GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Nitratiruptor tergarcus DSM 16512

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_084275692.1 B8779_RS06295 3-isopropylmalate dehydrogenase

Query= BRENDA::P93832
         (405 letters)



>NCBI__GCF_900176045.1:WP_084275692.1
          Length = 356

 Score =  409 bits (1050), Expect = e-119
 Identities = 215/351 (61%), Positives = 258/351 (73%), Gaps = 7/351 (1%)

Query: 41  KRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETI 100
           KRYT+ L+ GDGIGPE++  A  VL      EG E  ++E  +GGAA+D+ G P+PEETI
Sbjct: 2   KRYTVALIKGDGIGPEIIDEAVKVLDAVSVKEGFEITYKEALLGGAAIDVTGEPIPEETI 61

Query: 101 SAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTL 160
             AK +DAVL GAIGG +WD+  +  RPE GLL++R AL+VFANLRP TV  +LV+ASTL
Sbjct: 62  EIAKSADAVLFGAIGGPQWDDLPRDKRPETGLLKLRKALEVFANLRPVTVYDELVNASTL 121

Query: 161 KREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETA 220
           K EV +G DLMVVREL GGIYFG+PR  + +       +NT VY   E+ RIA+V FE A
Sbjct: 122 KPEVIQGTDLMVVRELIGGIYFGQPRAYEGDR-----AYNTMVYTKQEVYRIAKVGFEIA 176

Query: 221 RKRRGKLCSVDKANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTI 280
            KR  KL SVDKANVLE S LWR  V  +A EYP+V + HMYVDNAAMQLVRDPKQFD I
Sbjct: 177 MKRNKKLVSVDKANVLEVSQLWRDTVNEVAKEYPEVSVEHMYVDNAAMQLVRDPKQFDVI 236

Query: 281 VTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATIL 340
           +T NIFGDILSDEASM++GSIG+LPSAS+ +   GL+EPIHGSAPDIAGQ  ANP+ATI 
Sbjct: 237 LTGNIFGDILSDEASMLSGSIGLLPSASIGEK-YGLYEPIHGSAPDIAGQGIANPIATIA 295

Query: 341 SAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTK-LVGCKEMG 390
           SAAM+L+Y  GEE AAKRIEDA+   L  G+RT D+ S   K +V   EMG
Sbjct: 296 SAAMMLRYQFGEESAAKRIEDAIKRVLKEGYRTKDLSSFDAKEVVTTSEMG 346


Lambda     K      H
   0.316    0.134    0.374 

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: 418
Number of extensions: 12
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: 405
Length of database: 356
Length adjustment: 30
Effective length of query: 375
Effective length of database: 326
Effective search space:   122250
Effective search space used:   122250
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_084275692.1 B8779_RS06295 (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.2098316.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-164  533.0   0.2   1.8e-164  532.8   0.2    1.0  1  NCBI__GCF_900176045.1:WP_084275692.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900176045.1:WP_084275692.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.8   0.2  1.8e-164  1.8e-164       2     345 ..       6     345 ..       5     349 .. 0.97

  Alignments for each domain:
  == domain 1  score: 532.8 bits;  conditional E-value: 1.8e-164
                             TIGR00169   2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGp 74 
                                           +a+++GDgiGpe+++ea+kvL+av+ +++++++++eal+GGaaid tgeP+peet++ +k+adavL+ga+GGp
  NCBI__GCF_900176045.1:WP_084275692.1   6 VALIKGDGIGPEIIDEAVKVLDAVSVKEGFEITYKEALLGGAAIDVTGEPIPEETIEIAKSADAVLFGAIGGP 78 
                                           899********************************************************************** PP

                             TIGR00169  75 kWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkeree 147
                                           +Wd+lprd+rPe+gLLklrk l++fanLrP++++++L+++s+lk+e+++g+Dl+vvreL+gGiYfG+p+  e+
  NCBI__GCF_900176045.1:WP_084275692.1  79 QWDDLPRDKRPETGLLKLRKALEVFANLRPVTVYDELVNASTLKPEVIQGTDLMVVRELIGGIYFGQPRAYEG 151
                                           ************************************************************************9 PP

                             TIGR00169 148 aeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiD 220
                                               ++a++t++Ytk+e+ ria+v+fe+a+kr+kk++svDkanvLe+s+lWr+tv+e+akeyP+v++eh+y+D
  NCBI__GCF_900176045.1:WP_084275692.1 152 ----DRAYNTMVYTKQEVYRIAKVGFEIAMKRNKKLVSVDKANVLEVSQLWRDTVNEVAKEYPEVSVEHMYVD 220
                                           ....69******************************************************************* PP

                             TIGR00169 221 naamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpia 293
                                           naamqLv++P+q+dv++t+n+fGDilsDeas+++Gs+GlLPsas++ ++++l+ep+hgsapdiag+gianpia
  NCBI__GCF_900176045.1:WP_084275692.1 221 NAAMQLVRDPKQFDVILTGNIFGDILSDEASMLSGSIGLLPSASIG-EKYGLYEPIHGSAPDIAGQGIANPIA 292
                                           **********************************************.8899********************** PP

                             TIGR00169 294 ailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavs.tkev 345
                                           +i saa++lry+++ e aa++ie+a+k+vl+eg+rt+dl s ++++v+ t+e+
  NCBI__GCF_900176045.1:WP_084275692.1 293 TIASAAMMLRYQFGEESAAKRIEDAIKRVLKEGYRTKDLSSFDAKEVVtTSEM 345
                                           ***************************************99777666504555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (356 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 16.19
//
[ok]

This GapMind analysis is from Jul 25 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