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 3606654 Dshi_0085 3-isopropylmalate dehydratase, large subunit (RefSeq)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Dino:3606654
          Length = 467

 Score =  610 bits (1574), Expect = e-179
 Identities = 305/466 (65%), Positives = 374/466 (80%), Gaps = 4/466 (0%)

Query: 2   AKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATM 61
           A+TLY+K++DAH+ +EAE+ T LLYIDRHLVHEVTSPQAF+GLR  GR VR P KT A  
Sbjct: 3   ARTLYDKIWDAHLAHEAEDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRTVRAPDKTIAVP 62

Query: 62  DHNVSTQT--KDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
           DHNV T    ++ +   E +RIQ++ L KN K+FG+  Y ++   QGIVH++GPEQG TL
Sbjct: 63  DHNVPTTLGRENPDQMTEDSRIQVEALDKNAKDFGIHYYPVSDIRQGIVHIVGPEQGWTL 122

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGMT+VCGDSHTATHGAFGALA GIGTSEVEHVLATQTL Q ++K MK+E+ GK  PG+T
Sbjct: 123 PGMTVVCGDSHTATHGAFGALAHGIGTSEVEHVLATQTLIQKKSKNMKVEITGKLRPGVT 182

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
           AKDI L++IG TG+AGGTG+V+E+CGEAIRDLSMEGRMT+CNMAIE GA+AGL+APDE T
Sbjct: 183 AKDITLSVIGATGTAGGTGYVIEYCGEAIRDLSMEGRMTVCNMAIEGGARAGLIAPDEKT 242

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
           + YV+GR HAPKG  ++ A+A+WKTL +D+ A +D VVT++ E+I+P VTWGT+P  V+ 
Sbjct: 243 YEYVQGRPHAPKGAQWEAALAWWKTLYSDDDAHWDKVVTIKGEDIAPVVTWGTSPEDVLP 302

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           ++  +P P  F      A A ++L YMGL PG PL+E+ ID VFIGSCTN RIEDLRAAA
Sbjct: 303 ISAMVPAPEDFTGGKVDA-ARRSLDYMGLTPGTPLSEIEIDTVFIGSCTNGRIEDLRAAA 361

Query: 360 EIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
           EI KG+K+A   +A+VVPGSG V+AQAE EGL  IF +AGFEWR+ GCSMCLAMN D+L+
Sbjct: 362 EILKGKKIAV-KRAMVVPGSGLVRAQAEEEGLADIFKQAGFEWRMAGCSMCLAMNPDQLS 420

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
            GERCASTSNRNFEGRQG  GRTHLVSPAMAAAAAVTG   D+R++
Sbjct: 421 EGERCASTSNRNFEGRQGYKGRTHLVSPAMAAAAAVTGKLTDVRDL 466


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: 767
Number of extensions: 25
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: 467
Length adjustment: 33
Effective length of query: 433
Effective length of database: 434
Effective search space:   187922
Effective search space used:   187922
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 3606654 Dshi_0085 (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.3359.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.3e-241  787.2   0.2   2.7e-241  786.9   0.2    1.0  1  lcl|FitnessBrowser__Dino:3606654  Dshi_0085 3-isopropylmalate dehy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3606654  Dshi_0085 3-isopropylmalate dehydratase, large subunit (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  786.9   0.2  2.7e-241  2.7e-241       2     466 .]       3     466 ..       2     466 .. 0.98

  Alignments for each domain:
  == domain 1  score: 786.9 bits;  conditional E-value: 2.7e-241
                         TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr..dveike 76 
                                       a+tly+k++dah+ +eae++t llyidrhlvhevtspqafeglr agr vr +dkt+a  dhn++t+    + +++ 
  lcl|FitnessBrowser__Dino:3606654   3 ARTLYDKIWDAHLAHEAEDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRTVRAPDKTIAVPDHNVPTTLGreNPDQMT 79 
                                       89***************************************************************985423667899 PP

                         TIGR00170  77 ekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvl 153
                                       e++++qv++l+kn+k+fg++++ +s+ +qgivh+vgpe+g tlpg+t+vcgdshtathgafgala gigtsevehvl
  lcl|FitnessBrowser__Dino:3606654  80 EDSRIQVEALDKNAKDFGIHYYPVSDIRQGIVHIVGPEQGWTLPGMTVVCGDSHTATHGAFGALAHGIGTSEVEHVL 156
                                       9**************************************************************************** PP

                         TIGR00170 154 atqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagaka 230
                                       atqtl+q+++k++k+e+ gkl +g+takdi l +ig +g+aggtgyv+e++geairdlsme+rmtvcnmaie ga+a
  lcl|FitnessBrowser__Dino:3606654 157 ATQTLIQKKSKNMKVEITGKLRPGVTAKDITLSVIGATGTAGGTGYVIEYCGEAIRDLSMEGRMTVCNMAIEGGARA 233
                                       ***************************************************************************** PP

                         TIGR00170 231 gliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdp 307
                                       gliapde t+eyv++r++apkg+++e a+a wktl +d++a++dkvvt++++di+p vtwgt+p++vl+++  vp+p
  lcl|FitnessBrowser__Dino:3606654 234 GLIAPDEKTYEYVQGRPHAPKGAQWEAALAWWKTLYSDDDAHWDKVVTIKGEDIAPVVTWGTSPEDVLPISAMVPAP 310
                                       ***************************************************************************** PP

                         TIGR00170 308 ksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvk 384
                                       ++++   +   a ++l+y+gl+pgt+l +i++d vfigsctn+riedlraaae++kgkk+a  vk+a+vvpgsglv+
  lcl|FitnessBrowser__Dino:3606654 311 EDFTGG-KVDAARRSLDYMGLTPGTPLSEIEIDTVFIGSCTNGRIEDLRAAAEILKGKKIA--VKRAMVVPGSGLVR 384
                                       ***986.456789**********************************************98..99************ PP

                         TIGR00170 385 kqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfv 461
                                       +qae+egl  if +agfewr agcs+cl+mn+d+l+e+ercastsnrnfegrqg ++rthlvspamaaaaav+gk+ 
  lcl|FitnessBrowser__Dino:3606654 385 AQAEEEGLADIFKQAGFEWRMAGCSMCLAMNPDQLSEGERCASTSNRNFEGRQGYKGRTHLVSPAMAAAAAVTGKLT 461
                                       ***************************************************************************** PP

                         TIGR00170 462 direl 466
                                       d+r+l
  lcl|FitnessBrowser__Dino:3606654 462 DVRDL 466
                                       ***85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (467 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: 8.49
//
[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