GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Phyllobacterium endophyticum PEPV15

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_106714781.1 CU100_RS01435 3-isopropylmalate dehydrogenase

Query= BRENDA::P24404
         (370 letters)



>NCBI__GCF_003010935.1:WP_106714781.1
          Length = 370

 Score =  604 bits (1557), Expect = e-177
 Identities = 300/370 (81%), Positives = 334/370 (90%)

Query: 1   MTVRSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDAD 60
           M  + L LLPGDGIGPEAM EVRK+I YMNS   + F + EGLVGGSAYDAHG AIS+AD
Sbjct: 1   MASKKLLLLPGDGIGPEAMAEVRKIIGYMNSELKSEFVLDEGLVGGSAYDAHGAAISEAD 60

Query: 61  MEKALAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASS 120
           M KALAADA+LFGAVGGPKWD VPY+ RPEAGLLRLRKD+ELFANLRPAICYPALA +SS
Sbjct: 61  MAKALAADAVLFGAVGGPKWDSVPYDVRPEAGLLRLRKDMELFANLRPAICYPALADSSS 120

Query: 121 LKPELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFEL 180
           LK E+VEGLDILIVRELTGGVYFGEPK+I DLGNGQKRGIDTQ+YDT+EIERI+ VAFEL
Sbjct: 121 LKKEIVEGLDILIVRELTGGVYFGEPKEIRDLGNGQKRGIDTQVYDTYEIERISGVAFEL 180

Query: 181 ARSRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFD 240
           AR+R N+V SMEKRNVMKSGVLWN+VVT TH  KY DV+LEHMLADAGGMQLVR PKQFD
Sbjct: 181 ARTRGNKVTSMEKRNVMKSGVLWNEVVTATHKTKYSDVKLEHMLADAGGMQLVRWPKQFD 240

Query: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSI 300
           VIVTDNLFGDMLSD+AAMLTGSLGMLPSASLGAPDAKTGKRKA+YEPVHGSAPDIAG   
Sbjct: 241 VIVTDNLFGDMLSDIAAMLTGSLGMLPSASLGAPDAKTGKRKALYEPVHGSAPDIAGTGT 300

Query: 301 ANPIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDA 360
           ANPIAMIASFAMCLRYSFNM+ EA +LE+A+A VLD G+RTADIMA+G  ++GT++MGDA
Sbjct: 301 ANPIAMIASFAMCLRYSFNMIAEADRLESAVAGVLDDGLRTADIMAEGKTRIGTAEMGDA 360

Query: 361 VLAEFKALSA 370
           +LA+F+AL+A
Sbjct: 361 ILAKFRALAA 370


Lambda     K      H
   0.319    0.135    0.387 

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: 572
Number of extensions: 12
Number of successful extensions: 1
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: 370
Length of database: 370
Length adjustment: 30
Effective length of query: 340
Effective length of database: 340
Effective search space:   115600
Effective search space used:   115600
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate WP_106714781.1 CU100_RS01435 (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.2880579.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-136  438.9   0.0   7.3e-136  438.7   0.0    1.0  1  NCBI__GCF_003010935.1:WP_106714781.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010935.1:WP_106714781.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  438.7   0.0  7.3e-136  7.3e-136       2     348 ..       6     360 ..       5     361 .. 0.99

  Alignments for each domain:
  == domain 1  score: 438.7 bits;  conditional E-value: 7.3e-136
                             TIGR00169   2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGp 74 
                                           + +LpGDgiGpe +ae  k++  ++ + + ++  +e l+GG a da+g  ++e+ ++++ +adavL+gavGGp
  NCBI__GCF_003010935.1:WP_106714781.1   6 LLLLPGDGIGPEAMAEVRKIIGYMNSELKSEFVLDEGLVGGSAYDAHGAAISEADMAKALAADAVLFGAVGGP 78 
                                           679********************************************************************** PP

                             TIGR00169  75 kWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkeree 147
                                           kWd+ p dvrPe gLL+lrk+++lfanLrPa  +++L ++s+lk+eiv+g+D+++vreLtgG+YfGepke+++
  NCBI__GCF_003010935.1:WP_106714781.1  79 KWDSVPYDVRPEAGLLRLRKDMELFANLRPAICYPALADSSSLKKEIVEGLDILIVRELTGGVYFGEPKEIRD 151
                                           ************************************************************************9 PP

                             TIGR00169 148 aee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak.eyPdvelehly 218
                                            ++ +k+++dt++Y ++eieri  vafelar+r +kvts++k nv++s+ lW ++v++++k +y dv+leh++
  NCBI__GCF_003010935.1:WP_106714781.1 152 LGNgQKRGIDTQVYDTYEIERISGVAFELARTRGNKVTSMEKRNVMKSGVLWNEVVTATHKtKYSDVKLEHML 224
                                           9999********************************************************99*********** PP

                             TIGR00169 219 iDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss......kglalfepvhgsapdiag 285
                                            D+  mqLv+ P+q+dv+vt+nlfGD+lsD+a+++tGslG+LPsasl+       k++al+epvhgsapdiag
  NCBI__GCF_003010935.1:WP_106714781.1 225 ADAGGMQLVRWPKQFDVIVTDNLFGDMLSDIAAMLTGSLGMLPSASLGApdaktgKRKALYEPVHGSAPDIAG 297
                                           ************************************************999999999**************** PP

                             TIGR00169 286 kgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                            g anpia+i s a+ lrys+n+  +a+++e+av+ vl++g rt+d++ e+ t+ +t+e+++ 
  NCBI__GCF_003010935.1:WP_106714781.1 298 TGTANPIAMIASFAMCLRYSFNMIAEADRLESAVAGVLDDGLRTADIMAEGKTRIGTAEMGDA 360
                                           ************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (370 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: 25.26
//
[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