          ************************************************************************** PP

                            TIGR00170 150 ehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnma 223
                                          e v+a+q ++q+++k ++i+v+g+l kg+t+kdiil+ii ki+++ggtgy +e+ag ai++lsme+rmt+cnm+
  lcl|FitnessBrowser__Cola:Echvi_2059 151 EMVFASQCIMQSKPKRMRITVNGELGKGVTSKDIILYIISKISASGGTGYFIEYAGSAIQSLSMEARMTICNMS 224
                                          ************************************************************************** PP

                            TIGR00170 224 ieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqv 297
                                          ie+ga+ gliapde+tf+y+k++++apkg++++kav+ywk+l+tdega+fd + t +a+di p++t+gtnpg+ 
  lcl|FitnessBrowser__Cola:Echvi_2059 225 IEMGARGGLIAPDEVTFDYLKGKEHAPKGEDWDKAVEYWKSLRTDEGAEFDLEYTYDAEDIEPMITYGTNPGMG 298
                                          ************************************************************************** PP

                            TIGR00170 298 lsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnv 371
                                          + +++ +p  + +    +k++  k+l+y+g++pg ++k  k+d vf+gsctn+ried+ra ae vkgkk+adn+
  lcl|FitnessBrowser__Cola:Echvi_2059 299 IKIKDIIPTTEGMEGS-NKKTYLKSLDYMGFQPGEPIKGKKIDYVFVGSCTNGRIEDIRAVAEFVKGKKKADNI 371
                                          *********9999765.677889*************************************************** PP

                            TIGR00170 372 klalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthl 445
                                            a +vpgs  v  qa +egl  i+ eagf+ r++gcs cl+mn+d++++++   stsnrnfegrqg gart l
  lcl|FitnessBrowser__Cola:Echvi_2059 372 T-AWIVPGSREVESQAIEEGLVSILEEAGFKLRQPGCSACLAMNDDKIPAGKYAVSTSNRNFEGRQGPGARTLL 444
                                          9.9*********************************************************************** PP

                            TIGR00170 446 vspamaaaaavagkfvdirel 466
                                           sp   aa a++g+ +d re+
  lcl|FitnessBrowser__Cola:Echvi_2059 445 ASPLTVAAVAITGEVADPREV 465
                                          *****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (465 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: 00:00:00.02
# Mc/sec: 7.80
//
[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