GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Flavobacterium glycines Gm-149

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_066324126.1 BLR17_RS08000 branched-chain amino acid aminotransferase

Query= SwissProt::P39576
         (363 letters)



>NCBI__GCF_900100165.1:WP_066324126.1
          Length = 355

 Score =  295 bits (754), Expect = 2e-84
 Identities = 151/358 (42%), Positives = 221/358 (61%), Gaps = 8/358 (2%)

Query: 2   TKQTIRVELT---STKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMD 58
           T Q  ++E+    +TK  + D + L+FG VFTDH+F  DY  D  W +P I PY P  MD
Sbjct: 3   TTQANKIEIIKAPNTKINEVDFDNLNFGSVFTDHLFECDYK-DGEWQNPTIKPYAPFMMD 61

Query: 59  PAAMVYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLK 118
           P++ V+HYGQ +FEG+KAY  +++ + LFRP++N++R N S  R+ +P+I E   +EGL 
Sbjct: 62  PSSRVFHYGQAIFEGMKAYKDDNNDIWLFRPDENVKRFNSSAVRMAMPEIPESLFMEGLN 121

Query: 119 QLVAIDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVK 178
           QL+ +D+ WI    G SLYIRPF+IAT   +    S+ YK +IILSP  +YY      VK
Sbjct: 122 QLLKLDEAWIKKGLGNSLYIRPFMIATGYGVVANPSNEYKFMIILSPAKAYYS---GEVK 178

Query: 179 IAVESEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMN 238
           + +   F RA  GG G AKTAGNYA       +A + GF Q++W D      +EE G+MN
Sbjct: 179 VIIAEHFSRAANGGIGAAKTAGNYAGQFYPTSLANKDGFQQIIWTDDATHTKLEEAGTMN 238

Query: 239 IFFKINGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEA 298
           +FF+IN  +VT   +  IL+G+TR S+IA+ K  G+ + ER + + E+I+  K+G L+E 
Sbjct: 239 VFFRINDTLVTAPTSERILDGVTRKSIIAMAKKEGIAIEERPVLVSELIEGIKNGSLKEI 298

Query: 299 FGTGTAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356
           FG GTAAV+SP+    +++E   +   E   +A +L + +T IQ     D FGWT ++
Sbjct: 299 FGAGTAAVVSPIKGFAYKNEYFELPEIE-NSVALQLKEKLTNIQHKLAEDPFGWTVKI 355


Lambda     K      H
   0.316    0.135    0.390 

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: 27
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: 363
Length of database: 355
Length adjustment: 29
Effective length of query: 334
Effective length of database: 326
Effective search space:   108884
Effective search space used:   108884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_066324126.1 BLR17_RS08000 (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.255206.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-101  325.9   0.0   1.3e-101  325.7   0.0    1.0  1  NCBI__GCF_900100165.1:WP_066324126.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066324126.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.7   0.0  1.3e-101  1.3e-101       1     313 []      47     355 .]      47     355 .] 0.98

  Alignments for each domain:
  == domain 1  score: 325.7 bits;  conditional E-value: 1.3e-101
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W++++++++a++ +d++s v+hYgq++feG+kay+ ++  i+lfRpd+n+kR+++sa r+++Pe++e lf+e 
  NCBI__GCF_900100165.1:WP_066324126.1  47 WQNPTIKPYAPFMMDPSSRVFHYGQAIFEGMKAYKDDNNDIWLFRPDENVKRFNSSAVRMAMPEIPESLFMEG 119
                                           ************************************************************************* PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           l+ql+k+d++w+  ++ ++sLY+RPf+iat+  +  ++++ey f++++sP+ aY+ g++++    + +++ Ra
  NCBI__GCF_900100165.1:WP_066324126.1 120 LNQLLKLDEAWIK-KGLGNSLYIRPFMIATGYGVVANPSNEYKFMIILSPAKAYYSGEVKV---IIAEHFSRA 188
                                           ************9.566****************************************9888...99******* PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           a++G+Ga+k++GnYa  + + + a+++g++++++ d ++++k+ee+G++n+f+ ++d +lvt p se iL+gv
  NCBI__GCF_900100165.1:WP_066324126.1 189 ANGGIGAAKTAGNYAGQFYPTSLANKDGFQQIIWTDDATHTKLEEAGTMNVFFRIND-TLVTAPTSERILDGV 260
                                           ********************************************************9.*************** PP

                             TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290
                                           tr+s++ +ak+ g+++eer + + el +  ++G++  +f++Gtaav++P+++++ +++ +e+ +     v+ +
  NCBI__GCF_900100165.1:WP_066324126.1 261 TRKSIIAMAKKEGIAIEERPVLVSELIEGIKNGSLkeIFGAGTAAVVSPIKGFAYKNEYFELPEI-ENSVALQ 332
                                           *********************************9999**********************999887.678**** PP

                             TIGR01123 291 lrdeltdiqyGkledkegWivev 313
                                           l+++lt+iq+  +ed++gW+v++
  NCBI__GCF_900100165.1:WP_066324126.1 333 LKEKLTNIQHKLAEDPFGWTVKI 355
                                           ********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (355 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: 29.90
//
[ok]

This GapMind analysis is from Jul 26 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