Alignments for a candidate for leuC in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Paraburkholderia bryophila 376MFSha3.1

Align 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate H281DRAFT_06075 H281DRAFT_06075 3-isopropylmalate dehydratase, large subunit

Query= SwissProt::P15717
         (466 letters)



>FitnessBrowser__Burk376:H281DRAFT_06075
          Length = 469

 Score =  598 bits (1543), Expect = e-176
 Identities = 294/468 (62%), Positives = 361/468 (77%), Gaps = 3/468 (0%)

Query: 1   MAKTLYEKLFDAHVVFEAPNETPLLYIDRHLVHEVTSPQAFDGLRAHHRPVRQPGKTFAT 60
           M +TLY+KL++ HV+    + T +LYIDRHL+HEVTSPQAF+GL+   RPV +     A 
Sbjct: 1   MPQTLYDKLWNTHVIHTEEDGTTILYIDRHLLHEVTSPQAFEGLKLAQRPVWRISANLAV 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 GMTIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLLQKKSKNMLVKVEGPLPRGCTA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGDAIRALSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLAIIGK G+AGGTG+ +EF G  IR+LSMEGRMT+CNMAIE GA+AG+VA D+TT 
Sbjct: 181 KDIVLAIIGKIGTAGGTGYAIEFGGSTIRSLSMEGRMTVCNMAIEAGARAGMVAVDDTTI 240

Query: 241 NYVKGRLHAPKGRDFDEAVEYWKTLKTDDGATFDTVVALRAEEIAPQVTWGTNPGQVISV 300
            Y+KGR  +P+G ++D AVEYWK  K+D+GA FD VV L A +I PQVTWGT+P  V +V
Sbjct: 241 EYLKGRPFSPQGAEWDHAVEYWKQFKSDEGAQFDRVVELNAADIVPQVTWGTSPEMVTAV 300

Query: 301 TDIIPDPASFSDPVERASAEKALAYMGLQPGVPLTDVAIDKVFIGSCTNSRIEDLRAAAE 360
              +PDP    DPV+R + E+AL YM L+P  P+  +  DK+FIGSCTN+RIED+RAAA 
Sbjct: 301 DGRVPDPEREKDPVKRDAMERALKYMALEPNAPIESIKPDKIFIGSCTNARIEDIRAAAY 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: 758
Number of extensions: 20
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 H281DRAFT_06075 H281DRAFT_06075 (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.23473.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.8e-241  786.5   0.1   4.3e-241  786.3   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06075  H281DRAFT_06075 3-isopropylmalat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06075  H281DRAFT_06075 3-isopropylmalate dehydratase, large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  786.3   0.1  4.3e-241  4.3e-241       1     466 []       1     468 [.       1     468 [. 1.00

  Alignments for each domain:
  == domain 1  score: 786.3 bits;  conditional E-value: 4.3e-241
                                    TIGR00170   1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnis 66 
                                                  m++tly+kl+++hv++ +e++t++lyidrhl+hevtspqafegl+ a+r+v r++  la  dhn++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06075   1 MPQTLYDKLWNTHVIHTEEDGTTILYIDRHLLHEVTSPQAFEGLKLAQRPVWRISANLAVSDHNVP 66 
                                                  89**************************************************************** PP

                                    TIGR00170  67 tesrdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshta 132
                                                  t+ r   i + ++klqv +l+ n++++g+  f +++ +qgivh++gpe+g tlpg+tivcgdsht+
  lcl|FitnessBrowser__Burk376:H281DRAFT_06075  67 TTDRSHGIADPVSKLQVDTLDSNCDAYGITQFKMNDLRQGIVHIIGPEQGATLPGMTIVCGDSHTS 132
                                                  ****************************************************************** PP

                                    TIGR00170 133 thgafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtg 198
                                                  thgafgala gigtsevehvlatqtl q+++k++ ++veg l +g takdi+laiigkig+aggtg
  lcl|FitnessBrowser__Burk376:H281DRAFT_06075 133 THGAFGALAHGIGTSEVEHVLATQTLLQKKSKNMLVKVEGPLPRGCTAKDIVLAIIGKIGTAGGTG 198
                                                  ****************************************************************** PP

                                    TIGR00170 199 yvvefageairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywkt 264
                                                  y +ef g +ir+lsme+rmtvcnmaieaga+ag++a d+tt+ey+k+r+++p+g+e+++av+ywk 
  lcl|FitnessBrowser__Burk376:H281DRAFT_06075 199 YAIEFGGSTIRSLSMEGRMTVCNMAIEAGARAGMVAVDDTTIEYLKGRPFSPQGAEWDHAVEYWKQ 264
                                                  ****************************************************************** PP

                                    TIGR00170 265 lktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglep 330
                                                  +k+dega+fd+vv l+a di+pqvtwgt+p++v +v++ vpdp+   dpv++  +e+al+y+ lep
  lcl|FitnessBrowser__Burk376:H281DRAFT_06075 265 FKSDEGAQFDRVVELNAADIVPQVTWGTSPEMVTAVDGRVPDPEREKDPVKRDAMERALKYMALEP 330
                                                  ****************************************************************** PP

                                    TIGR00170 331 gtklkdikvdkvfigsctnsriedlraaaevvk..gkkvadnvklalvvpgsglvkkqaekegldk 394
                                                  + ++++ik dk+figsctn+ried+raaa vvk  g++va+n++la+vvpgsglvk+qae+egldk
  lcl|FitnessBrowser__Burk376:H281DRAFT_06075 331 NAPIESIKPDKIFIGSCTNARIEDIRAAAYVVKklGRRVAPNIRLAMVVPGSGLVKAQAEREGLDK 396
                                                  ********************************9889****************************** PP

                                    TIGR00170 395 ifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkf 460
                                                  +f +agfewre+gcs+cl+mn d+ld++ercastsnrnfegrqg+g+rthlvspamaaaaa+ g+f
  lcl|FitnessBrowser__Burk376:H281DRAFT_06075 397 VFTDAGFEWREPGCSMCLAMNADRLDPGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAIEGHF 462
                                                  ****************************************************************** PP

                                    TIGR00170 461 vdirel 466
                                                  vdir+l
  lcl|FitnessBrowser__Burk376:H281DRAFT_06075 463 VDIRKL 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: 10.85
//
[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