Alignments for a candidate for leuC in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Dinoroseobacter shibae DFL-12

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate 3607280 Dshi_0695 3-isopropylmalate dehydratase, large subunit (RefSeq)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Dino:3607280
          Length = 464

 Score =  482 bits (1240), Expect = e-140
 Identities = 250/461 (54%), Positives = 307/461 (66%), Gaps = 10/461 (2%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TL EKL+ AH V   E+   LL++DRHL+HE  S  AF  L   G  V  P +TFA MD
Sbjct: 5   RTLLEKLWAAHEVTRREDGASLLWVDRHLLHE-GSHHAFAKLAERGLSVAAPAQTFAVMD 63

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           H   T+ +         R  +  L +N +   + L+DL    QGIVHV+GPEQG+TLPG+
Sbjct: 64  HYAPTRDRAAEGATPEIRAMIARLRENAEIHQIRLFDLFDRDQGIVHVIGPEQGLTLPGL 123

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
           TI CGDSHT+THGAFGALAFGIG +EV HVLATQT+ Q R KT+++   G+  PG+ AKD
Sbjct: 124 TINCGDSHTSTHGAFGALAFGIGATEVAHVLATQTVWQTRPKTLRLRFDGRLGPGVGAKD 183

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           + LA I   GS G  GH +E+ GEA+R LSMEGRMTLCN++IE GAK GL+APDETTF Y
Sbjct: 184 LALAWIAALGSDGARGHAIEYTGEAVRRLSMEGRMTLCNLSIEGGAKLGLIAPDETTFAY 243

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           ++GR HAP G D+  AV  W  L++DE A FD   TL    I+P VTWGT P Q I V +
Sbjct: 244 LRGRPHAPDGADWGRAVEDWAALRSDEDAVFDREETLDCAAIAPVVTWGTRPDQAIPVTE 303

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
           N+P         E +    AL YMGL+ G P+    +D+VFIGSCTN RIEDLRAAA + 
Sbjct: 304 NLPRG-------EGSEVNSALTYMGLRAGAPIAGTPVDQVFIGSCTNGRIEDLRAAAAVL 356

Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422
            GR+    V   V PGS  +KAQAE EGL +IFI AG EW   GC+MC+ MN D + PG+
Sbjct: 357 AGRRAR--VPGQVTPGSARIKAQAEQEGLAEIFIAAGLEWTEAGCAMCVGMNGDLVAPGK 414

Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           RCAS++NRNF GRQG G RTHL+SPAM AAAAVTG   D+R
Sbjct: 415 RCASSTNRNFRGRQGPGARTHLMSPAMVAAAAVTGEITDVR 455


Lambda     K      H
   0.317    0.134    0.396 

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: 717
Number of extensions: 31
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: 466
Length of database: 464
Length adjustment: 33
Effective length of query: 433
Effective length of database: 431
Effective search space:   186623
Effective search space used:   186623
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: 51 (24.3 bits)

Align candidate 3607280 Dshi_0695 (3-isopropylmalate dehydratase, large subunit (RefSeq))
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.13179.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.2e-186  605.9   0.0   2.6e-186  605.7   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607280  Dshi_0695 3-isopropylmalate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607280  Dshi_0695 3-isopropylmalate dehydratase, large subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  605.7   0.0  2.6e-186  2.6e-186       2     465 ..       4     456 ..       3     457 .. 0.98

  Alignments for each domain:
  == domain 1  score: 605.7 bits;  conditional E-value: 2.6e-186
                         TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveikeek 78 
                                       ++tl+ekl+ ah v + e++++ll++drhl+he  s  af  l ++g  v  + +t+a +dh  +t+ r  e    +
  lcl|FitnessBrowser__Dino:3607280   4 PRTLLEKLWAAHEVTRREDGASLLWVDRHLLHE-GSHHAFAKLAERGLSVAAPAQTFAVMDHYAPTRDRAAEGATPE 79 
                                       8********************************.5899*************************************** PP

                         TIGR00170  79 aklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvlat 155
                                        +  +  l +n++   ++lfdl + +qgivhv+gpe+gltlpg ti cgdsht+thgafgalafgig++ev hvlat
  lcl|FitnessBrowser__Dino:3607280  80 IRAMIARLRENAEIHQIRLFDLFDRDQGIVHVIGPEQGLTLPGLTINCGDSHTSTHGAFGALAFGIGATEVAHVLAT 156
                                       ***************************************************************************** PP

                         TIGR00170 156 qtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagl 232
                                       qt++q+r+ktl+++ +g+l +g+ akd+ la i  +g+ g  g+ +e++gea+r lsme+rmt+cn++ie gak gl
  lcl|FitnessBrowser__Dino:3607280 157 QTVWQTRPKTLRLRFDGRLGPGVGAKDLALAWIAALGSDGARGHAIEYTGEAVRRLSMEGRMTLCNLSIEGGAKLGL 233
                                       ***************************************************************************** PP

                         TIGR00170 233 iapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpks 309
                                       iapdettf+y+++r++ap g+++  av+ w +l++de+a+fd++ tl++  i+p vtwgt p+q+++v+e++p  + 
  lcl|FitnessBrowser__Dino:3607280 234 IAPDETTFAYLRGRPHAPDGADWGRAVEDWAALRSDEDAVFDREETLDCAAIAPVVTWGTRPDQAIPVTENLPRGE- 309
                                       *************************************************************************875. PP

                         TIGR00170 310 ladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkq 386
                                              ++++ al+y+gl++g ++    vd+vfigsctn+riedlraaa+v+ g++     +   v pgs  +k+q
  lcl|FitnessBrowser__Dino:3607280 310 ------GSEVNSALTYMGLRAGAPIAGTPVDQVFIGSCTNGRIEDLRAAAAVLAGRRARVPGQ---VTPGSARIKAQ 377
                                       ......578899********************************************9876666...99********* PP

                         TIGR00170 387 aekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdi 463
                                       ae+egl +if++ag+ew eagc++c+gmn d + +++rcas++nrnf grqg garthl+spam aaaav+g++ d+
  lcl|FitnessBrowser__Dino:3607280 378 AEQEGLAEIFIAAGLEWTEAGCAMCVGMNGDLVAPGKRCASSTNRNFRGRQGPGARTHLMSPAMVAAAAVTGEITDV 454
                                       ***************************************************************************** PP

                         TIGR00170 464 re 465
                                       r 
  lcl|FitnessBrowser__Dino:3607280 455 RP 456
                                       95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (464 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: 00:00:00.01
# Mc/sec: 12.51
//
[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:

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