Alignments for a candidate for ilvE in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Flavobacterium beibuense F44-8

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_035131886.1 Q763_RS05105 branched-chain amino acid aminotransferase

Query= SwissProt::P39576
         (363 letters)



>NCBI__GCF_000769915.1:WP_035131886.1
          Length = 352

 Score =  286 bits (731), Expect = 8e-82
 Identities = 147/357 (41%), Positives = 217/357 (60%), Gaps = 6/357 (1%)

Query: 1   MTKQTIRVELT-STKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDP 59
           M +  I V L   +K    D   L+FG VFTDHM + DY  +  W  P I PY+P  +DP
Sbjct: 1   MNENDITVNLAPGSKIDSVDFENLTFGNVFTDHMLICDYK-NGVWEKPVIKPYEPFLIDP 59

Query: 60  AAMVYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQ 119
           +A V+HYGQ +FEG+KAY  E+D V LFRP++N ER N+S  RL +P++ E   + GLK+
Sbjct: 60  SAKVFHYGQAIFEGMKAYKDENDDVWLFRPDQNYERFNKSATRLAMPEVPENVFMGGLKK 119

Query: 120 LVAIDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKI 179
           LV I+K W+   +G SLYIRPF+IAT P +  A +  Y+ +IILSP  SYY      VK+
Sbjct: 120 LVEIEKAWVKKGKGNSLYIRPFMIATGPGVLAAPALFYRFMIILSPAKSYYS---GEVKV 176

Query: 180 AVESEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNI 239
            +   F RA  GG G AK AGNY++     ++A E+G+ Q++W D      +EE G+MN+
Sbjct: 177 LIAEHFSRAANGGIGAAKAAGNYSAQFYPTKLANEQGYQQIIWTDDATHTKLEEAGTMNV 236

Query: 240 FFKINGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAF 299
           FF+IN  + T   +  IL+G+TR S+I + K  G+ V  R + + E+++A ++G L+E F
Sbjct: 237 FFRINDTLYTAPTSERILDGVTRKSLIDVAKREGINVEVRPVLVSELVEATENGTLQEVF 296

Query: 300 GTGTAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356
           G GTAAV++P+    ++++   +   E   +A  L + +  IQ     D FGWT ++
Sbjct: 297 GAGTAAVVNPIVGFSYKEKYYELPKQE-NSVALFLKEKLNNIQYKLAEDTFGWTVKI 352


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: 376
Number of extensions: 25
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: 352
Length adjustment: 29
Effective length of query: 334
Effective length of database: 323
Effective search space:   107882
Effective search space used:   107882
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_035131886.1 Q763_RS05105 (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.carbon/TIGR01123.hmm
# target sequence database:        /tmp/gapView.1713412.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.5e-100  320.3   0.0   6.2e-100  320.2   0.0    1.0  1  NCBI__GCF_000769915.1:WP_035131886.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000769915.1:WP_035131886.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.2   0.0  6.2e-100  6.2e-100       1     313 []      44     352 .]      44     352 .] 0.98

  Alignments for each domain:
  == domain 1  score: 320.2 bits;  conditional E-value: 6.2e-100
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W+++ +++++++ +d++++v+hYgq++feG+kay+ ++  ++lfRpd+n +R+++sa rl++Pe++e++f+  
  NCBI__GCF_000769915.1:WP_035131886.1  44 WEKPVIKPYEPFLIDPSAKVFHYGQAIFEGMKAYKDENDDVWLFRPDQNYERFNKSATRLAMPEVPENVFMGG 116
                                           999********************************************************************** PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           lk+lv+++k+wv k k ++sLY+RPf+iat++ +  ++a  y+f++++sP+ +Y+ g++++   ++ +++ Ra
  NCBI__GCF_000769915.1:WP_035131886.1 117 LKKLVEIEKAWVKKGK-GNSLYIRPFMIATGPGVLAAPALFYRFMIILSPAKSYYSGEVKV---LIAEHFSRA 185
                                           ************9777.9***************************************9887...********* PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           a++G+Ga+k +GnY+a + + k a+eqg++++++ d ++++k+ee+G++n+f+ ++d +l t p se iL+gv
  NCBI__GCF_000769915.1:WP_035131886.1 186 ANGGIGAAKAAGNYSAQFYPTKLANEQGYQQIIWTDDATHTKLEEAGTMNVFFRIND-TLYTAPTSERILDGV 257
                                           ********************************************************9.*************** PP

                             TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290
                                           tr+sl+ +ak  g++ve r + + el +a+e+G +  vf++Gtaav+ P+ +++ ++k +e+ ++    v+  
  NCBI__GCF_000769915.1:WP_035131886.1 258 TRKSLIDVAKREGINVEVRPVLVSELVEATENGTLqeVFGAGTAAVVNPIVGFSYKEKYYELPKQ-ENSVALF 329
                                           *********************************9899************************9988.6799*** PP

                             TIGR01123 291 lrdeltdiqyGkledkegWivev 313
                                           l+++l +iqy  +ed++gW+v++
  NCBI__GCF_000769915.1:WP_035131886.1 330 LKEKLNNIQYKLAEDTFGWTVKI 352
                                           ********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (352 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 22.42
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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 2024 update 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

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 catabolism of small carbon sources