GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Xanthobacter autotrophicus Py2

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_012114576.1 XAUT_RS12870 branched-chain amino acid aminotransferase

Query= BRENDA::O86428
         (307 letters)



>NCBI__GCF_000017645.1:WP_012114576.1
          Length = 297

 Score =  222 bits (565), Expect = 9e-63
 Identities = 122/294 (41%), Positives = 173/294 (58%), Gaps = 9/294 (3%)

Query: 6   RDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYDTPQGTAIFRLQAHTDRLFDS 65
           RDG IWYDG  V W DA  HVL+H LHYG  VFEG RAY    G  IF+   H++RL  S
Sbjct: 11  RDGWIWYDGVFVPWADAKLHVLSHGLHYGSTVFEGERAY----GGTIFKSAEHSERLRLS 66

Query: 66  AHIMNMQIPYSRDEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHVIIAAW 125
           A +++  IPY+  EI+ A +A + +NNL  AYIRP+ + GSE MG+ A    +H+ I  W
Sbjct: 67  AEMLDFTIPYTIGEIDAAKKATLEKNNLVDAYIRPVAWRGSEMMGVAAQKNTIHLAIGVW 126

Query: 126 SWGAYMGEEALQQGIKVRTSSFTRHHVNISMTRAKSNGAYINSMLALQEAISGGADEAMM 185
            W +Y   E  Q+G+++  S + R        +AK+ G Y+   ++   A   G  +A+M
Sbjct: 127 EWPSYFDPEQRQKGLRLDLSEWRRPDPATIPCKAKAAGLYMICTISKHRAERRGFADALM 186

Query: 186 LDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRNTILTLAAEHGFKLVEKRITRDE 245
           LD  GYVAE +G N+F +KDGVI+TP     L+G+TR T++ +A  HG ++VE+ I  +E
Sbjct: 187 LDYRGYVAECTGANVFFVKDGVIHTPTPDCFLDGLTRRTVIDIARRHGMEVVERHIKPEE 246

Query: 246 VYIADEAFFTGTAAEVTPIREV-DGRKIGAGRRGPVTEKLQKAYFDLVSGKTEA 298
           +    E F TGTAAEVTP+  + D     +G    +T +L  +Y   V  K +A
Sbjct: 247 LSSFTECFITGTAAEVTPVGSIADWHFAPSG----ITHQLMDSYTAEVRPKQQA 296


Lambda     K      H
   0.319    0.134    0.394 

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: 281
Number of extensions: 9
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: 307
Length of database: 297
Length adjustment: 27
Effective length of query: 280
Effective length of database: 270
Effective search space:    75600
Effective search space used:    75600
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_012114576.1 XAUT_RS12870 (branched-chain amino acid aminotransferase)
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.1505101.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.8e-88  281.9   0.0    3.1e-88  281.8   0.0    1.0  1  NCBI__GCF_000017645.1:WP_012114576.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017645.1:WP_012114576.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.8   0.0   3.1e-88   3.1e-88       1     287 [.      16     293 ..      16     297 .] 0.97

  Alignments for each domain:
  == domain 1  score: 281.8 bits;  conditional E-value: 3.1e-88
                             TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 
                                           w+dG +v+++dak+hvl+h+lhYG++vfeG RaY +    +if+  eh eRl  sa++l++ ipy+  e+  +
  NCBI__GCF_000017645.1:WP_012114576.1  16 WYDGVFVPWADAKLHVLSHGLHYGSTVFEGERAYGG----TIFKSAEHSERLRLSAEMLDFTIPYTIGEIDAA 84 
                                           9*********************************99....9******************************** PP

                             TIGR01122  74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146
                                            k +l knnl +aYiRp++++G+e +g+ +  + +++++i +wew+ y++ e  +kG++  +s +rr ++ +i
  NCBI__GCF_000017645.1:WP_012114576.1  85 KKATLEKNNLVDAYIRPVAWRGSEMMGVAA-QKNTIHLAIGVWEWPSYFDPEQRQKGLRLDLSEWRRPDPATI 156
                                           ******************************.6669************************************** PP

                             TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219
                                           p kakaag Y+  ++ k+ a r+G+ +a++Ld  Gyvae +G n+f vkdgv+ tP   +  L+g+tr +vi+
  NCBI__GCF_000017645.1:WP_012114576.1 157 PCKAKAAGLYMICTISKHRAERRGFADALMLDYRGYVAECTGANVFFVKDGVIHTPTP-DCFLDGLTRRTVID 228
                                           *********************************************************9.99************ PP

                             TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegk 287
                                           +a+++g+ev+e++i  eel    e f+tGtaaevtP+ ++ + +        +t++l++++   v+ k
  NCBI__GCF_000017645.1:WP_012114576.1 229 IARRHGMEVVERHIKPEELSSFTECFITGTAAEVTPVGSIADWHFAP---SGITHQLMDSYTAEVRPK 293
                                           ****************************************9998865...469999999998777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (297 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: 14.97
//
[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