Alignments for a candidate for ilvE in Anaerobutyricum hallii DSM 3353

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Anaerobutyricum hallii DSM 3353

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_005348665.1 EUBHAL_RS09600 branched-chain amino acid aminotransferase

Query= BRENDA::Q9RTX5
         (358 letters)



>NCBI__GCF_000173975.1:WP_005348665.1
          Length = 346

 Score =  356 bits (914), Expect = e-103
 Identities = 179/334 (53%), Positives = 231/334 (69%), Gaps = 2/334 (0%)

Query: 23  DIDWSTLGFSYIRTDLRYLAHWKDGEWDAGTLTEDNQIHLAEGSTALHYGQQCFEGLKAY 82
           +I+W  LGFSY +T+ R++A++KDG WD GTLTED  I L E +    Y Q CFEGLKAY
Sbjct: 5   NINWGELGFSYQQTEKRFVANFKDGAWDDGTLTEDATITLNECAGVFQYAQTCFEGLKAY 64

Query: 83  RCADGSINLFRPDQNAARMRMSCRRLLMPELSDEQFIDACLQVVRANEHFLPPYGTGGSL 142
              +G I  FRPD NAARM  SCRRL MP   +++F++A ++ V+AN  ++ PYG+G +L
Sbjct: 65  TTENGDIVCFRPDLNAARMADSCRRLEMPVFPEDKFVEAVVETVKANAGYVAPYGSGATL 124

Query: 143 YLRPFVIGVGDNIGVRTAPEFIFSVFCVPVGPYFKGGLTPTNFITSDYDRAAPHGTGAAK 202
           Y+RP++ G    IGV+ A E+ F +F  PVGPYFKGG  P     SD+DRAAP+GTG  K
Sbjct: 125 YIRPYMFGSNPVIGVKPADEYQFRIFVTPVGPYFKGGAKPITIRVSDFDRAAPNGTGHIK 184

Query: 203 VGGNYAASLLPGYEAKKRDFADVIYLDPATHTTIEEAGAANFFAITQDGQKFVTPQSPSI 262
            G NYA SL    +A  + + + +YLDPAT T +EE G ANF  IT+DG KFVTP+S SI
Sbjct: 185 AGLNYAMSLHAIVDAHNQGYDENMYLDPATRTKVEETGGANFIFITKDG-KFVTPKSDSI 243

Query: 263 LPSITKYSLLWLAEHRLGLEVEEGDIRIDELGKFSEAGACGTAAVITPIGGI-QHGDDFH 321
           LPSIT+ SL+++AEH LG+EVE  ++R DE+  F+E G CGTAAVI+P+G I  HG +  
Sbjct: 244 LPSITRRSLMYIAEHYLGMEVEHREVRFDEVKDFAECGLCGTAAVISPVGKIVDHGKEIC 303

Query: 322 VFYSESEPGPVTRRLYDELVGIQYGDKEAPEGWI 355
                 E GPVT++LYD L GIQ G  EAPEGWI
Sbjct: 304 FPSGMEEMGPVTKKLYDTLTGIQMGHIEAPEGWI 337


Lambda     K      H
   0.320    0.139    0.430 

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: 416
Number of extensions: 17
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: 358
Length of database: 346
Length adjustment: 29
Effective length of query: 329
Effective length of database: 317
Effective search space:   104293
Effective search space used:   104293
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_005348665.1 EUBHAL_RS09600 (branched-chain amino acid aminotransferase)
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

# 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/TIGR01123.hmm
# target sequence database:        /tmp/gapView.1365128.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01123  [M=313]
Accession:   TIGR01123
Description: ilvE_II: branched-chain amino acid aminotransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-119  384.2   0.0   2.3e-119  384.0   0.0    1.0  1  NCBI__GCF_000173975.1:WP_005348665.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000173975.1:WP_005348665.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.0   0.0  2.3e-119  2.3e-119       1     311 [.      31     338 ..      31     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: 384.0 bits;  conditional E-value: 2.3e-119
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           Wd+++l+++a+++l+e + v+ Y+q +feGlkay t++G i+ fRpd na+R+  s++rl +P  +e+ f+ea
  NCBI__GCF_000173975.1:WP_005348665.1  31 WDDGTLTEDATITLNECAGVFQYAQTCFEGLKAYTTENGDIVCFRPDLNAARMADSCRRLEMPVFPEDKFVEA 103
                                           ************************************************************************* PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           + + vka++ +v++++s+a+LY+RP++++ ++++Gvk+a ey f ++++PvG+Yfkgg +p++i v+ +++Ra
  NCBI__GCF_000173975.1:WP_005348665.1 104 VVETVKANAGYVAPYGSGATLYIRPYMFGSNPVIGVKPADEYQFRIFVTPVGPYFKGGAKPITIRVS-DFDRA 175
                                           *************************************************************888885.8**** PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           ap+GtG +k g nYa sl+a   a++qg+d+ +yldp++++k+ee+G+an+++itkd  +++tp+s+siL+++
  NCBI__GCF_000173975.1:WP_005348665.1 176 APNGTGHIKAGLNYAMSLHAIVDAHNQGYDENMYLDPATRTKVEETGGANFIFITKD-GKFVTPKSDSILPSI 247
                                           *********************************************************.578899********* PP

                             TIGR01123 220 tresllelakd.lgleveereiaidelkaaveaGeivfacGtaavitPvgelkiegkevevkse..evGevtk 289
                                           tr+sl+ +a++ lg+eve re++ de+k+++e G    +cGtaavi+Pvg++  +gke+ + s+  e+G+vtk
  NCBI__GCF_000173975.1:WP_005348665.1 248 TRRSLMYIAEHyLGMEVEHREVRFDEVKDFAECG----LCGTAAVISPVGKIVDHGKEICFPSGmeEMGPVTK 316
                                           **********************************....***********************997779****** PP

                             TIGR01123 290 klrdeltdiqyGkledkegWiv 311
                                           kl+d+lt+iq+G++e++egWi 
  NCBI__GCF_000173975.1:WP_005348665.1 317 KLYDTLTGIQMGHIEAPEGWIK 338
                                           ********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (346 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: 11.72
//
[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