GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Thermophagus xiamenensis HS1

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_010526307.1 GQW_RS0101545 3-isopropylmalate dehydrogenase

Query= BRENDA::P54354
         (353 letters)



>NCBI__GCF_000220155.1:WP_010526307.1
          Length = 355

 Score =  439 bits (1128), Expect = e-128
 Identities = 227/354 (64%), Positives = 272/354 (76%), Gaps = 6/354 (1%)

Query: 1   MDFKIAVLAGDGIGPEISVQGVEVMSAVCEKFGHKVNYEYAICGADAIDKVGDPFPEETY 60
           M   IAVL GDGIGPEI  Q  + + AV +K GH+ NY  A  GA AID+ GDP+PEET+
Sbjct: 1   MKLNIAVLPGDGIGPEIVEQAKKSLDAVLKKKGHEANYTEAPVGAVAIDQTGDPYPEETH 60

Query: 61  RVCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCLVHKSP 120
           ++C NADAVLF A+GDPK+DNDP AKVRPEQGLLAMRKKLGL+ANIRPV TF  L+HKSP
Sbjct: 61  QICMNADAVLFGAIGDPKYDNDPKAKVRPEQGLLAMRKKLGLYANIRPVTTFPSLIHKSP 120

Query: 121 LRAELVEGADFLCIRELTGGMYFGE---KYQDNDKAYDTNMYTRPEIERILKVGFEYAMK 177
           LR++LV+GADF+ IRELTGG+YFG    + +D   AYDTN+YT  EIERI ++ F++AMK
Sbjct: 121 LRSDLVDGADFVAIRELTGGIYFGRPQGRSEDGRTAYDTNVYTVEEIERITRLAFDFAMK 180

Query: 178 RRKHLTVVDKANVLASSRLWRQIAQEMAPQYPEVTTDYMFVDNAAMKMIQEPKFFDVMVT 237
           RRK LTVVDKANVLA+SRLWR+  Q +AP + EV  +YMFVDNAAM++IQ PK FDVM+T
Sbjct: 181 RRKKLTVVDKANVLATSRLWRETVQAIAPDFLEVEVEYMFVDNAAMQIIQWPKRFDVMLT 240

Query: 238 ENTFGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVA 297
           EN FGDILTDE SVI+GS+GLLPSAS G  T VFEPIHGS+PQA G NIANPLA ILS A
Sbjct: 241 ENMFGDILTDEASVITGSLGLLPSASIGVHTSVFEPIHGSYPQAAGKNIANPLATILSAA 300

Query: 298 MLFE-YFDCKAEGALIRKAVDASLDANVRTPEIQVEGGEKFGTKEVGAWIVDYI 350
           ++ E  F+ K E  +IR AV+ASL+    T +I  +      T EVG WI +YI
Sbjct: 301 LMLESAFNLKEEANMIRTAVEASLEQGKVTEDI--DKSNALSTSEVGDWIAEYI 352


Lambda     K      H
   0.319    0.136    0.403 

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: 416
Number of extensions: 13
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: 353
Length of database: 355
Length adjustment: 29
Effective length of query: 324
Effective length of database: 326
Effective search space:   105624
Effective search space used:   105624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_010526307.1 GQW_RS0101545 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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/TIGR00169.hmm
# target sequence database:        /tmp/gapView.3087436.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.2e-144  464.8   0.0   9.7e-144  464.6   0.0    1.0  1  NCBI__GCF_000220155.1:WP_010526307.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000220155.1:WP_010526307.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  464.6   0.0  9.7e-144  9.7e-144       1     345 [.       4     344 ..       4     348 .. 0.97

  Alignments for each domain:
  == domain 1  score: 464.6 bits;  conditional E-value: 9.7e-144
                             TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 
                                           +iavLpGDgiGpe+v++a k L+av ++++++ ++ ea +G  aid+tg+P peet + c +adavL+ga+G 
  NCBI__GCF_000220155.1:WP_010526307.1   4 NIAVLPGDGIGPEIVEQAKKSLDAVLKKKGHEANYTEAPVGAVAIDQTGDPYPEETHQICMNADAVLFGAIGD 76 
                                           69*********************************************************************** PP

                             TIGR00169  74 pkWdnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepker 145
                                           pk+dn p+ +vrPe+gLL++rk+l+l+an+rP++ f+sL++ spl++++v+g D+v +reLtgGiYfG+p++r
  NCBI__GCF_000220155.1:WP_010526307.1  77 PKYDNDPKaKVRPEQGLLAMRKKLGLYANIRPVTTFPSLIHKSPLRSDLVDGADFVAIRELTGGIYFGRPQGR 149
                                           *****986379************************************************************** PP

                             TIGR00169 146 eeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehly 218
                                           +e+   ++a+dt +Yt+eeieri+r+af  a+krrkk+t vDkanvL++srlWr+tv++ia ++ +ve+e ++
  NCBI__GCF_000220155.1:WP_010526307.1 150 SED--GRTAYDTNVYTVEEIERITRLAFDFAMKRRKKLTVVDKANVLATSRLWRETVQAIAPDFLEVEVEYMF 220
                                           *95..889***************************************************************** PP

                             TIGR00169 219 iDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianp 291
                                           +Dnaamq+++ P+++dv++t+n+fGDil DeasvitGslGlLPsas++   + +fep+hgs p+ agk+ianp
  NCBI__GCF_000220155.1:WP_010526307.1 221 VDNAAMQIIQWPKRFDVMLTENMFGDILTDEASVITGSLGLLPSASIG-VHTSVFEPIHGSYPQAAGKNIANP 292
                                           ************************************************.8899******************** PP

                             TIGR00169 292 iaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkev 345
                                           +a+ilsaal+l++++nl+e+a++i +av+  le+gk ted+ +++  a st+ev
  NCBI__GCF_000220155.1:WP_010526307.1 293 LATILSAALMLESAFNLKEEANMIRTAVEASLEQGKVTEDIDKSN--ALSTSEV 344
                                           *****************************************9887..5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (355 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: 00:00:00.00
# Mc/sec: 19.28
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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