Alignments for a candidate for leuC in Sinorhizobium fredii NGR234

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Sinorhizobium fredii NGR234

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate YP_002827628.1 NGR_c31400 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000018545.1:YP_002827628.1
          Length = 469

 Score =  632 bits (1629), Expect = 0.0
 Identities = 311/465 (66%), Positives = 371/465 (79%), Gaps = 1/465 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TLY+K++D H+V + ++ T LLYIDRHLVHEVTSPQAF+GLR  GR VR P KT A +D
Sbjct: 5   RTLYDKIWDDHLVNQQDDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPEKTLAVVD 64

Query: 63  HNVSTQT-KDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPG 121
           HNV T   + +    E +RIQ++ L +N  +FGVE Y  N   QGIVH++GPEQG TLPG
Sbjct: 65  HNVPTSPDRHLGIKNEESRIQVEALARNAADFGVEYYSENDKRQGIVHIVGPEQGFTLPG 124

Query: 122 MTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAK 181
           MTIVCGDSHT+THGAFGALA GIGTSEVEHVLATQTL Q +AK M + V G+  PG+TAK
Sbjct: 125 MTIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLIQKKAKNMLVRVDGQLPPGVTAK 184

Query: 182 DIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFN 241
           DI+LAIIG+ G+AGGTGHV+EF GEAIR LSMEGRMT+CNM IE GA+AGL+APDETTF+
Sbjct: 185 DIILAIIGEIGTAGGTGHVIEFAGEAIRSLSMEGRMTICNMTIEGGARAGLIAPDETTFD 244

Query: 242 YVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVN 301
           Y+K +  APKGK +D A+ YWKTL TDEGA +D +V L A ++ P V+WG++P  VISV 
Sbjct: 245 YIKDKPRAPKGKAWDMALDYWKTLHTDEGAHYDRIVVLDAADLPPIVSWGSSPEDVISVQ 304

Query: 302 DNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEI 361
             +P+P    +  +RAS  +AL YMGLKPG  +T++A+D+VFIGSCTN RIEDLRA A++
Sbjct: 305 GAVPNPDDIQEETKRASKWRALDYMGLKPGTKITDIAVDRVFIGSCTNGRIEDLRAVAKV 364

Query: 362 AKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421
            +GRKVA  V A++VPGSG VK QAEAEGLDKIF EAGF+WR PGCSMCLAMN+DRL PG
Sbjct: 365 VEGRKVASTVSAMIVPGSGLVKEQAEAEGLDKIFKEAGFDWREPGCSMCLAMNDDRLKPG 424

Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNIK 466
           ERCASTSNRNFEGRQG  GRTHLVSPAMAAAAAV GHF DIR  K
Sbjct: 425 ERCASTSNRNFEGRQGFKGRTHLVSPAMAAAAAVAGHFVDIREWK 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: 794
Number of extensions: 27
Number of successful extensions: 2
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: 469
Length adjustment: 33
Effective length of query: 433
Effective length of database: 436
Effective search space:   188788
Effective search space used:   188788
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 YP_002827628.1 NGR_c31400 (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.15997.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-251  821.0   0.1   1.5e-251  820.8   0.1    1.0  1  lcl|NCBI__GCF_000018545.1:YP_002827628.1  NGR_c31400 3-isopropylmalate deh


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000018545.1:YP_002827628.1  NGR_c31400 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  820.8   0.1  1.5e-251  1.5e-251       2     465 ..       4     467 ..       3     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 820.8 bits;  conditional E-value: 1.5e-251
                                 TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhniste.s 69 
                                               ++tly+k++d h+v++++++t llyidrhlvhevtspqafeglr agrkvr ++ktla +dhn++t   
  lcl|NCBI__GCF_000018545.1:YP_002827628.1   4 PRTLYDKIWDDHLVNQQDDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPEKTLAVVDHNVPTSpD 72 
                                               8*****************************************************************846 PP

                                 TIGR00170  70 rdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafg 138
                                               r + ik+e++++qv++l +n+ +fgv+++  ++++qgivh+vgpe+g+tlpg+tivcgdsht+thgafg
  lcl|NCBI__GCF_000018545.1:YP_002827628.1  73 RHLGIKNEESRIQVEALARNAADFGVEYYSENDKRQGIVHIVGPEQGFTLPGMTIVCGDSHTSTHGAFG 141
                                               89******************************************************************* PP

                                 TIGR00170 139 alafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefagea 207
                                               ala gigtsevehvlatqtl+q++ak++ ++v+g+l +g+takdiilaiig ig+aggtg+v+efagea
  lcl|NCBI__GCF_000018545.1:YP_002827628.1 142 ALAHGIGTSEVEHVLATQTLIQKKAKNMLVRVDGQLPPGVTAKDIILAIIGEIGTAGGTGHVIEFAGEA 210
                                               ********************************************************************* PP

                                 TIGR00170 208 irdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkv 276
                                               ir+lsme+rmt+cnm+ie ga+agliapdettf+y+kd++ apkgk ++ a++ywktl+tdega++d+ 
  lcl|NCBI__GCF_000018545.1:YP_002827628.1 211 IRSLSMEGRMTICNMTIEGGARAGLIAPDETTFDYIKDKPRAPKGKAWDMALDYWKTLHTDEGAHYDRI 279
                                               ********************************************************************* PP

                                 TIGR00170 277 vtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfig 345
                                               v+l+a d+ p v+wg +p++v+sv++ vp+p+++ ++ ++as  +al+y+gl+pgtk++di+vd+vfig
  lcl|NCBI__GCF_000018545.1:YP_002827628.1 280 VVLDAADLPPIVSWGSSPEDVISVQGAVPNPDDIQEETKRASKWRALDYMGLKPGTKITDIAVDRVFIG 348
                                               ********************************************************************* PP

                                 TIGR00170 346 sctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgm 414
                                               sctn+riedlra a+vv g+kva++v  a++vpgsglvk+qae+egldkif eagf+wre+gcs+cl+m
  lcl|NCBI__GCF_000018545.1:YP_002827628.1 349 SCTNGRIEDLRAVAKVVEGRKVASTVS-AMIVPGSGLVKEQAEAEGLDKIFKEAGFDWREPGCSMCLAM 416
                                               **************************9.***************************************** PP

                                 TIGR00170 415 nndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                               n+d+l+++ercastsnrnfegrqg ++rthlvspamaaaaavag+fvdire
  lcl|NCBI__GCF_000018545.1:YP_002827628.1 417 NDDRLKPGERCASTSNRNFEGRQGFKGRTHLVSPAMAAAAAVAGHFVDIRE 467
                                               **************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (469 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: 00:00:00.01
# Mc/sec: 11.33
//
[ok]

This GapMind analysis is from Apr 10 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