Alignments for a candidate for leuB in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Azospirillum brasilense Sp245

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate AZOBR_RS14130 AZOBR_RS14130 3-isopropylmalate dehydrogenase

Query= BRENDA::P24404
         (370 letters)



>FitnessBrowser__azobra:AZOBR_RS14130
          Length = 371

 Score =  472 bits (1214), Expect = e-138
 Identities = 235/368 (63%), Positives = 291/368 (79%), Gaps = 2/368 (0%)

Query: 4   RSLFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDADMEK 63
           + L  LPGDGIGPE M +VR++I++++   N  F V+EGLVGG+A DA+GV + D  +  
Sbjct: 5   KKLLFLPGDGIGPEVMRQVRRVIDWLDRKRNVTFDVTEGLVGGAAIDAYGVPLKDETLAD 64

Query: 64  ALAADAILFGAVGGPKWDG-VPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASSLK 122
           ALAADA++ GAVGGPKWD    Y  RPEAGLL LRK+L LFANLRPA+ + AL  AS+LK
Sbjct: 65  ALAADAVMLGAVGGPKWDNPTDYTKRPEAGLLSLRKELNLFANLRPAVVFDALVDASTLK 124

Query: 123 PELVEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFELAR 182
            ++++GLDILIVRELTGGVYFGEP+ I D+GNG++RG++TQ+Y T EI R+A VAFELAR
Sbjct: 125 ADVIKGLDILIVRELTGGVYFGEPRGITDIGNGERRGVNTQVYTTSEIRRVARVAFELAR 184

Query: 183 SRDNRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFDVI 242
            R N++ SMEK NVM+SG+LW Q VT+ H  ++ DV LEHM AD G MQL++ PKQFDVI
Sbjct: 185 KRGNKLHSMEKANVMESGLLWRQEVTKLHQEEFSDVTLEHMYADNGAMQLLKNPKQFDVI 244

Query: 243 VTDNLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSIAN 302
           VTDNLFGD+LSD AAM+TGSLGMLPSASLGAPDA  G+RKA+YEPVHGSAPDIAG+ +AN
Sbjct: 245 VTDNLFGDILSDEAAMMTGSLGMLPSASLGAPDA-NGQRKALYEPVHGSAPDIAGRDLAN 303

Query: 303 PIAMIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCRQVGTSDMGDAVL 362
           P A + SFAMCLRYSFNM +EA  LE A+ NVL  G+RTADIMA G  +  T+ MGD++L
Sbjct: 304 PCATLLSFAMCLRYSFNMDEEAKMLEKAVQNVLSGGMRTADIMAPGMARCSTTVMGDSIL 363

Query: 363 AEFKALSA 370
            E   L++
Sbjct: 364 RELDKLAS 371


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: 450
Number of extensions: 11
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: 370
Length of database: 371
Length adjustment: 30
Effective length of query: 340
Effective length of database: 341
Effective search space:   115940
Effective search space used:   115940
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 AZOBR_RS14130 AZOBR_RS14130 (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.27765.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-148  480.0   0.0   2.4e-148  479.8   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS14130  AZOBR_RS14130 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS14130  AZOBR_RS14130 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  479.8   0.0  2.4e-148  2.4e-148       2     348 ..       7     361 ..       6     362 .. 0.98

  Alignments for each domain:
  == domain 1  score: 479.8 bits;  conditional E-value: 2.4e-148
                                 TIGR00169   2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 
                                               +  LpGDgiGpev+ +  +v++ ++ + ++ ++  e l+GGaaida+g Pl +etl+ + +adav+lga
  lcl|FitnessBrowser__azobra:AZOBR_RS14130   7 LLFLPGDGIGPEVMRQVRRVIDWLDRKRNVTFDVTEGLVGGAAIDAYGVPLKDETLADALAADAVMLGA 75 
                                               5689***************************************************************** PP

                                 TIGR00169  71 vGGpkWdnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138
                                               vGGpkWdn     +rPe gLL+lrkel+lfanLrPa +f++L+++s+lk++++kg+D+++vreLtgG+Y
  lcl|FitnessBrowser__azobra:AZOBR_RS14130  76 VGGPKWDNPTDyTKRPEAGLLSLRKELNLFANLRPAVVFDALVDASTLKADVIKGLDILIVRELTGGVY 144
                                               ********864368******************************************************* PP

                                 TIGR00169 139 fGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206
                                               fGep+++++ ++ e+++++t++Yt++ei+r+arvafelarkr +k+ s++kanv+es+ lWr+ v++++
  lcl|FitnessBrowser__azobra:AZOBR_RS14130 145 FGEPRGITDIGNgERRGVNTQVYTTSEIRRVARVAFELARKRGNKLHSMEKANVMESGLLWRQEVTKLH 213
                                               *********9999*******************************************************9 PP

                                 TIGR00169 207 k.eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss.....kg 269
                                               + e+ dv+leh+y Dn amqL+k+P+q+dv+vt+nlfGDilsDea+++tGslG+LPsasl+      ++
  lcl|FitnessBrowser__azobra:AZOBR_RS14130 214 QeEFSDVTLEHMYADNGAMQLLKNPKQFDVIVTDNLFGDILSDEAAMMTGSLGMLPSASLGApdangQR 282
                                               999**********************************************************99999999 PP

                                 TIGR00169 270 lalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatt 338
                                               +al+epvhgsapdiag+++anp+a++ls a+ lrys+n++e+a+++e+av++vl+ g+rt+d++  + +
  lcl|FitnessBrowser__azobra:AZOBR_RS14130 283 KALYEPVHGSAPDIAGRDLANPCATLLSFAMCLRYSFNMDEEAKMLEKAVQNVLSGGMRTADIMAPGMA 351
                                               *******************************************************************99 PP

                                 TIGR00169 339 avstkeveee 348
                                               + st+ ++++
  lcl|FitnessBrowser__azobra:AZOBR_RS14130 352 RCSTTVMGDS 361
                                               9999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (371 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.55
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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