Alignments for a candidate for leuC in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Azospirillum brasilense Sp245

Align 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate AZOBR_RS15565 AZOBR_RS15565 isopropylmalate isomerase

Query= SwissProt::P15717
         (466 letters)



>FitnessBrowser__azobra:AZOBR_RS15565
          Length = 468

 Score =  511 bits (1317), Expect = e-149
 Identities = 261/464 (56%), Positives = 330/464 (71%), Gaps = 5/464 (1%)

Query: 3   KTLYEKLFDAHVVFEAPNETPLLYIDRHLVHEVTSPQAFDGLRAHHRPVRQPGKTFATMD 62
           ++L++K++DAH+V   P+   LL IDRH +HE  S  AF  +    RPVR+P  TFA  D
Sbjct: 6   RSLFDKVWDAHLVATRPDGQALLAIDRHFLHE-GSFHAFGMIDHAKRPVRRPELTFAVAD 64

Query: 63  HNVSTQTKDINASGEMARIQMQELIKNCNEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           H V + ++    +       +  L  N    G+  + L+ P QGIVHV+ PEQG+TLPG+
Sbjct: 65  HYVPSHSRAKPIADPEIANMVTMLEANAERHGLRHFGLHDPAQGIVHVLAPEQGLTLPGL 124

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVTGNAAPGITAKD 182
           TIVCGDSHT+THGAFGALAFGIG +EV HVLATQTL Q R KTM+I + G     +TAKD
Sbjct: 125 TIVCGDSHTSTHGAFGALAFGIGATEVSHVLATQTLWQRRPKTMRIIIDGELGAHVTAKD 184

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGDAIRALSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           ++LA+IG  G+ G  GHV+E+ G AIRALSMEGR+T+CNM+IE GA+AG++APD+ TF++
Sbjct: 185 LILAVIGFIGADGAAGHVIEYAGSAIRALSMEGRLTVCNMSIEAGARAGMIAPDDITFSW 244

Query: 243 VKGRLHAPKGRDFDEAVEYWKTLKTDDGATFDTVVALRAEEIAPQVTWGTNPGQVISVTD 302
           ++GR +APKG  FD AV +W+TL +D  A FD  V+L A  IAP VTWGT+P   + VT 
Sbjct: 245 IEGRNYAPKGDLFDRAVAHWRTLPSDPEAAFDREVSLDAAAIAPLVTWGTSPETAVPVTG 304

Query: 303 IIPDPASFSDPVERASAEKALAYMGLQPGVPLTDVAIDKVFIGSCTNSRIEDLRAAAEVA 362
            +PDP + SDPV      K L YMGL PG  L +V ID+VFIGSCTN+R+EDLRAAA V 
Sbjct: 305 TVPDPGAESDPVRAGQMRKMLDYMGLTPGTRLEEVGIDRVFIGSCTNARLEDLRAAAAVL 364

Query: 363 KGRK-VAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421
           +GR+ V PG   LVV GS PV+ QAEAEGLD++FI AG EW  PGCSMC+ +N D +  G
Sbjct: 365 RGRRAVVPG---LVVAGSVPVRRQAEAEGLDRVFIGAGLEWGEPGCSMCVGINGDLVPAG 421

Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRSI 465
           ERCAST+NRNF GRQG   RTHL+SPAMAAAAAVTG   D+R +
Sbjct: 422 ERCASTTNRNFPGRQGPNARTHLMSPAMAAAAAVTGRLTDVRKL 465


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: 770
Number of extensions: 32
Number of successful extensions: 4
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: 468
Length adjustment: 33
Effective length of query: 433
Effective length of database: 435
Effective search space:   188355
Effective search space used:   188355
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 AZOBR_RS15565 AZOBR_RS15565 (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.30047.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-203  661.9   0.0   2.7e-203  661.7   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS15565  AZOBR_RS15565 isopropylmalate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS15565  AZOBR_RS15565 isopropylmalate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  661.7   0.0  2.7e-203  2.7e-203       2     466 .]       5     465 ..       4     465 .. 0.99

  Alignments for each domain:
  == domain 1  score: 661.7 bits;  conditional E-value: 2.7e-203
                                 TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr 70 
                                               +++l++k++dah+v    +++ ll idrh++he  s  af  + +a r+vrr++ t+a  dh ++++sr
  lcl|FitnessBrowser__azobra:AZOBR_RS15565   5 PRSLFDKVWDAHLVATRPDGQALLAIDRHFLHE-GSFHAFGMIDHAKRPVRRPELTFAVADHYVPSHSR 72 
                                               799******************************.5899******************************* PP

                                 TIGR00170  71 dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafga 139
                                                  i + +    v+ le n+++ g++ f+l++  qgivhv+ pe+gltlpg tivcgdsht+thgafga
  lcl|FitnessBrowser__azobra:AZOBR_RS15565  73 AKPIADPEIANMVTMLEANAERHGLRHFGLHDPAQGIVHVLAPEQGLTLPGLTIVCGDSHTSTHGAFGA 141
                                               ********99*********************************************************** PP

                                 TIGR00170 140 lafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageai 208
                                               lafgig++ev hvlatqtl+q r+kt++i ++g+l   +takd+ila+ig ig+ g +g+v+e+ag ai
  lcl|FitnessBrowser__azobra:AZOBR_RS15565 142 LAFGIGATEVSHVLATQTLWQRRPKTMRIIIDGELGAHVTAKDLILAVIGFIGADGAAGHVIEYAGSAI 210
                                               ********************************************************************* PP

                                 TIGR00170 209 rdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvv 277
                                               r+lsme+r+tvcnm+ieaga+ag+iapd++tf+++ +r+yapkg+ f+ ava+w+tl +d++a fd++v
  lcl|FitnessBrowser__azobra:AZOBR_RS15565 211 RALSMEGRLTVCNMSIEAGARAGMIAPDDITFSWIEGRNYAPKGDLFDRAVAHWRTLPSDPEAAFDREV 279
                                               ********************************************************************* PP

                                 TIGR00170 278 tleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigs 346
                                               +l+a  i+p vtwgt+p+++++v+++vpdp   +dpv+  ++ k l+y+gl+pgt+l+++ +d+vfigs
  lcl|FitnessBrowser__azobra:AZOBR_RS15565 280 SLDAAAIAPLVTWGTSPETAVPVTGTVPDPGAESDPVRAGQMRKMLDYMGLTPGTRLEEVGIDRVFIGS 348
                                               ********************************************************************* PP

                                 TIGR00170 347 ctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmn 415
                                               ctn+r+edlraaa+v++g++    v   lvv gs +v++qae+egld++f+ ag+ew e+gcs+c+g+n
  lcl|FitnessBrowser__azobra:AZOBR_RS15565 349 CTNARLEDLRAAAAVLRGRRA---VVPGLVVAGSVPVRRQAEAEGLDRVFIGAGLEWGEPGCSMCVGIN 414
                                               *******************85...44589**************************************** PP

                                 TIGR00170 416 ndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                                d ++++ercast+nrnf grqg +arthl+spamaaaaav+g++ d+r+l
  lcl|FitnessBrowser__azobra:AZOBR_RS15565 415 GDLVPAGERCASTTNRNFPGRQGPNARTHLMSPAMAAAAAVTGRLTDVRKL 465
                                               *************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (468 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: 8.55
//
[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