Alignments for a candidate for leuB in Rhizobium leguminosarum bv. trifolii WSM1325

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Rhizobium leguminosarum bv. trifolii WSM1325

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_012759505.1 RLEG_RS20910 3-isopropylmalate dehydrogenase

Query= BRENDA::P24404
         (370 letters)



>NCBI__GCF_000023185.1:WP_012759505.1
          Length = 370

 Score =  653 bits (1684), Expect = 0.0
 Identities = 326/370 (88%), Positives = 344/370 (92%)

Query: 1   MTVRSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDAD 60
           MT R+LFLLPGDGIGPEAM EVRK+I YMN A NAGF   EGLVGG AYDAHG AIS+AD
Sbjct: 1   MTARNLFLLPGDGIGPEAMGEVRKIIAYMNEAMNAGFVTDEGLVGGCAYDAHGAAISEAD 60

Query: 61  MEKALAADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASS 120
           M+KA+AADA+LFGAVGGPKWD VPYE RPEAGLLRLRKDL+LFANLRPAICYPALAAASS
Sbjct: 61  MQKAIAADAVLFGAVGGPKWDSVPYEVRPEAGLLRLRKDLQLFANLRPAICYPALAAASS 120

Query: 121 LKPELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFEL 180
           LKPELVEGLDILI+RELTGGVYFGEPK+IIDLGNGQKRGIDTQ+YDT+EIERIA VAFE+
Sbjct: 121 LKPELVEGLDILIIRELTGGVYFGEPKEIIDLGNGQKRGIDTQVYDTYEIERIAGVAFEM 180

Query: 181 ARSRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFD 240
           AR+R NRVCSMEKRNVMKSGVLWNQVVTETH AKY DVQLEHMLADAGGMQLVR+PKQFD
Sbjct: 181 ARTRQNRVCSMEKRNVMKSGVLWNQVVTETHKAKYSDVQLEHMLADAGGMQLVRQPKQFD 240

Query: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSI 300
           VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPD KTGKRKA+YEPVHGSAPDIAGK I
Sbjct: 241 VIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDGKTGKRKALYEPVHGSAPDIAGKGI 300

Query: 301 ANPIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDA 360
           ANPIAMIASFAMCLRYSFN+V EA  LE AIANVLDKGIRT DIMADG RQVGT +MGDA
Sbjct: 301 ANPIAMIASFAMCLRYSFNLVKEADDLEKAIANVLDKGIRTGDIMADGARQVGTIEMGDA 360

Query: 361 VLAEFKALSA 370
           +LAEFK LSA
Sbjct: 361 ILAEFKTLSA 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: 601
Number of extensions: 14
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_012759505.1 RLEG_RS20910 (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.3470214.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.8e-138  445.0   0.0     1e-137  444.8   0.0    1.0  1  NCBI__GCF_000023185.1:WP_012759505.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023185.1:WP_012759505.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.8   0.0    1e-137    1e-137       3     348 ..       7     360 ..       5     361 .. 0.99

  Alignments for each domain:
  == domain 1  score: 444.8 bits;  conditional E-value: 1e-137
                             TIGR00169   3 avLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpk 75 
                                            +LpGDgiGpe + e  k++  ++e ++  + ++e l+GG a da+g  ++e+ ++++ +adavL+gavGGpk
  NCBI__GCF_000023185.1:WP_012759505.1   7 FLLPGDGIGPEAMGEVRKIIAYMNEAMNAGFVTDEGLVGGCAYDAHGAAISEADMQKAIAADAVLFGAVGGPK 79 
                                           68*********************************************************************** PP

                             TIGR00169  76 WdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkereea 148
                                           Wd+ p +vrPe gLL+lrk+l+lfanLrPa  +++L ++s+lk+e+v+g+D++++reLtgG+YfGepke+ + 
  NCBI__GCF_000023185.1:WP_012759505.1  80 WDSVPYEVRPEAGLLRLRKDLQLFANLRPAICYPALAAASSLKPELVEGLDILIIRELTGGVYFGEPKEIIDL 152
                                           **********************************************************************999 PP

                             TIGR00169 149 ee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak.eyPdvelehlyi 219
                                           ++ +k+++dt++Y ++eieria vafe+ar+r+++v+s++k nv++s+ lW ++v+e++k +y dv+leh++ 
  NCBI__GCF_000023185.1:WP_012759505.1 153 GNgQKRGIDTQVYDTYEIERIAGVAFEMARTRQNRVCSMEKRNVMKSGVLWNQVVTETHKaKYSDVQLEHMLA 225
                                           999*********************************************************9************ PP

                             TIGR00169 220 DnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss......kglalfepvhgsapdiagk 286
                                           D+  mqLv++P+q+dv+vt+nlfGD+lsD a+++tGslG+LPsasl+       k++al+epvhgsapdiagk
  NCBI__GCF_000023185.1:WP_012759505.1 226 DAGGMQLVRQPKQFDVIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGApdgktgKRKALYEPVHGSAPDIAGK 298
                                           ***********************************************999999999***************** PP

                             TIGR00169 287 gianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                           gianpia+i s a+ lrys+nl ++a+ +e+a+++vl++g+rt d++ +++ +v+t e+++ 
  NCBI__GCF_000023185.1:WP_012759505.1 299 GIANPIAMIASFAMCLRYSFNLVKEADDLEKAIANVLDKGIRTGDIMADGARQVGTIEMGDA 360
                                           **********************************************************9986 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 15.94
//
[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:

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