GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Streptacidiphilus oryzae TH49

Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_037572526.1 BS73_RS14595 3-isopropylmalate dehydratase large subunit

Query= SwissProt::Q7TXH6
         (473 letters)



>NCBI__GCF_000744815.1:WP_037572526.1
          Length = 474

 Score =  743 bits (1917), Expect = 0.0
 Identities = 357/465 (76%), Positives = 407/465 (87%), Gaps = 1/465 (0%)

Query: 9   RTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELTLATE 68
           RTLAEK+WDDH+V    G  PDL++IDLHL+HEVTSPQAFDGLRLAGR+VRR +LT+ATE
Sbjct: 3   RTLAEKVWDDHVVRRVDG-EPDLLFIDLHLLHEVTSPQAFDGLRLAGRKVRRTDLTIATE 61

Query: 69  DHNVPTVDIDQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGPQLGLTQPG 128
           DHN PT+DID+PIADPVSRTQ+ETLR+NCAEFG+RLH +GD+EQG+VHVVGPQLGLTQPG
Sbjct: 62  DHNTPTLDIDKPIADPVSRTQLETLRKNCAEFGVRLHPLGDVEQGVVHVVGPQLGLTQPG 121

Query: 129 MTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGRLPDGVSAK 188
            T+VCGDSHTSTHGAFGALA GIGTS+VEHVLATQTLP+ PFKTMAV V+G LP+GV+AK
Sbjct: 122 TTVVCGDSHTSTHGAFGALAFGIGTSQVEHVLATQTLPMAPFKTMAVTVEGELPEGVTAK 181

Query: 189 DIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMVAPDETTYA 248
           D+ILA+IA+IGTGGGQG+VIEYRGSA+E LSME RMT+CNMSIEAGARAGM+APDETT+A
Sbjct: 182 DLILAVIARIGTGGGQGYVIEYRGSAVEKLSMEARMTVCNMSIEAGARAGMIAPDETTFA 241

Query: 249 FLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTNPGQGVPLA 308
           +L+GRPHAP G  WD A+ YW+ LRTD  AVFD EV +DAA LSPFVTWGTNPGQG PL 
Sbjct: 242 YLKGRPHAPAGEDWDAAVAYWKTLRTDEDAVFDHEVVIDAAELSPFVTWGTNPGQGAPLG 301

Query: 309 AAVPDPQLMTDDAERQAAEKALAYMDLRPGTAMREIAVDAVFVGSCTNGRIEDLRVVAEV 368
           A+VPDP    D +ER AAE AL YM L  GT +RE+ VDAVFVGSCTNGRIEDLR  AEV
Sbjct: 302 ASVPDPADYADPSERVAAENALKYMGLTAGTPLREVEVDAVFVGSCTNGRIEDLRAAAEV 361

Query: 369 LRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGMNPDQLASG 428
           L+ R++AD VRML+VPGS+RV  QA  EGL ++FT AGA+WR AGCSMCLGMNPDQLA G
Sbjct: 362 LKDRQIADDVRMLVVPGSVRVALQAVEEGLDKVFTAAGAEWRHAGCSMCLGMNPDQLAPG 421

Query: 429 ERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLSSPADLN 473
           ERCA+TSNRNFEGRQG GGRTHLVSP VAAATAV G L+SPADL+
Sbjct: 422 ERCASTSNRNFEGRQGKGGRTHLVSPQVAAATAVLGHLASPADLS 466


Lambda     K      H
   0.319    0.135    0.402 

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: 814
Number of extensions: 23
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: 473
Length of database: 474
Length adjustment: 33
Effective length of query: 440
Effective length of database: 441
Effective search space:   194040
Effective search space used:   194040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_037572526.1 BS73_RS14595 (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.2880919.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-229  748.6   0.0   1.3e-229  748.4   0.0    1.0  1  NCBI__GCF_000744815.1:WP_037572526.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_037572526.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  748.4   0.0  1.3e-229  1.3e-229       1     461 [.       1     460 [.       1     465 [. 0.99

  Alignments for each domain:
  == domain 1  score: 748.4 bits;  conditional E-value: 1.3e-229
                             TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 
                                           m +tl ek++d hvv++ ++e+dll+id+hl+hevtspqaf+glr agrkvrr+d t+at dhn +t   d  
  NCBI__GCF_000744815.1:WP_037572526.1   1 MGRTLAEKVWDDHVVRRVDGEPDLLFIDLHLLHEVTSPQAFDGLRLAGRKVRRTDLTIATEDHNTPTLDIDKP 73 
                                           789********************************************************************** PP

                             TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146
                                           i + +++ q+++l kn+ efgv+l+ l ++eqg+vhvvgp+ glt pg+t+vcgdsht+thgafgalafgigt
  NCBI__GCF_000744815.1:WP_037572526.1  74 IADPVSRTQLETLRKNCAEFGVRLHPLGDVEQGVVHVVGPQLGLTQPGTTVVCGDSHTSTHGAFGALAFGIGT 146
                                           ************************************************************************* PP

                             TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219
                                           s+vehvlatqtl  a  kt+ ++veg+l +g+takd+ila+i +ig+ gg gyv+e+ g a+++lsme+rmtv
  NCBI__GCF_000744815.1:WP_037572526.1 147 SQVEHVLATQTLPMAPFKTMAVTVEGELPEGVTAKDLILAVIARIGTGGGQGYVIEYRGSAVEKLSMEARMTV 219
                                           ************************************************************************* PP

                             TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292
                                           cnm+ieaga+ag+iapdettf+y+k+r++ap g++++ avaywktl+tde+a+fd++v+++a ++sp vtwgt
  NCBI__GCF_000744815.1:WP_037572526.1 220 CNMSIEAGARAGMIAPDETTFAYLKGRPHAPAGEDWDAAVAYWKTLRTDEDAVFDHEVVIDAAELSPFVTWGT 292
                                           ************************************************************************* PP

                             TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365
                                           npgq  ++  +vpdp++ adp e+  ae+al+y+gl++gt+l++++vd vf+gsctn+riedlraaaev+k +
  NCBI__GCF_000744815.1:WP_037572526.1 293 NPGQGAPLGASVPDPADYADPSERVAAENALKYMGLTAGTPLREVEVDAVFVGSCTNGRIEDLRAAAEVLKDR 365
                                           ************************************************************************* PP

                             TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438
                                           ++ad+v+ +lvvpgs  v  qa +egldk+f +ag+ewr+agcs+clgmn+d+l ++ercastsnrnfegrqg
  NCBI__GCF_000744815.1:WP_037572526.1 366 QIADDVR-MLVVPGSVRVALQAVEEGLDKVFTAAGAEWRHAGCSMCLGMNPDQLAPGERCASTSNRNFEGRQG 437
                                           *******.9**************************************************************** PP

                             TIGR00170 439 kgarthlvspamaaaaavagkfv 461
                                           kg+rthlvsp +aaa+av g+++
  NCBI__GCF_000744815.1:WP_037572526.1 438 KGGRTHLVSPQVAAATAVLGHLA 460
                                           *********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (474 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: 00:00:00.00
# Mc/sec: 24.00
//
[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