GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Clostridium tyrobutyricum FAM22553

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_017751620.1 PN53_RS13955 branched-chain amino acid transaminase

Query= BRENDA::F2L0W0
         (295 letters)



>NCBI__GCF_000816635.1:WP_017751620.1
          Length = 304

 Score =  266 bits (680), Expect = 4e-76
 Identities = 137/299 (45%), Positives = 191/299 (63%), Gaps = 6/299 (2%)

Query: 3   VWLDGRLVDEEEAKVTVLSPSLNYGFGVFEGIRAYWNGEN--LYVFRLRDHMERLLRSAK 60
           V+  G++VDE E  + + S + NYG G FEGIRAYW+ E   L+ FRL+DH  RLL+S+K
Sbjct: 6   VFYQGKIVDESEVTIGIRSKAFNYGLGCFEGIRAYWDEEQKQLFGFRLKDHYTRLLQSSK 65

Query: 61  IIGLDVPYTAEELSKAVVETVRANGFKEDLYIRPVAYISKPQISLDVRGLQASVAIAAIP 120
            + L++PYTA+ELSK  +E ++ N  K   YIRP+ Y     I  ++      V I   P
Sbjct: 66  SLNLNIPYTADELSKWTIELLKKNNCKRTTYIRPIVYNDAQDIGPNLSKPDTKVVIYCQP 125

Query: 121 FGKYLKVEGVRAAVVSWRRVHTSMMPVMAKATGIYLNSIMAAVEARARGYDEAIMLNAEG 180
             KY     +   + SWRR+  +M+P   KAT  YLNS +A++EA+  G+DEAI L +  
Sbjct: 126 LDKYAGKSELSVGITSWRRLEDNMLPPRTKATAAYLNSALASLEAKRAGFDEAIFLTSGN 185

Query: 181 KVVEGSGENIFIVRRGVLMTPPLEDGILEGITRETVISIA-GDLGIPLLEKSITREELYA 239
            V EG GENIFI ++G L+TPP  D ILEGITR+ V+ +   +LG+ + E+SI R ELYA
Sbjct: 186 HVCEGPGENIFIYKKGKLITPPASDNILEGITRDLVMQLGKEELGLEVQERSIARTELYA 245

Query: 240 ADEAFFVGTAAEITPIIEIDGRVL---QRGPITQKIAETYRRIVLGKEEKYLPWLTPVY 295
           +DE FF GTA E+TPIIE+D RV+   ++G + +KI E +  + +GK  KY  + TPVY
Sbjct: 246 SDEVFFSGTAMEVTPIIEVDHRVVGDGKQGEVCKKIKELFFNLTVGKNPKYAHYCTPVY 304


Lambda     K      H
   0.320    0.138    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: 272
Number of extensions: 7
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: 295
Length of database: 304
Length adjustment: 27
Effective length of query: 268
Effective length of database: 277
Effective search space:    74236
Effective search space used:    74236
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: 48 (23.1 bits)

Align candidate WP_017751620.1 PN53_RS13955 (branched-chain amino acid transaminase)
to HMM TIGR01122 (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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.1875827.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.2e-100  319.8   0.0   9.3e-100  319.6   0.0    1.0  1  NCBI__GCF_000816635.1:WP_017751620.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000816635.1:WP_017751620.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.6   0.0  9.3e-100  9.3e-100       1     298 []       7     303 ..       7     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 319.6 bits;  conditional E-value: 9.3e-100
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglai..frlkehveRlydsakilrleipyskeelv 71 
                                           +++G++vd+ + ++ + ++a+ YG g feGiRaY+ ++++++  frlk+h+ Rl++s+k+l+l+ipy+++el+
  NCBI__GCF_000816635.1:WP_017751620.1   7 FYQGKIVDESEVTIGIRSKAFNYGLGCFEGIRAYWDEEQKQLfgFRLKDHYTRLLQSSKSLNLNIPYTADELS 79 
                                           789*******************************998866652379*************************** PP

                             TIGR01122  72 evtkevlrknnlks.aYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraav 143
                                           + t+e+l+knn k  +YiRp+vy  a+d+g +  ++ +++v+i+  ++ +y g+  l+ G    ++s+rr ++
  NCBI__GCF_000816635.1:WP_017751620.1  80 KWTIELLKKNNCKRtTYIRPIVYNDAQDIGPNL-SKPDTKVVIYCQPLDKYAGKSELSVG----ITSWRRLED 147
                                           ************9889*************9988.8889***************9766666....579****** PP

                             TIGR01122 144 nsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrda 216
                                           n++p+++ka+++Ylns+la  ea+raG+deai+L +  +v eG+Genifi k+g+l+tPp s++iL+gitrd 
  NCBI__GCF_000816635.1:WP_017751620.1 148 NMLPPRTKATAAYLNSALASLEAKRAGFDEAIFLTSGNHVCEGPGENIFIYKKGKLITPPASDNILEGITRDL 220
                                           ************************************************************************* PP

                             TIGR01122 217 viklak.elgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegkt 288
                                           v++l k elg+ev+e++i+r+ely +Devf++Gta evtPi evD+r +g+gk+G+v kk++e ff+l+ gk+
  NCBI__GCF_000816635.1:WP_017751620.1 221 VMQLGKeELGLEVQERSIARTELYASDEVFFSGTAMEVTPIIEVDHRVVGDGKQGEVCKKIKELFFNLTVGKN 293
                                           ****98689**************************************************************** PP

                             TIGR01122 289 ekkeewltyv 298
                                           +k++++ t+v
  NCBI__GCF_000816635.1:WP_017751620.1 294 PKYAHYCTPV 303
                                           ****998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (304 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: 11.63
//
[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