Alignments for a candidate for leuB in Caminibacter mediatlanticus TB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Caminibacter mediatlanticus TB-2

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_007473884.1 CMTB2_RS02910 3-isopropylmalate dehydrogenase

Query= BRENDA::P43860
         (358 letters)



>NCBI__GCF_000170735.1:WP_007473884.1
          Length = 354

 Score =  390 bits (1002), Expect = e-113
 Identities = 205/358 (57%), Positives = 269/358 (75%), Gaps = 10/358 (2%)

Query: 1   MQSYNIAVLAGDGIGPEVMAEAIKVLNRVQEKFGFKLNFNEFFVGGAAIEHCGYPLPAET 60
           M++Y IAVL GDGIGPE++ EAIKVL+ V EK G    FNE+ +GG+A++    P P ET
Sbjct: 1   MKTYKIAVLKGDGIGPEIVDEAIKVLDAVAEKEGINFEFNEYLIGGSAVDVFDNPCPDET 60

Query: 61  LKGCDQADAILFGSVGGPKWTNLPPDQQPERGALLPLRKHFKLFCNLRPATLYKGLEKFC 120
           +KGC  +DAILFGS+GGPKW  LP +++PE G LL LRK   LF N+RPA ++  L    
Sbjct: 61  IKGCLNSDAILFGSIGGPKWDKLPKEKRPESG-LLKLRKSLGLFANIRPAIIFDELVNAS 119

Query: 121 PLRADIAAKGFDMVVVRELTGGIYFGQPKGREGDGVQTKAFDTEVYYKYEIERIARAAFE 180
            L+ ++  KG D+ VVRELTGGIYFG+P+ ++ +    KA++T +Y + EIE+IA  AF+
Sbjct: 120 TLKPEVI-KGVDLTVVRELTGGIYFGEPRYKDDN----KAYNTMIYTREEIEKIAHVAFK 174

Query: 181 AAMKRNKKVTSVDKANVLQSSILWRETVTEMAKDYPEVTLEHIYIDNATMQLIKSPESFD 240
            A KRNKKVTSVDKANVL+ S LWRE V E+AK+YP+V LEH+Y+DNA MQLI+ P+ FD
Sbjct: 175 EASKRNKKVTSVDKANVLEVSELWREVVEEVAKNYPDVELEHMYVDNAAMQLIRDPKQFD 234

Query: 241 VLLCSNIFGDIISDEAAMITGSMGMLPSASLNEEGFGLYEPAGGSAPDIAGKGIANPIAQ 300
           V+L  NIFGDI+SDEA+MI GS+G+LPSAS+  +  GL+EP  GSAPDIAG+GIANPIA 
Sbjct: 235 VILTGNIFGDILSDEASMIVGSIGLLPSASIGGK-VGLFEPIHGSAPDIAGQGIANPIAT 293

Query: 301 ILSAAMMLRYSFNLNEAADAIESAVQKVLASGHRTADLA--DDSTPVSTAEMGTLITQ 356
           ILSA+MML Y  +  +AAD I+ +++KVLA G+RT DL+  D    V+T+EMG+LI +
Sbjct: 294 ILSASMMLDY-LDEKKAADRIKKSIKKVLADGYRTKDLSSFDAKEIVTTSEMGSLIAE 350


Lambda     K      H
   0.318    0.135    0.392 

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: 377
Number of extensions: 17
Number of successful extensions: 6
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: 358
Length of database: 354
Length adjustment: 29
Effective length of query: 329
Effective length of database: 325
Effective search space:   106925
Effective search space used:   106925
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: 49 (23.5 bits)

Align candidate WP_007473884.1 CMTB2_RS02910 (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.940406.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.7e-162  525.6   0.1   3.1e-162  525.5   0.1    1.0  1  NCBI__GCF_000170735.1:WP_007473884.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000170735.1:WP_007473884.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.5   0.1  3.1e-162  3.1e-162       1     346 [.       5     345 ..       5     348 .. 0.97

  Alignments for each domain:
  == domain 1  score: 525.5 bits;  conditional E-value: 3.1e-162
                             TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 
                                           kiavL+GDgiGpe+v+ea+kvL+av+e++++++ef+e+liGG a+d   +P p+et+k+c ++da+L+g++GG
  NCBI__GCF_000170735.1:WP_007473884.1   5 KIAVLKGDGIGPEIVDEAIKVLDAVAEKEGINFEFNEYLIGGSAVDVFDNPCPDETIKGCLNSDAILFGSIGG 77 
                                           79*********************************************************************** PP

                             TIGR00169  74 pkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkere 146
                                           pkWd+lp+++rPe+gLLklrk+l+lfan+rPa +f++L+++s+lk+e++kgvDl vvreLtgGiYfGep+ ++
  NCBI__GCF_000170735.1:WP_007473884.1  78 PKWDKLPKEKRPESGLLKLRKSLGLFANIRPAIIFDELVNASTLKPEVIKGVDLTVVRELTGGIYFGEPRYKD 150
                                           **********************************************************************998 PP

                             TIGR00169 147 eaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyi 219
                                           +    +ka++t+ Yt+eeie+ia+vaf+ a kr+kkvtsvDkanvLe+s+lWr++vee+ak+yPdveleh+y+
  NCBI__GCF_000170735.1:WP_007473884.1 151 D----NKAYNTMIYTREEIEKIAHVAFKEASKRNKKVTSVDKANVLEVSELWREVVEEVAKNYPDVELEHMYV 219
                                           8....79****************************************************************** PP

                             TIGR00169 220 DnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpi 292
                                           DnaamqL+++P+q+dv++t+n+fGDilsDeas+i+Gs+GlLPsas++  +++lfep+hgsapdiag+gianpi
  NCBI__GCF_000170735.1:WP_007473884.1 220 DNAAMQLIRDPKQFDVILTGNIFGDILSDEASMIVGSIGLLPSASIG-GKVGLFEPIHGSAPDIAGQGIANPI 291
                                           ***********************************************.6679********************* PP

                             TIGR00169 293 aailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatta.vstkeve 346
                                           a+ilsa+++l y l+ ++aa++i++++kkvl++g+rt+dl s ++++ v+t+e++
  NCBI__GCF_000170735.1:WP_007473884.1 292 ATILSASMMLDY-LDEKKAADRIKKSIKKVLADGYRTKDLSSFDAKEiVTTSEMG 345
                                           **********99.68899**********************996655415666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (354 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 22.33
//
[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