Alignments for a candidate for leuC in Klebsiella michiganensis M5al

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Klebsiella michiganensis M5al

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate BWI76_RS04670 BWI76_RS04670 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Koxy:BWI76_RS04670
          Length = 466

 Score =  900 bits (2326), Expect = 0.0
 Identities = 446/466 (95%), Positives = 458/466 (98%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           MAKTLYEKLFDAHVVYEA+NETPLLYIDRHLVHEVTSPQAFDGLRAH RPVRQPGKTFAT
Sbjct: 1   MAKTLYEKLFDAHVVYEAQNETPLLYIDRHLVHEVTSPQAFDGLRAHKRPVRQPGKTFAT 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
           MDHNVSTQTKDINA GEMARIQMQELIKNCKEFGVELYDLNHP+QGIVHVMGPEQGVTLP
Sbjct: 61  MDHNVSTQTKDINASGEMARIQMQELIKNCKEFGVELYDLNHPFQGIVHVMGPEQGVTLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEV+GKAAPGITA
Sbjct: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVKGKAAPGITA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD+TTF
Sbjct: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDQTTF 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
           +YVKGRLHAPKG DF DAVAYWKTL TD+GATFD+VVTLQAEEI+PQVTWGTNPGQVISV
Sbjct: 241 DYVKGRLHAPKGVDFADAVAYWKTLTTDDGATFDSVVTLQAEEIAPQVTWGTNPGQVISV 300

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
            D IPDPASF+DPVERASAEKALAYMGLK G+PLTEVAIDKVFIGSCTNSRIEDLRAAAE
Sbjct: 301 TDIIPDPASFSDPVERASAEKALAYMGLKSGVPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360

Query: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420
           IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP
Sbjct: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420

Query: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNIK 466
           GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR++K
Sbjct: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRSLK 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: 973
Number of extensions: 21
Number of successful extensions: 1
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: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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 BWI76_RS04670 BWI76_RS04670 (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.19882.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   7.3e-280  914.1   0.8   8.2e-280  914.0   0.8    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04670  BWI76_RS04670 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04670  BWI76_RS04670 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  914.0   0.8  8.2e-280  8.2e-280       1     465 [.       1     464 [.       1     465 [. 1.00

  Alignments for each domain:
  == domain 1  score: 914.0 bits;  conditional E-value: 8.2e-280
                               TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrd 71 
                                             maktlyeklfdahvv+ea+net+llyidrhlvhevtspqaf+glra+ r+vr+++kt+at+dhn+st+++d
  lcl|FitnessBrowser__Koxy:BWI76_RS04670   1 MAKTLYEKLFDAHVVYEAQNETPLLYIDRHLVHEVTSPQAFDGLRAHKRPVRQPGKTFATMDHNVSTQTKD 71 
                                             89********************************************************************* PP

                               TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalaf 142
                                             +++ +e+a++q++el kn+kefgv+l+dl++  qgivhv+gpe+g+tlpg+tivcgdshtathgafgalaf
  lcl|FitnessBrowser__Koxy:BWI76_RS04670  72 INASGEMARIQMQELIKNCKEFGVELYDLNHPFQGIVHVMGPEQGVTLPGMTIVCGDSHTATHGAFGALAF 142
                                             *********************************************************************** PP

                               TIGR00170 143 gigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsm 213
                                             gigtsevehvlatqtlkq+rakt+kiev+gk+a+gitakdi+laiigk+g+aggtg+vvef+geairdlsm
  lcl|FitnessBrowser__Koxy:BWI76_RS04670 143 GIGTSEVEHVLATQTLKQGRAKTMKIEVKGKAAPGITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSM 213
                                             *********************************************************************** PP

                               TIGR00170 214 eermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdi 284
                                             e+rmt+cnmaie+gakagl+apd+ttf+yvk+r +apkg +f +avaywktl td+ga+fd vvtl+a++i
  lcl|FitnessBrowser__Koxy:BWI76_RS04670 214 EGRMTLCNMAIEMGAKAGLVAPDQTTFDYVKGRLHAPKGVDFADAVAYWKTLTTDDGATFDSVVTLQAEEI 284
                                             *********************************************************************** PP

                               TIGR00170 285 spqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedl 355
                                             +pqvtwgtnpgqv+sv++ +pdp+s++dpve+asaekalay+gl++g++l+++++dkvfigsctnsriedl
  lcl|FitnessBrowser__Koxy:BWI76_RS04670 285 APQVTWGTNPGQVISVTDIIPDPASFSDPVERASAEKALAYMGLKSGVPLTEVAIDKVFIGSCTNSRIEDL 355
                                             *********************************************************************** PP

                               TIGR00170 356 raaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyerca 426
                                             raaae++kg+kva++v+ alvvpgsg+vk+qae+egldkif+eagfewr +gcs+cl+mnnd+l+++erca
  lcl|FitnessBrowser__Koxy:BWI76_RS04670 356 RAAAEIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGERCA 425
                                             *****************.***************************************************** PP

                               TIGR00170 427 stsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                             stsnrnfegrqg+g+rthlvspamaaaaav+g+f+dir 
  lcl|FitnessBrowser__Koxy:BWI76_RS04670 426 STSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRS 464
                                             **************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (466 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: 12.33
//
[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