Alignments for a candidate for leuC in Burkholderia phytofirmans PsJN

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.22832.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: 9.74
//
[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