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.7918.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.34
//
[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