Alignments for a candidate for leuC in Thiomicrorhabdus arctica DSM 13458

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Thiomicrorhabdus arctica DSM 13458

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_019555900.1 F612_RS0101120 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000381085.1:WP_019555900.1
          Length = 471

 Score =  562 bits (1449), Expect = e-165
 Identities = 285/467 (61%), Positives = 345/467 (73%), Gaps = 4/467 (0%)

Query: 2   AKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATM 61
           AKTLY+KL+DAH+V + ++ T L+YIDR L+HEVTSPQAF+GLR   R   +     AT 
Sbjct: 3   AKTLYDKLWDAHIVRQEDDGTALIYIDRQLLHEVTSPQAFEGLRMAHRTPWRIDTNLATP 62

Query: 62  DHNVSTQTKD---INACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118
           DHNV T        +    ++RIQ++ L  N +EFG+  Y +    QGIVHV+GPE G T
Sbjct: 63  DHNVPTTDLSNGIASITDPVSRIQVETLGMNTREFGITEYAMGDIRQGIVHVVGPESGAT 122

Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178
           LPGMT+VCGDSHTATHGA GALA GIGTSEVEHVLATQ L Q + K M ++V GK + G+
Sbjct: 123 LPGMTVVCGDSHTATHGALGALAHGIGTSEVEHVLATQCLIQKKMKNMLVKVDGKLSAGV 182

Query: 179 TAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDET 238
           T KD+VLAIIGK G+AGG GH +EF G+  RD+S+EGRMT+CNMAIE GA+ GL+A DE 
Sbjct: 183 TPKDVVLAIIGKIGTAGGNGHAIEFGGQVFRDMSIEGRMTVCNMAIEGGARVGLIAVDEK 242

Query: 239 TFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVI 298
           T  YVKGR  APKG+ +D AV  W  L +D  A FDT+V L    I PQVTWGT+P  V+
Sbjct: 243 TVEYVKGRTFAPKGEQWDMAVTAWMDLTSDADAVFDTLVELDGSMIEPQVTWGTSPEMVL 302

Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358
            VN  +P+PA+  D V+     +ALAYMGL+  + + ++  + VFIGSCTNSRIEDLRAA
Sbjct: 303 DVNGRVPNPANEMDAVKADGIRRALAYMGLEADMAIKDIPAEYVFIGSCTNSRIEDLRAA 362

Query: 359 AEIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417
           A + KGRK++  V+ AL VPGSG VK QAEAEGLDKIFIEAGFEWR PGCSMCLAMN D+
Sbjct: 363 ATVLKGRKISDKVELALAVPGSGLVKQQAEAEGLDKIFIEAGFEWRNPGCSMCLAMNADK 422

Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRN 464
           L  G+ CASTSNRNFEGRQG GGRTHLVSP MAAAAA+ GHF D+R+
Sbjct: 423 LPTGKHCASTSNRNFEGRQGAGGRTHLVSPEMAAAAAIAGHFVDVRD 469


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: 729
Number of extensions: 23
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: 471
Length adjustment: 33
Effective length of query: 433
Effective length of database: 438
Effective search space:   189654
Effective search space used:   189654
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 WP_019555900.1 F612_RS0101120 (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.2839655.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-227  741.6   1.7   1.8e-227  741.4   1.7    1.0  1  NCBI__GCF_000381085.1:WP_019555900.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000381085.1:WP_019555900.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  741.4   1.7  1.8e-227  1.8e-227       2     465 ..       3     469 ..       2     470 .. 0.99

  Alignments for each domain:
  == domain 1  score: 741.4 bits;  conditional E-value: 1.8e-227
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr...d 71 
                                           aktly+kl+dah+v++++++t l+yidr l+hevtspqafeglr a r   r+d+ lat dhn++t+      
  NCBI__GCF_000381085.1:WP_019555900.1   3 AKTLYDKLWDAHIVRQEDDGTALIYIDRQLLHEVTSPQAFEGLRMAHRTPWRIDTNLATPDHNVPTTDLsngI 75 
                                           89***************************************************************98653334 PP

                             TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgi 144
                                             i++ ++++qv++l  n++efg+  + + + +qgivhvvgpe g tlpg+t+vcgdshtathga+gala gi
  NCBI__GCF_000381085.1:WP_019555900.1  76 ASITDPVSRIQVETLGMNTREFGITEYAMGDIRQGIVHVVGPESGATLPGMTVVCGDSHTATHGALGALAHGI 148
                                           678999******************************************************************* PP

                             TIGR00170 145 gtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeerm 217
                                           gtsevehvlatq l+q++ k++ ++v+gkl+ g+t kd++laiigkig+agg g+ +ef g+++rd+s+e+rm
  NCBI__GCF_000381085.1:WP_019555900.1 149 GTSEVEHVLATQCLIQKKMKNMLVKVDGKLSAGVTPKDVVLAIIGKIGTAGGNGHAIEFGGQVFRDMSIEGRM 221
                                           ************************************************************************* PP

                             TIGR00170 218 tvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtw 290
                                           tvcnmaie ga+ glia de t eyvk+r++apkg++++ av+ w  l +d +a+fd+ v l+++ i pqvtw
  NCBI__GCF_000381085.1:WP_019555900.1 222 TVCNMAIEGGARVGLIAVDEKTVEYVKGRTFAPKGEQWDMAVTAWMDLTSDADAVFDTLVELDGSMIEPQVTW 294
                                           ************************************************************************* PP

                             TIGR00170 291 gtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvk 363
                                           gt+p++vl vn+ vp+p++  d v+  ++ +alay+gle+++ +kdi  + vfigsctnsriedlraaa v+k
  NCBI__GCF_000381085.1:WP_019555900.1 295 GTSPEMVLDVNGRVPNPANEMDAVKADGIRRALAYMGLEADMAIKDIPAEYVFIGSCTNSRIEDLRAAATVLK 367
                                           ************************************************************************* PP

                             TIGR00170 364 gkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegr 436
                                           g+k++d+v+lal vpgsglvk+qae+egldkif+eagfewr++gcs+cl+mn d+l++++ castsnrnfegr
  NCBI__GCF_000381085.1:WP_019555900.1 368 GRKISDKVELALAVPGSGLVKQQAEAEGLDKIFIEAGFEWRNPGCSMCLAMNADKLPTGKHCASTSNRNFEGR 440
                                           ************************************************************************* PP

                             TIGR00170 437 qgkgarthlvspamaaaaavagkfvdire 465
                                           qg+g+rthlvsp maaaaa+ag+fvd+r+
  NCBI__GCF_000381085.1:WP_019555900.1 441 QGAGGRTHLVSPEMAAAAAIAGHFVDVRD 469
                                           ****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (471 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: 18.02
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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