GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Phyllobacterium endophyticum PEPV15

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_106714736.1 CU100_RS01185 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_003010935.1:WP_106714736.1
          Length = 469

 Score =  614 bits (1584), Expect = e-180
 Identities = 307/467 (65%), Positives = 366/467 (78%), Gaps = 5/467 (1%)

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

Query: 63  HNVST---QTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
           HN+ T   +TK I      +RIQ++ L +N  +FGVE Y      QGIVH++GPEQG TL
Sbjct: 65  HNIPTSPDRTKRIE--NNESRIQVEALARNALDFGVEYYSEKDIRQGIVHIIGPEQGFTL 122

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGMTIVCGDSHT+THGAFGALA GIGTSEVEHVLATQTL Q +AK M + V G    G+T
Sbjct: 123 PGMTIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLIQSKAKNMLVRVDGVLPAGVT 182

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
           AKDI+LAIIG+ G+AGGTG+V+E+ GEAIR LSMEGRMT+CNM+IE GA+AGL+APDETT
Sbjct: 183 AKDIILAIIGEIGTAGGTGYVIEYAGEAIRALSMEGRMTICNMSIEGGARAGLIAPDETT 242

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
           F YVK +  APKG+ +D A+ YWKTLQ+DEGA FD VV L A ++ P V+WG++P  VIS
Sbjct: 243 FAYVKDKPRAPKGEAWDMALEYWKTLQSDEGAHFDKVVVLNAADLPPIVSWGSSPEDVIS 302

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           V   +P+P    D  +R+S  +AL YMGLKPG P+T++ +D+VFIGSCTN RIEDLR  A
Sbjct: 303 VTGAVPNPDEIPDETKRSSKWRALDYMGLKPGTPITDIKLDRVFIGSCTNGRIEDLREVA 362

Query: 360 EIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
           ++ +G  VAP V A++VPGSG VK QAEAEGLDKIF  AGF+WR PGCSMCLAMN+DRL 
Sbjct: 363 KVVEGHTVAPTVDAMIVPGSGLVKQQAEAEGLDKIFKAAGFDWREPGCSMCLAMNDDRLK 422

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNIK 466
           PGERCASTSNRNFEGRQG  GRTHLVSPAMAAAAA+ GHF DIR  K
Sbjct: 423 PGERCASTSNRNFEGRQGFKGRTHLVSPAMAAAAAIAGHFVDIREWK 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: 790
Number of extensions: 30
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 WP_106714736.1 CU100_RS01185 (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.2425373.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.5e-248  809.3   0.0   5.2e-248  809.1   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106714736.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106714736.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  809.1   0.0  5.2e-248  5.2e-248       2     465 ..       4     467 ..       3     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 809.1 bits;  conditional E-value: 5.2e-248
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes.rdve 73 
                                           ++tly+k++d h+v  +e++t llyidrhlvhevtspqafeglr +grkvr+++ktla +dhni+t   r   
  NCBI__GCF_003010935.1:WP_106714736.1   4 PRTLYDKIWDDHLVDSQEDGTCLLYIDRHLVHEVTSPQAFEGLRLTGRKVRHPEKTLAVVDHNIPTSPdRTKR 76 
                                           8*****************************************************************8625667 PP

                             TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146
                                           i ++++++qv++l +n+ +fgv+++  ++ +qgivh++gpe+g+tlpg+tivcgdsht+thgafgala gigt
  NCBI__GCF_003010935.1:WP_106714736.1  77 IENNESRIQVEALARNALDFGVEYYSEKDIRQGIVHIIGPEQGFTLPGMTIVCGDSHTSTHGAFGALAHGIGT 149
                                           88899******************************************************************** PP

                             TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219
                                           sevehvlatqtl+q++ak++ ++v+g l  g+takdiilaiig ig+aggtgyv+e+ageair+lsme+rmt+
  NCBI__GCF_003010935.1:WP_106714736.1 150 SEVEHVLATQTLIQSKAKNMLVRVDGVLPAGVTAKDIILAIIGEIGTAGGTGYVIEYAGEAIRALSMEGRMTI 222
                                           ************************************************************************* PP

                             TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292
                                           cnm+ie ga+agliapdettf+yvkd++ apkg+ ++ a++ywktl++dega+fdkvv+l+a d+ p v+wg 
  NCBI__GCF_003010935.1:WP_106714736.1 223 CNMSIEGGARAGLIAPDETTFAYVKDKPRAPKGEAWDMALEYWKTLQSDEGAHFDKVVVLNAADLPPIVSWGS 295
                                           ************************************************************************* PP

                             TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365
                                           +p++v+sv++ vp+p+++ d+ +++s  +al+y+gl+pgt+++dik+d+vfigsctn+riedlr+ a+vv g+
  NCBI__GCF_003010935.1:WP_106714736.1 296 SPEDVISVTGAVPNPDEIPDETKRSSKWRALDYMGLKPGTPITDIKLDRVFIGSCTNGRIEDLREVAKVVEGH 368
                                           ************************************************************************* PP

                             TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438
                                            va++v  a++vpgsglvk+qae+egldkif +agf+wre+gcs+cl+mn+d+l+++ercastsnrnfegrqg
  NCBI__GCF_003010935.1:WP_106714736.1 369 TVAPTVD-AMIVPGSGLVKQQAEAEGLDKIFKAAGFDWREPGCSMCLAMNDDRLKPGERCASTSNRNFEGRQG 440
                                           *******.***************************************************************** PP

                             TIGR00170 439 kgarthlvspamaaaaavagkfvdire 465
                                            ++rthlvspamaaaaa+ag+fvdire
  NCBI__GCF_003010935.1:WP_106714736.1 441 FKGRTHLVSPAMAAAAAIAGHFVDIRE 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 16.43
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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