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; EC 4.2.1.33 (characterized)
to candidate BPHYT_RS13520 BPHYT_RS13520 isopropylmalate isomerase

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__BFirm:BPHYT_RS13520
          Length = 471

 Score =  489 bits (1258), Expect = e-142
 Identities = 246/465 (52%), Positives = 318/465 (68%), Gaps = 1/465 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TLY+KL D+HVV   + +  LLY+D HL++E TSPQAF  L A  R VR+P +  A + 
Sbjct: 4   RTLYQKLVDSHVVTRVDEQNVLLYVDLHLMNEYTSPQAFSALAAKTRRVRRPKQQLAVVS 63

Query: 63  HNVSTQTKDINACGEMARIQM-QELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPG 121
           H + T  +      + A + +   L +NC E G+ L+  N P QGI H++ PE+G+  PG
Sbjct: 64  HIIPTHAEAPRVIRDAASLLLANNLARNCAEAGIALHAANDPLQGIEHIVAPERGLVRPG 123

Query: 122 MTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAK 181
           M ++CGDSHT T+GA GAL FGIGTSEVEHVLATQTL    A+TM+I ++G    G ++K
Sbjct: 124 MVVLCGDSHTTTYGALGALGFGIGTSEVEHVLATQTLVYRVAQTMRITIEGPMPYGTSSK 183

Query: 182 DIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFN 241
           D++L II + G+ G  G+ VEF G  I  LS E RMTLCNM +E GA+A L+APD TTF+
Sbjct: 184 DLILWIISRIGAQGARGYAVEFAGSTIASLSAEARMTLCNMTVEAGARAALIAPDATTFD 243

Query: 242 YVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVN 301
           Y++          +  A++ W+ L++D GA FD+     A +ISP VTWGT+P Q I+V+
Sbjct: 244 YIRAHATQLDEIAWYAAMSDWRELKSDPGARFDSEYRFDACDISPFVTWGTSPDQAIAVD 303

Query: 302 DNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEI 361
           + IP  A+   P   A+  +AL Y+GL    P+    ID+VFIGSCTN RIEDLR  A I
Sbjct: 304 ERIPAAAAQKTPEAAAALRRALDYIGLDADQPIAGTPIDRVFIGSCTNGRIEDLRIVASI 363

Query: 362 AKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421
             GR VA GV+A+VVPGSG V+ QAEAEG+     EAGFEWR PGCSMCLAMN+D L PG
Sbjct: 364 VAGRHVAQGVRAMVVPGSGSVRRQAEAEGVAATLREAGFEWREPGCSMCLAMNDDFLTPG 423

Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNIK 466
           ERCAST+NRNFEGRQGRGGRTHL+SPAMAAAAA+TG   D+R ++
Sbjct: 424 ERCASTTNRNFEGRQGRGGRTHLMSPAMAAAAALTGRITDVRTLE 468


Lambda     K      H
   0.317    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: 665
Number of extensions: 25
Number of successful extensions: 3
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: 471
Length adjustment: 33
Effective length of query: 433
Effective length of database: 438
Effective search space:   189654
Effective search space used:   189654
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_RS13520 BPHYT_RS13520 (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.588.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   5.9e-188  611.1   0.0     7e-188  610.8   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS13520  BPHYT_RS13520 isopropylmalate is


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS13520  BPHYT_RS13520 isopropylmalate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  610.8   0.0    7e-188    7e-188       2     465 ..       3     466 ..       2     467 .. 0.98

  Alignments for each domain:
  == domain 1  score: 610.8 bits;  conditional E-value: 7e-188
                                TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrd 71 
                                              ++tly+kl d+hvv + ++++ lly+d+hl+ e tspqaf  l a++r+vrr+++ la + h i+t++  
  lcl|FitnessBrowser__BFirm:BPHYT_RS13520   3 TRTLYQKLVDSHVVTRVDEQNVLLYVDLHLMNEYTSPQAFSALAAKTRRVRRPKQQLAVVSHIIPTHAEA 72 
                                              69*****************************************************************997 PP

                                TIGR00170  72 veik.eekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgal 140
                                                +  +  + l  ++l +n+ e g+ l+  ++  qgi h+v pe+gl  pg+ ++cgdsht+t+ga+gal
  lcl|FitnessBrowser__BFirm:BPHYT_RS13520  73 PRVIrDAASLLLANNLARNCAEAGIALHAANDPLQGIEHIVAPERGLVRPGMVVLCGDSHTTTYGALGAL 142
                                              665505556667789******************************************************* PP

                                TIGR00170 141 afgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageaird 210
                                               fgigtsevehvlatqtl+   a+t++i++eg +  g ++kd+il ii +ig++g  gy vefag +i +
  lcl|FitnessBrowser__BFirm:BPHYT_RS13520 143 GFGIGTSEVEHVLATQTLVYRVAQTMRITIEGPMPYGTSSKDLILWIISRIGAQGARGYAVEFAGSTIAS 212
                                              ********************************************************************** PP

                                TIGR00170 211 lsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtle 280
                                              ls e+rmt+cnm++eaga+a liapd ttf+y++          +  a++ w+ lk+d+ga+fd +  ++
  lcl|FitnessBrowser__BFirm:BPHYT_RS13520 213 LSAEARMTLCNMTVEAGARAALIAPDATTFDYIRAHATQLDEIAWYAAMSDWRELKSDPGARFDSEYRFD 282
                                              *********************************99999999999************************** PP

                                TIGR00170 281 akdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctns 350
                                              a disp vtwgt+p+q+++v+e +p+ +    p   a   +al+y+gl++++++    +d+vfigsctn+
  lcl|FitnessBrowser__BFirm:BPHYT_RS13520 283 ACDISPFVTWGTSPDQAIAVDERIPAAAAQKTPEAAAALRRALDYIGLDADQPIAGTPIDRVFIGSCTNG 352
                                              ********************************************************************** PP

                                TIGR00170 351 riedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvld 420
                                              riedlr  a++v g++va++v+ a+vvpgsg+v++qae+eg+   + eagfewre+gcs+cl+mn+d l 
  lcl|FitnessBrowser__BFirm:BPHYT_RS13520 353 RIEDLRIVASIVAGRHVAQGVR-AMVVPGSGSVRRQAEAEGVAATLREAGFEWREPGCSMCLAMNDDFLT 421
                                              **********************.*********************************************** PP

                                TIGR00170 421 eyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                              ++ercast+nrnfegrqg+g+rthl+spamaaaaa++g++ d+r 
  lcl|FitnessBrowser__BFirm:BPHYT_RS13520 422 PGERCASTTNRNFEGRQGRGGRTHLMSPAMAAAAALTGRITDVRT 466
                                              *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (471 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: 10.50
//
[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