Alignments for a candidate for ilvE in Bacillus alkalinitrilicus DSM 22532

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Bacillus alkalinitrilicus DSM 22532

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_078428432.1 BK574_RS09430 branched-chain amino acid aminotransferase

Query= SwissProt::P39576
         (363 letters)



>NCBI__GCF_002019605.1:WP_078428432.1
          Length = 357

 Score =  476 bits (1226), Expect = e-139
 Identities = 228/354 (64%), Positives = 287/354 (81%)

Query: 3   KQTIRVELTSTKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAM 62
           K+ + +  ++ KK +   +QL FG+ FTDHMFVMDY+ DKGW+DPRI PY+ +++DPAAM
Sbjct: 2   KEQLTIIESTNKKNRLADDQLVFGKHFTDHMFVMDYSIDKGWHDPRITPYETITLDPAAM 61

Query: 63  VYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVA 122
           ++HYGQTVFEGLKAY +ED+ +LLFRPEKN ER+N+S++RL IP +DE+ VL  LK+L+ 
Sbjct: 62  IFHYGQTVFEGLKAYRTEDNRILLFRPEKNFERMNRSSERLSIPSVDEKLVLHYLKELLR 121

Query: 123 IDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVE 182
           ID+DW+P  EG SLYIRPFIIATEP L +A S TY+  IILSPVGSYY EGI PVKI VE
Sbjct: 122 IDQDWVPATEGYSLYIRPFIIATEPNLSLAPSSTYQFYIILSPVGSYYSEGIHPVKIFVE 181

Query: 183 SEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFK 242
            E+ RAV+GGTG AKTAGNY+++  AQ+ A EKG+SQVLWLDGIEKKYIEEVGSMN+FFK
Sbjct: 182 EEYTRAVRGGTGTAKTAGNYSAAYIAQEKATEKGYSQVLWLDGIEKKYIEEVGSMNVFFK 241

Query: 243 INGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTG 302
           INGE+VTP LNGSILEGITR S+I LLK W + V E++I++DE+ QA++ G LEE FGTG
Sbjct: 242 INGEVVTPQLNGSILEGITRLSIIELLKDWQIPVVEKRISMDEIFQAYEKGELEEVFGTG 301

Query: 303 TAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356
           TAAV+SPVGEL W D  ++IN+ +TG ++KKLY+T+T IQ G   D + WT EV
Sbjct: 302 TAAVVSPVGELTWNDCHMTINDKQTGNLSKKLYETLTRIQTGKDDDPYSWTVEV 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: 486
Number of extensions: 13
Number of successful extensions: 1
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: 357
Length adjustment: 29
Effective length of query: 334
Effective length of database: 328
Effective search space:   109552
Effective search space used:   109552
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_078428432.1 BK574_RS09430 (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.24607.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-126  406.0   0.0   5.3e-126  405.8   0.0    1.0  1  lcl|NCBI__GCF_002019605.1:WP_078428432.1  BK574_RS09430 branched-chain ami


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002019605.1:WP_078428432.1  BK574_RS09430 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.8   0.0  5.3e-126  5.3e-126       1     313 []      43     355 ..      43     355 .. 0.99

  Alignments for each domain:
  == domain 1  score: 405.8 bits;  conditional E-value: 5.3e-126
                                 TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 
                                               W++++++++++++ld++++++hYgq vfeGlkayRt+d +illfRp++n +R++rs+erl++P ++e+l
  lcl|NCBI__GCF_002019605.1:WP_078428432.1  43 WHDPRITPYETITLDPAAMIFHYGQTVFEGLKAYRTEDNRILLFRPEKNFERMNRSSERLSIPSVDEKL 111
                                               ********************************************************************* PP

                                 TIGR01123  70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138
                                               +l+ lk+l+++d+dwvp ++ + sLY+RPf+iate+nl  +++++y f++++sPvG+Y+ +g++pv+if
  lcl|NCBI__GCF_002019605.1:WP_078428432.1 112 VLHYLKELLRIDQDWVPATE-GYSLYIRPFIIATEPNLSLAPSSTYQFYIILSPVGSYYSEGIHPVKIF 179
                                               *****************777.9*********************************************** PP

                                 TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207
                                               ve+ey+Ra+ +GtG++k++GnY+a+  aq+ka+e+g+++v++ld +ekk+ieevG++n+f+ ++ ge+v
  lcl|NCBI__GCF_002019605.1:WP_078428432.1 180 VEEEYTRAVRGGTGTAKTAGNYSAAYIAQEKATEKGYSQVLWLDGIEKKYIEEVGSMNVFFKIN-GEVV 247
                                               *************************************************************998.8*** PP

                                 TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274
                                               t++l +siLeg+tr s++el kd+++ v e++i++de+ +a e+Ge+  vf++Gtaav++Pvgel+ ++
  lcl|NCBI__GCF_002019605.1:WP_078428432.1 248 TPQLNGSILEGITRLSIIELLKDWQIPVVEKRISMDEIFQAYEKGELeeVFGTGTAAVVSPVGELTWND 316
                                               *********************************************9999******************** PP

                                 TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313
                                                +++++++++G+++kkl+++lt iq+Gk +d++ W+vev
  lcl|NCBI__GCF_002019605.1:WP_078428432.1 317 CHMTINDKQTGNLSKKLYETLTRIQTGKDDDPYSWTVEV 355
                                               *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (357 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: 00:00:00.01
# Mc/sec: 10.74
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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