Alignments for a candidate for ilvE in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Shewanella amazonensis SB2B

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate 6939205 Sama_3299 branched-chain amino acid aminotransferase (RefSeq)

Query= SwissProt::P39576
         (363 letters)



>FitnessBrowser__SB2B:6939205
          Length = 361

 Score =  280 bits (716), Expect = 4e-80
 Identities = 144/344 (41%), Positives = 214/344 (62%), Gaps = 4/344 (1%)

Query: 15  KPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFEGL 74
           +P      + FG++ TDHMF+MDY  D  W + RI+PY P  M P AM  HYGQ++FEG 
Sbjct: 16  EPFEPQGDVGFGKLRTDHMFMMDYK-DGQWQNARILPYGPFEMMPGAMALHYGQSIFEGA 74

Query: 75  KAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAEGT 134
           KA++ +D  +  FR +KN +RLN+S D +CIP I E   LE +  L+ +D+ W P  EG 
Sbjct: 75  KAFMHDDGEIYTFRLDKNAQRLNRSADIVCIPNIPEAVQLEAINALIDVDRLWFPRQEGA 134

Query: 135 SLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIAVESEFVRAVKGGTG 194
            LYIRPF+ ATE  L V+ ++ Y   ++LSP G+YY + +  +++ + ++F RAV GGTG
Sbjct: 135 CLYIRPFVFATEDRLSVSPANQYTFCVVLSPSGAYYGKNLNAIRLLITTQFHRAVSGGTG 194

Query: 195 NAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIF-FKINGEIVTPMLN 253
            +K AGNYA+SL+A + A E G +QVL+LD    +YIEEVG+MN F  + +G ++ P   
Sbjct: 195 ASKAAGNYAASLRAGKAAAEHGAAQVLYLDS-TNQYIEEVGAMNHFHIRKDGTLIIPEFT 253

Query: 254 GSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPVGEL 313
            +IL  IT  S++AL +  G +V +  + + + I   + G + EA G GTAAV+SPVG  
Sbjct: 254 DTILRSITSESILALGEELGCEVRQETVKLSDFIADIEAGEIVEAGGFGTAAVVSPVGSY 313

Query: 314 IWQD-ETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356
           I++D   +++ +G+ GE    +Y   T +QKG      GW  +V
Sbjct: 314 IFEDGRIVTVGDGKVGERISHIYKVYTEMQKGLRPAPEGWVRKV 357


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: 334
Number of extensions: 17
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: 361
Length adjustment: 29
Effective length of query: 334
Effective length of database: 332
Effective search space:   110888
Effective search space used:   110888
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 6939205 Sama_3299 (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.17316.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.8e-104  334.4   0.0   3.2e-104  334.2   0.0    1.0  1  lcl|FitnessBrowser__SB2B:6939205  Sama_3299 branched-chain amino a


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6939205  Sama_3299 branched-chain amino acid aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.2   0.0  3.2e-104  3.2e-104       1     313 []      44     357 ..      44     357 .. 0.97

  Alignments for each domain:
  == domain 1  score: 334.2 bits;  conditional E-value: 3.2e-104
                         TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkql 77 
                                       W++a++ +++++e+ +g+++lhYgq +feG ka+ ++dG+i++fR d+na+Rl+rsa+++ +P+++e++ lea++ l
  lcl|FitnessBrowser__SB2B:6939205  44 WQNARILPYGPFEMMPGAMALHYGQSIFEGAKAFMHDDGEIYTFRLDKNAQRLNRSADIVCIPNIPEAVQLEAINAL 120
                                       ***************************************************************************** PP

                         TIGR01123  78 vkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkGtGav 154
                                       + +d+ w p ++ +a LY+RPf++ated l v +a++y+f+v++sP GaY+ ++l+ ++ +++t++ Ra+ +GtGa 
  lcl|FitnessBrowser__SB2B:6939205 121 IDVDRLWFPRQE-GACLYIRPFVFATEDRLSVSPANQYTFCVVLSPSGAYYGKNLNAIRLLITTQFHRAVSGGTGAS 196
                                       *********888.**************************************************************** PP

                         TIGR01123 155 kvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresllelakdl 231
                                       k +GnYaasl+a k aae+g ++v+yld++++ +ieevGa+n f i kdg+l++++ ++ iL ++t es+l l ++l
  lcl|FitnessBrowser__SB2B:6939205 197 KAAGNYAASLRAGKAAAEHGAAQVLYLDSTNQ-YIEEVGAMNHFHIRKDGTLIIPEFTDTILRSITSESILALGEEL 272
                                       ****************************9887.******************************************** PP

                         TIGR01123 232 gleveereiaidelkaaveaGei..vfacGtaavitPvge.lkiegkevevkseevGevtkklrdeltdiqyGkled 305
                                       g ev+ + +++ ++ a  eaGei  + + Gtaav++Pvg+ +  +g+ v+v +++vGe+  ++++  t++q G   +
  lcl|FitnessBrowser__SB2B:6939205 273 GCEVRQETVKLSDFIADIEAGEIveAGGFGTAAVVSPVGSyIFEDGRIVTVGDGKVGERISHIYKVYTEMQKGLRPA 349
                                       ***********************4444568********9835566788999999*********************** PP

                         TIGR01123 306 kegWivev 313
                                       +egW+ +v
  lcl|FitnessBrowser__SB2B:6939205 350 PEGWVRKV 357
                                       ****9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (361 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: 00:00:00.00
# Mc/sec: 11.94
//
[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