Alignments for a candidate for ilvE in Desulfuromusa kysingii DSM 7343

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Desulfuromusa kysingii DSM 7343

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate WP_092349638.1 BLU87_RS13210 branched-chain amino acid aminotransferase

Query= SwissProt::P39576
         (363 letters)



>NCBI__GCF_900107645.1:WP_092349638.1
          Length = 354

 Score =  373 bits (957), Expect = e-108
 Identities = 173/347 (49%), Positives = 248/347 (71%)

Query: 8   VELTSTKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYG 67
           + LT+ K+   D ++L+FGR ++D M +M+Y + KGW+  RI PY PLS+DPAAMV+HY 
Sbjct: 6   IPLTAPKEKYKDEDKLAFGRQYSDRMLIMEYDSGKGWHSARIQPYGPLSLDPAAMVFHYS 65

Query: 68  QTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDW 127
           Q +FEG+K +   D  + +FRP  N+ R N+S +R+C+P++DE+  L+ + +L+ ++ DW
Sbjct: 66  QEIFEGMKVFRRADGTLSMFRPADNITRFNRSAERMCMPKVDEKFFLDAILKLIRMEADW 125

Query: 128 IPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVR 187
           +P++EGTSLYIRP +IATEP LGV  ++ Y   +ILSPVG YYK GI PVKI +   +VR
Sbjct: 126 VPHSEGTSLYIRPTMIATEPMLGVRPANQYLCYVILSPVGPYYKGGIAPVKIWISDFYVR 185

Query: 188 AVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKINGEI 247
           A +GGTG AKT GNYA+SL A + A EKG+ QVLWLD  EK+++EEVGSMN+ F  +G+I
Sbjct: 186 ATEGGTGEAKTGGNYAASLYAAKEAAEKGYDQVLWLDAKEKRFVEEVGSMNMLFLYDGKI 245

Query: 248 VTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVI 307
           VT  L+G++L+GITR S + LLK  G +V ER +++DE+I+   +G L+EAFGTGTA VI
Sbjct: 246 VTSPLHGTVLDGITRRSALTLLKEMGYEVEERALSVDEIIEGANNGRLQEAFGTGTAVVI 305

Query: 308 SPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTT 354
           SPVG   ++D  + + +G+ G++  +LY  +T IQ G   D   W T
Sbjct: 306 SPVGSFCYKDTCVQLGDGQPGKLTMELYHKLTAIQYGKEPDNHNWVT 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: 403
Number of extensions: 17
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: 354
Length adjustment: 29
Effective length of query: 334
Effective length of database: 325
Effective search space:   108550
Effective search space used:   108550
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_092349638.1 BLU87_RS13210 (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.29598.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.5e-126  405.5   0.0   7.4e-126  405.3   0.0    1.0  1  lcl|NCBI__GCF_900107645.1:WP_092349638.1  BLU87_RS13210 branched-chain ami


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900107645.1:WP_092349638.1  BLU87_RS13210 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.3   0.0  7.4e-126  7.4e-126       1     311 [.      42     352 ..      42     354 .] 0.99

  Alignments for each domain:
  == domain 1  score: 405.3 bits;  conditional E-value: 7.4e-126
                                 TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 
                                               W++a+++++++l+ld++++v+hY+qe+feG+k +R adG + +fRp +n+ R++rsaer+ +P+++e+ 
  lcl|NCBI__GCF_900107645.1:WP_092349638.1  42 WHSARIQPYGPLSLDPAAMVFHYSQEIFEGMKVFRRADGTLSMFRPADNITRFNRSAERMCMPKVDEKF 110
                                               ********************************************************************* PP

                                 TIGR01123  70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138
                                               fl+a+ +l+++++dwvp+ + ++sLY+RP++iate+ lGv++a++yl +v++sPvG+Y+kgg+apv+i+
  lcl|NCBI__GCF_900107645.1:WP_092349638.1 111 FLDAILKLIRMEADWVPHSE-GTSLYIRPTMIATEPMLGVRPANQYLCYVILSPVGPYYKGGIAPVKIW 178
                                               *****************888.************************************************ PP

                                 TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207
                                               +++ yvRa+++GtG +k+gGnYaasl a k+aae+g+d+v++ld++ek+ +eevG++n++++++ g++v
  lcl|NCBI__GCF_900107645.1:WP_092349638.1 179 ISDFYVRATEGGTGEAKTGGNYAASLYAAKEAAEKGYDQVLWLDAKEKRFVEEVGSMNMLFLYD-GKIV 246
                                               *************************************************************987.9*** PP

                                 TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274
                                               t+pl + +L+g+tr+s+l+l k++g+eveer +++de+ + +++G +  +f++Gta vi+Pvg++  ++
  lcl|NCBI__GCF_900107645.1:WP_092349638.1 247 TSPLHGTVLDGITRRSALTLLKEMGYEVEERALSVDEIIEGANNGRLqeAFGTGTAVVISPVGSFCYKD 315
                                               *********************************************9899******************** PP

                                 TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWiv 311
                                               + v++ ++++G++t++l+++lt iqyGk  d+++W++
  lcl|NCBI__GCF_900107645.1:WP_092349638.1 316 TCVQLGDGQPGKLTMELYHKLTAIQYGKEPDNHNWVT 352
                                               ***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (354 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.23
//
[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