GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Burkholderia phytofirmans PsJN

Align 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate BPHYT_RS33915 BPHYT_RS33915 isopropylmalate isomerase

Query= SwissProt::P15717
         (466 letters)



>FitnessBrowser__BFirm:BPHYT_RS33915
          Length = 469

 Score =  603 bits (1554), Expect = e-177
 Identities = 298/468 (63%), Positives = 362/468 (77%), Gaps = 3/468 (0%)

Query: 1   MAKTLYEKLFDAHVVFEAPNETPLLYIDRHLVHEVTSPQAFDGLRAHHRPVRQPGKTFAT 60
           MA+TLY+KL++ HV+    + T +LYIDRHL+HEVTSPQAF+GL+   RPV +     A 
Sbjct: 1   MAQTLYDKLWNTHVIHTEEDGTTILYIDRHLLHEVTSPQAFEGLKLAERPVWRISANLAV 60

Query: 61  MDHNVSTQTKDINASGEMARIQMQELIKNCNEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
            DHNV T  +    +  ++++Q+  L  NC+ +G+  + +N   QGIVH++GPEQG TLP
Sbjct: 61  SDHNVPTTDRSHGIADPVSKLQVDTLDSNCDAYGITQFKMNDLRQGIVHIIGPEQGATLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVTGNAAPGITA 180
           GMTIVCGDSHT+THGAFGALA GIGTSEVEHVLATQTL Q ++K M ++V G    G TA
Sbjct: 121 GMTIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLLQKKSKNMLVKVEGALPRGCTA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGDAIRALSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLAIIGK G+AGGTG+ +EF G  IRALSMEGRMT+CNMAIE GA+AG+VA D+TT 
Sbjct: 181 KDIVLAIIGKIGTAGGTGYAIEFGGSTIRALSMEGRMTVCNMAIEAGARAGMVAVDDTTI 240

Query: 241 NYVKGRLHAPKGRDFDEAVEYWKTLKTDDGATFDTVVALRAEEIAPQVTWGTNPGQVISV 300
            Y+KGR  +P+G ++D AVEYWK  KTD+GA FD VV L A EI PQVTWGT+P  V +V
Sbjct: 241 EYLKGRPFSPEGVEWDHAVEYWKQFKTDEGAHFDRVVELNAAEIVPQVTWGTSPEMVTAV 300

Query: 301 TDIIPDPASFSDPVERASAEKALAYMGLQPGVPLTDVAIDKVFIGSCTNSRIEDLRAAAE 360
              +PDP    DPV+R + E+AL YM L+P  P+  +  DK+FIGSCTN+RIED+RAAA 
Sbjct: 301 DGRVPDPDREKDPVKRDAMERALKYMALEPNAPIESIKPDKIFIGSCTNARIEDIRAAAY 360

Query: 361 VAK--GRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417
           V K  GR+VAP ++ A+VVPGSG VKAQAE EGLDK+F +AGFEWR PGCSMCLAMN DR
Sbjct: 361 VVKKLGRRVAPNIRLAMVVPGSGLVKAQAEREGLDKVFTDAGFEWREPGCSMCLAMNADR 420

Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRSI 465
           L+PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAAA+ GHF DIR +
Sbjct: 421 LDPGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAIEGHFVDIRKL 468


Lambda     K      H
   0.318    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: 766
Number of extensions: 24
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 BPHYT_RS33915 BPHYT_RS33915 (isopropylmalate isomerase)
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.32566.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-240  784.9   0.2   1.3e-240  784.7   0.2    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS33915  BPHYT_RS33915 isopropylmalate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS33915  BPHYT_RS33915 isopropylmalate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  784.7   0.2  1.3e-240  1.3e-240       1     466 []       1     468 [.       1     468 [. 1.00

  Alignments for each domain:
  == domain 1  score: 784.7 bits;  conditional E-value: 1.3e-240
                                TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr 70 
                                              ma+tly+kl+++hv++ +e++t++lyidrhl+hevtspqafegl+ a+r+v r++  la  dhn++t+ r
  lcl|FitnessBrowser__BFirm:BPHYT_RS33915   1 MAQTLYDKLWNTHVIHTEEDGTTILYIDRHLLHEVTSPQAFEGLKLAERPVWRISANLAVSDHNVPTTDR 70 
                                              89******************************************************************** PP

                                TIGR00170  71 dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgal 140
                                                 i + ++klqv +l+ n++++g+  f +++ +qgivh++gpe+g tlpg+tivcgdsht+thgafgal
  lcl|FitnessBrowser__BFirm:BPHYT_RS33915  71 SHGIADPVSKLQVDTLDSNCDAYGITQFKMNDLRQGIVHIIGPEQGATLPGMTIVCGDSHTSTHGAFGAL 140
                                              ********************************************************************** PP

                                TIGR00170 141 afgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageaird 210
                                              a gigtsevehvlatqtl q+++k++ ++veg l +g takdi+laiigkig+aggtgy +ef g +ir+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33915 141 AHGIGTSEVEHVLATQTLLQKKSKNMLVKVEGALPRGCTAKDIVLAIIGKIGTAGGTGYAIEFGGSTIRA 210
                                              ********************************************************************** PP

                                TIGR00170 211 lsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtle 280
                                              lsme+rmtvcnmaieaga+ag++a d+tt+ey+k+r+++p g e+++av+ywk +ktdega+fd+vv l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33915 211 LSMEGRMTVCNMAIEAGARAGMVAVDDTTIEYLKGRPFSPEGVEWDHAVEYWKQFKTDEGAHFDRVVELN 280
                                              ********************************************************************** PP

                                TIGR00170 281 akdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctns 350
                                              a +i+pqvtwgt+p++v +v++ vpdp+   dpv++  +e+al+y+ lep+ ++++ik dk+figsctn+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33915 281 AAEIVPQVTWGTSPEMVTAVDGRVPDPDREKDPVKRDAMERALKYMALEPNAPIESIKPDKIFIGSCTNA 350
                                              ********************************************************************** PP

                                TIGR00170 351 riedlraaaevvk..gkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndv 418
                                              ried+raaa vvk  g++va+n++la+vvpgsglvk+qae+egldk+f +agfewre+gcs+cl+mn d+
  lcl|FitnessBrowser__BFirm:BPHYT_RS33915 351 RIEDIRAAAYVVKklGRRVAPNIRLAMVVPGSGLVKAQAEREGLDKVFTDAGFEWREPGCSMCLAMNADR 420
                                              ************9889****************************************************** PP

                                TIGR00170 419 ldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                              ld++ercastsnrnfegrqg+g+rthlvspamaaaaa+ g+fvdir+l
  lcl|FitnessBrowser__BFirm:BPHYT_RS33915 421 LDPGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAIEGHFVDIRKL 468
                                              **********************************************85 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: 00:00:00.02
# Mc/sec: 8.36
//
[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:

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