Alignments for a candidate for leuC in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Magnetospirillum magneticum AMB-1

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_011386418.1 AMB_RS20560 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000009985.1:WP_011386418.1
          Length = 467

 Score =  623 bits (1607), Expect = 0.0
 Identities = 310/463 (66%), Positives = 364/463 (78%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TL++K++DAH+V   ++ T L+YIDRH+VHEVTSPQAF+GL   GR VR P  T A  D
Sbjct: 5   RTLFDKIWDAHLVDVQDDGTCLIYIDRHMVHEVTSPQAFEGLEMSGRKVRHPELTLAVAD 64

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           HNV T  +      E +RIQ++ L  N K+FGVE   ++   QG+VH++GPEQG TLPG 
Sbjct: 65  HNVPTTDRSKGIENEESRIQVETLEANAKKFGVEYLRMDDIRQGVVHIVGPEQGFTLPGT 124

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
           TIVCGDSHTATHGAFG+LAFGIGTSEVEHVLATQTL Q  AK M+I V GK  PG+TAKD
Sbjct: 125 TIVCGDSHTATHGAFGSLAFGIGTSEVEHVLATQTLVQKPAKNMRITVTGKPGPGVTAKD 184

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           IVLAIIGK G+AGGTG+VVEF GEAIRDLSMEGRMT+CNM IE GA+AGLVAPDE TF Y
Sbjct: 185 IVLAIIGKIGTAGGTGYVVEFAGEAIRDLSMEGRMTVCNMTIEAGARAGLVAPDEKTFAY 244

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           + G+  +PKG  F+ AV+YWKTL TDEGA FD  VTL A  + PQ+TWGT+P  VI++  
Sbjct: 245 IAGKPRSPKGAAFEAAVSYWKTLFTDEGAHFDAEVTLDASTLVPQITWGTSPEDVIAITG 304

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
            +P+PA   D  +R + E++L YMGL  G+  T++AID VFIGSCTN RIED RAAAEI 
Sbjct: 305 TVPNPADIKDEAKRKAVERSLDYMGLTAGMKATDIAIDVVFIGSCTNGRIEDFRAAAEIF 364

Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422
           KGRKVA  VQAL+VPGSG VK QAE EGLDKIFIEAG EWR PGCSMCLAMN D+L PG+
Sbjct: 365 KGRKVAASVQALIVPGSGLVKEQAEQEGLDKIFIEAGAEWREPGCSMCLAMNADQLKPGQ 424

Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           R ASTSNRNFEGRQGRGGRTHLVSPAMAAAAA+TG   D+R++
Sbjct: 425 RSASTSNRNFEGRQGRGGRTHLVSPAMAAAAAITGKLTDVRSL 467


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: 760
Number of extensions: 27
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: 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 WP_011386418.1 AMB_RS20560 (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.26039.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-243  793.8   1.7   2.8e-243  793.5   1.7    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011386418.1  AMB_RS20560 3-isopropylmalate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011386418.1  AMB_RS20560 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  793.5   1.7  2.8e-243  2.8e-243       3     465 ..       5     466 ..       3     467 .] 1.00

  Alignments for each domain:
  == domain 1  score: 793.5 bits;  conditional E-value: 2.8e-243
                                 TIGR00170   3 ktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrd 71 
                                               +tl++k++dah+v  ++++t l+yidrh+vhevtspqafegl+  grkvr+++ tla  dhn++t+ r 
  lcl|NCBI__GCF_000009985.1:WP_011386418.1   5 RTLFDKIWDAHLVDVQDDGTCLIYIDRHMVHEVTSPQAFEGLEMSGRKVRHPELTLAVADHNVPTTDRS 73 
                                               8******************************************************************** PP

                                 TIGR00170  72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgal 140
                                                 i +e++++qv++le n+k+fgv+++ +++ +qg+vh+vgpe+g+tlpg+tivcgdshtathgafg+l
  lcl|NCBI__GCF_000009985.1:WP_011386418.1  74 KGIENEESRIQVETLEANAKKFGVEYLRMDDIRQGVVHIVGPEQGFTLPGTTIVCGDSHTATHGAFGSL 142
                                               ********************************************************************* PP

                                 TIGR00170 141 afgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageair 209
                                               afgigtsevehvlatqtl+q+ ak+++i+v gk  +g+takdi+laiigkig+aggtgyvvefageair
  lcl|NCBI__GCF_000009985.1:WP_011386418.1 143 AFGIGTSEVEHVLATQTLVQKPAKNMRITVTGKPGPGVTAKDIVLAIIGKIGTAGGTGYVVEFAGEAIR 211
                                               ********************************************************************* PP

                                 TIGR00170 210 dlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvt 278
                                               dlsme+rmtvcnm+ieaga+agl+apde tf+y+ +++ +pkg+ fe av+ywktl tdega+fd +vt
  lcl|NCBI__GCF_000009985.1:WP_011386418.1 212 DLSMEGRMTVCNMTIEAGARAGLVAPDEKTFAYIAGKPRSPKGAAFEAAVSYWKTLFTDEGAHFDAEVT 280
                                               ********************************************************************* PP

                                 TIGR00170 279 leakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsc 347
                                               l+a+ ++pq+twgt+p++v++++++vp+p+++ d+ +++ +e++l+y+gl++g+k +di++d vfigsc
  lcl|NCBI__GCF_000009985.1:WP_011386418.1 281 LDASTLVPQITWGTSPEDVIAITGTVPNPADIKDEAKRKAVERSLDYMGLTAGMKATDIAIDVVFIGSC 349
                                               ********************************************************************* PP

                                 TIGR00170 348 tnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnn 416
                                               tn+ried+raaae+ kg+kva +v+ al+vpgsglvk+qae+egldkif+eag+ewre+gcs+cl+mn 
  lcl|NCBI__GCF_000009985.1:WP_011386418.1 350 TNGRIEDFRAAAEIFKGRKVAASVQ-ALIVPGSGLVKEQAEQEGLDKIFIEAGAEWREPGCSMCLAMNA 417
                                               *************************.******************************************* PP

                                 TIGR00170 417 dvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                               d+l++++r astsnrnfegrqg+g+rthlvspamaaaaa++gk+ d+r 
  lcl|NCBI__GCF_000009985.1:WP_011386418.1 418 DQLKPGQRSASTSNRNFEGRQGRGGRTHLVSPAMAAAAAITGKLTDVRS 466
                                               ***********************************************97 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.76
//
[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