GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuB in Azoarcus olearius BH72

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_011764775.1 AZO_RS05285 3-isopropylmalate dehydrogenase

Query= SwissProt::Q56268
         (358 letters)



>NCBI__GCF_000061505.1:WP_011764775.1
          Length = 354

 Score =  427 bits (1098), Expect = e-124
 Identities = 225/357 (63%), Positives = 276/357 (77%), Gaps = 9/357 (2%)

Query: 3   KIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLA 62
           KI +  GDGIGPEI A A +VL A+D    L +   E L+GG+A+DA+  P P A+ +LA
Sbjct: 2   KICVLPGDGIGPEITAEAVRVLRALD----LKIELEEALLGGSAVDATGTPYPEATQKLA 57

Query: 63  MAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPE 122
            AADAV+LGAVGGP+WD  P  +RPE+GLL +RK L L+ANLRPA ++P+L +AS L+PE
Sbjct: 58  RAADAVLLGAVGGPKWDTLPREQRPERGLLGIRKDLSLFANLRPAILYPELANASTLKPE 117

Query: 123 LVRDVDILVVRELTGDIYFGQPRGLEV--IDG--KRRGFNTMVYDEDEIRRIAHVAFRAA 178
           +V  +DIL+VRELTGDIYFGQPRG+E   ++G  +R G+NTM+Y E EIRRI  VAF AA
Sbjct: 118 VVSGLDILIVRELTGDIYFGQPRGIETREVNGAQQRVGWNTMIYAEYEIRRILKVAFEAA 177

Query: 179 QGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVL 238
           Q R K+LCSVDK NVLETT+LWR++  E+A+D+PDV LSHM VDNAAMQL+R P QFDV+
Sbjct: 178 QKRGKKLCSVDKMNVLETTQLWRDIADEMAKDFPDVELSHMLVDNAAMQLVRNPKQFDVM 237

Query: 239 LTGNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATIL 297
           +TGNMFGDILSDEAS LTGSIGMLPSASL    + +YEP HGSAPDIAG+  ANPLATIL
Sbjct: 238 VTGNMFGDILSDEASMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGKGVANPLATIL 297

Query: 298 SVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           S AMMLR++ N E  A R+E AV++VL QG RT DI   GT  +GT+ MG AV+ AL
Sbjct: 298 SAAMMLRYTFNQEEAAVRIERAVKKVLAQGFRTGDIYEAGTKKVGTREMGDAVLAAL 354


Lambda     K      H
   0.320    0.137    0.396 

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: 404
Number of extensions: 14
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: 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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate WP_011764775.1 AZO_RS05285 (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.2481481.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-159  516.5   0.0   1.8e-159  516.3   0.0    1.0  1  NCBI__GCF_000061505.1:WP_011764775.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000061505.1:WP_011764775.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.3   0.0  1.8e-159  1.8e-159       1     348 [.       2     349 ..       2     350 .. 0.97

  Alignments for each domain:
  == domain 1  score: 516.3 bits;  conditional E-value: 1.8e-159
                             TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 
                                           ki vLpGDgiGpe++aea++vL a+    +lk+e eeal+GG a+datg+P pe+t k +++adavLlgavGG
  NCBI__GCF_000061505.1:WP_011764775.1   2 KICVLPGDGIGPEITAEAVRVLRAL----DLKIELEEALLGGSAVDATGTPYPEATQKLARAADAVLLGAVGG 70 
                                           79********************997....58999*************************************** PP

                             TIGR00169  74 pkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkere 146
                                           pkWd+lpr++rPe+gLL +rk+l lfanLrPa l+++L ++s+lk+e+v+g+D+++vreLtg iYfG+p+++e
  NCBI__GCF_000061505.1:WP_011764775.1  71 PKWDTLPREQRPERGLLGIRKDLSLFANLRPAILYPELANASTLKPEVVSGLDILIVRELTGDIYFGQPRGIE 143
                                           **********************************************************************987 PP

                             TIGR00169 147 eaee....ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvele 215
                                             e     ++ +++t+ Y ++ei+ri +vafe+a+kr kk++svDk nvLe+++lWr++++e+ak++Pdvel+
  NCBI__GCF_000061505.1:WP_011764775.1 144 TREVngaqQRVGWNTMIYAEYEIRRILKVAFEAAQKRGKKLCSVDKMNVLETTQLWRDIADEMAKDFPDVELS 216
                                           65432224889************************************************************** PP

                             TIGR00169 216 hlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgi 288
                                           h+++DnaamqLv++P+q+dv+vt+n+fGDilsDeas++tGs+G+LPsasl  + ++l+ep hgsapdiagkg+
  NCBI__GCF_000061505.1:WP_011764775.1 217 HMLVDNAAMQLVRNPKQFDVMVTGNMFGDILSDEASMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIAGKGV 289
                                           ************************************************************************* PP

                             TIGR00169 289 anpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                           anp+a+ilsaa++lry++n+eeaa +ie+avkkvl++g rt d+++ +t++v+t+e+++ 
  NCBI__GCF_000061505.1:WP_011764775.1 290 ANPLATILSAAMMLRYTFNQEEAAVRIERAVKKVLAQGFRTGDIYEAGTKKVGTREMGDA 349
                                           *********************************************************986 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.17
//
[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