Alignments for a candidate for leuC in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Sphingomonas koreensis DSMZ 15582

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate Ga0059261_4223 Ga0059261_4223 3-isopropylmalate dehydratase, large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Korea:Ga0059261_4223
          Length = 478

 Score =  597 bits (1538), Expect = e-175
 Identities = 297/470 (63%), Positives = 367/470 (78%), Gaps = 9/470 (1%)

Query: 4   TLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMDH 63
           TLYEK++ AHVV   ++ T L+YIDRHLVHEVTSPQAF+GLRA+GR VR+P  T A  DH
Sbjct: 7   TLYEKIWAAHVVERRDDGTCLIYIDRHLVHEVTSPQAFEGLRANGRRVRRPDLTLAVPDH 66

Query: 64  NVSTQTKDINACGEMARI-------QMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQG 116
           N+ T T  ++A G    I       Q+  L +N  EFG++ +      QGIVHV+GPEQG
Sbjct: 67  NLPT-TPRVDAAGNRLPIADRESAQQLAALERNVAEFGIDYFGATAAEQGIVHVVGPEQG 125

Query: 117 VTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAP 176
            TLPG T+VCGDSHT+ HGA GALAFGIGTSEVEHVLATQTL   ++KTM+I V G    
Sbjct: 126 FTLPGTTLVCGDSHTSAHGALGALAFGIGTSEVEHVLATQTLLLSQSKTMEIRVDGTLGF 185

Query: 177 GITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD 236
           G++AKD+VLAIIGKTG+AGGTG+VVE+ GE IR LS+EGR+T+ NM+IE GA++GL+APD
Sbjct: 186 GVSAKDVVLAIIGKTGAAGGTGYVVEYTGEVIRALSIEGRLTVSNMSIEGGARSGLIAPD 245

Query: 237 ETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQ 296
           E TF Y+KGR  APKG+ ++ AVA+WKTL TD GA +D VVTL   +I+P +TWGT+P  
Sbjct: 246 EKTFAYLKGRPMAPKGEQWEQAVAWWKTLPTDAGAQYDRVVTLNGSDIAPSLTWGTSPED 305

Query: 297 VISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLR 356
           V+ +   +PDP SFADP +R +A+K+L YMGL PG  + ++A++ +FIGSCTNSRIEDLR
Sbjct: 306 VVPITGVVPDPESFADPAKRVAAQKSLDYMGLAPGTRMQDIAVENIFIGSCTNSRIEDLR 365

Query: 357 AAAEIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNN 415
           AAA++ KGR VA G+ QAL+VPGSG VK QAEAEGLD+IF++AGFEWR PGCSMCLAMN 
Sbjct: 366 AAADVVKGRHVADGIRQALIVPGSGLVKRQAEAEGLDRIFLDAGFEWREPGCSMCLAMNP 425

Query: 416 DRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           D++  GERCASTSNRNF GRQG G RTHLVSPAMAAAAAVTG   D+R++
Sbjct: 426 DKVPAGERCASTSNRNFVGRQGPGARTHLVSPAMAAAAAVTGRLTDVRDL 475


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: 768
Number of extensions: 26
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: 466
Length of database: 478
Length adjustment: 33
Effective length of query: 433
Effective length of database: 445
Effective search space:   192685
Effective search space used:   192685
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 Ga0059261_4223 Ga0059261_4223 (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.9738.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.4e-239  778.8   0.0   9.8e-239  778.5   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_4223  Ga0059261_4223 3-isopropylmalate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_4223  Ga0059261_4223 3-isopropylmalate dehydratase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  778.5   0.0  9.8e-239  9.8e-239       2     466 .]       5     475 ..       4     475 .. 0.99

  Alignments for each domain:
  == domain 1  score: 778.5 bits;  conditional E-value: 9.8e-239
                                 TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr 70 
                                               + tlyek++ ahvv++ +++t l+yidrhlvhevtspqafeglra+gr+vrr+d tla  dhn++t+ r
  lcl|FitnessBrowser__Korea:Ga0059261_4223   5 PLTLYEKIWAAHVVERRDDGTCLIYIDRHLVHEVTSPQAFEGLRANGRRVRRPDLTLAVPDHNLPTTPR 73 
                                               569****************************************************************99 PP

                                 TIGR00170  71 ......dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtat 133
                                                      + i + ++  q+ +le+nv efg+++f+ + aeqgivhvvgpe+g+tlpg+t+vcgdsht++
  lcl|FitnessBrowser__Korea:Ga0059261_4223  74 vdaagnRLPIADRESAQQLAALERNVAEFGIDYFGATAAEQGIVHVVGPEQGFTLPGTTLVCGDSHTSA 142
                                               98888778899********************************************************** PP

                                 TIGR00170 134 hgafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvve 202
                                               hga+galafgigtsevehvlatqtl  +++kt++i+v+g+l  g++akd++laiigk+g+aggtgyvve
  lcl|FitnessBrowser__Korea:Ga0059261_4223 143 HGALGALAFGIGTSEVEHVLATQTLLLSQSKTMEIRVDGTLGFGVSAKDVVLAIIGKTGAAGGTGYVVE 211
                                               ********************************************************************* PP

                                 TIGR00170 203 fageairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdega 271
                                               ++ge+ir+ls+e+r+tv nm+ie ga++gliapde tf+y+k+r++apkg+++e+ava wktl td ga
  lcl|FitnessBrowser__Korea:Ga0059261_4223 212 YTGEVIRALSIEGRLTVSNMSIEGGARSGLIAPDEKTFAYLKGRPMAPKGEQWEQAVAWWKTLPTDAGA 280
                                               ********************************************************************* PP

                                 TIGR00170 272 kfdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvd 340
                                               ++d+vvtl+++di+p +twgt+p++v+++++ vpdp+s+adp ++  a+k+l+y+gl pgt+++di+v+
  lcl|FitnessBrowser__Korea:Ga0059261_4223 281 QYDRVVTLNGSDIAPSLTWGTSPEDVVPITGVVPDPESFADPAKRVAAQKSLDYMGLAPGTRMQDIAVE 349
                                               ********************************************************************* PP

                                 TIGR00170 341 kvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcs 409
                                               ++figsctnsriedlraaa+vvkg++vad++++al+vpgsglvk+qae+egld+ifl+agfewre+gcs
  lcl|FitnessBrowser__Korea:Ga0059261_4223 350 NIFIGSCTNSRIEDLRAAADVVKGRHVADGIRQALIVPGSGLVKRQAEAEGLDRIFLDAGFEWREPGCS 418
                                               ********************************************************************* PP

                                 TIGR00170 410 lclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                               +cl+mn+d+++++ercastsnrnf grqg garthlvspamaaaaav+g++ d+r+l
  lcl|FitnessBrowser__Korea:Ga0059261_4223 419 MCLAMNPDKVPAGERCASTSNRNFVGRQGPGARTHLVSPAMAAAAAVTGRLTDVRDL 475
                                               *******************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (478 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: 10.56
//
[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