Alignments for a candidate for ilvE in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Shewanella loihica PV-4

Align Branched-chain-amino-acid transaminase 1; BCAT 1; EC 2.6.1.42 (characterized)
to candidate 5207757 Shew_0278 branched-chain amino acid aminotransferase (RefSeq)

Query= SwissProt::O31461
         (356 letters)



>FitnessBrowser__PV4:5207757
          Length = 363

 Score =  295 bits (756), Expect = 1e-84
 Identities = 152/343 (44%), Positives = 221/343 (64%), Gaps = 5/343 (1%)

Query: 16  KPDPSSLGFGQYFTDYMFVMDYEEGIGWHHPRIAPYAPLTLDPSSSVFHYGQAVFEGLKA 75
           KP+ +++GFG   TD+MF+MDY +G  W  PR+ PY P  + P +   HYGQ++FEG KA
Sbjct: 19  KPE-TNVGFGNLRTDHMFLMDYRDG-EWRDPRVVPYGPFEMAPGAMALHYGQSIFEGAKA 76

Query: 76  YRTDDGRVLLFRPDQNIKRLNRSCERMSMPPLDEELVLEALTQLVELEKDWVPKEKGTSL 135
           +  DDG +  FR ++N +RLN S E + +PP+ E + L  +  L+++++ W P + G  L
Sbjct: 77  FMHDDGEIYTFRLNKNAERLNLSGEVVCIPPVPEAMQLAGINALIDVDRLWFPMQDGACL 136

Query: 136 YIRPFVIATEPSLGVKASRSYTFMIVLSPVGSYYGDDQLKPVRIYVEDEYVRAVNGGVGF 195
           YIRPFV ATE  L V  S+ YTF ++LSP G+YY D   K +R+ + + + RAV+GG G 
Sbjct: 137 YIRPFVFATEDRLSVSPSQQYTFCVMLSPSGAYYADGFDKAIRLLITERFHRAVSGGTGA 196

Query: 196 AKTAGNYAASLQAQRKANELGYDQVLWLDAIEKKYVEEVGSMNIFFVI-NGEAVTPALSG 254
           +K AGNYAASL+A + A E G  QVL+LDA   K +EEVG+MN F V+ +G  + P  + 
Sbjct: 197 SKAAGNYAASLRAGKAAAEYGAAQVLYLDA-NNKQIEEVGAMNHFHVLKDGTIIIPKFTD 255

Query: 255 SILSGVTRASAIELIRSWGIPVREERISIDEVYAASARGELTEVFGTGTAAVVTPVGELN 314
           +IL  +T  S +EL  + G  VR+E + +D+  A    GE+ E  G GTAAVV+PVG   
Sbjct: 256 TILKSITSQSIMELGEALGCEVRQETVMLDQFIADIESGEIVEAGGFGTAAVVSPVGSYI 315

Query: 315 IHGKTVI-VGDGQIGDLSKKLYETITDIQLGKVKGPFNWTVEV 356
                V+ VGDGQ+G+ ++++Y+ +TDIQ GK +GP  W  +V
Sbjct: 316 FEDHRVLTVGDGQVGEHTRRIYQVLTDIQKGKRQGPEGWMQKV 358


Lambda     K      H
   0.317    0.137    0.400 

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: 359
Number of extensions: 27
Number of successful extensions: 5
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: 356
Length of database: 363
Length adjustment: 29
Effective length of query: 327
Effective length of database: 334
Effective search space:   109218
Effective search space used:   109218
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 5207757 Shew_0278 (branched-chain amino acid aminotransferase (RefSeq))
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.18264.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.4e-104  334.1   0.0     4e-104  333.9   0.0    1.0  1  lcl|FitnessBrowser__PV4:5207757  Shew_0278 branched-chain amino a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207757  Shew_0278 branched-chain amino acid aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.9   0.0    4e-104    4e-104       1     313 []      44     358 ..      44     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 333.9 bits;  conditional E-value: 4e-104
                        TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkqlv 78 
                                      W ++++++++++e+++g+++lhYgq +feG ka+ ++dG+i++fR ++na+Rl+ s e + +P ++e++ l  ++ l+
  lcl|FitnessBrowser__PV4:5207757  44 WRDPRVVPYGPFEMAPGAMALHYGQSIFEGAKAFMHDDGEIYTFRLNKNAERLNLSGEVVCIPPVPEAMQLAGINALI 121
                                      99**************************************************************************** PP

                        TIGR01123  79 kadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglap.vsifveteyvRaapkGtGavk 155
                                       +d+ w p ++ +a LY+RPf++ated l v ++++y+f+v++sP GaY+++g ++ ++ ++++ + Ra+ +GtGa k
  lcl|FitnessBrowser__PV4:5207757 122 DVDRLWFPMQD-GACLYIRPFVFATEDRLSVSPSQQYTFCVMLSPSGAYYADGFDKaIRLLITERFHRAVSGGTGASK 198
                                      ********888.*****************************************887589999**************** PP

                        TIGR01123 156 vgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresllelakdlgl 233
                                       +GnYaasl+a k aae g ++v+yld+++k +ieevGa+n f ++kdg++++++ ++ iL+++t +s++el + lg 
  lcl|FitnessBrowser__PV4:5207757 199 AAGNYAASLRAGKAAAEYGAAQVLYLDANNK-QIEEVGAMNHFHVLKDGTIIIPKFTDTILKSITSQSIMELGEALGC 275
                                      ****************************987.9********************************************* PP

                        TIGR01123 234 eveereiaidelkaaveaGei..vfacGtaavitPvgelkiegke.vevkseevGevtkklrdeltdiqyGkledkeg 308
                                      ev+ + + +d++ a  e+Gei  + + Gtaav++Pvg+   e++  ++v +++vGe t+++++ ltdiq Gk +++eg
  lcl|FitnessBrowser__PV4:5207757 276 EVRQETVMLDQFIADIESGEIveAGGFGTAAVVSPVGSYIFEDHRvLTVGDGQVGEHTRRIYQVLTDIQKGKRQGPEG 353
                                      *********************4444568*********988777651578899************************** PP

                        TIGR01123 309 Wivev 313
                                      W+ +v
  lcl|FitnessBrowser__PV4:5207757 354 WMQKV 358
                                      **987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (363 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: 8.87
//
[ok]

This GapMind analysis is from Apr 09 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