GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Shewanella sp. ANA-3

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate 7026697 Shewana3_3830 branched-chain amino acid aminotransferase (RefSeq)

Query= SwissProt::P39576
         (363 letters)



>FitnessBrowser__ANA3:7026697
          Length = 363

 Score =  287 bits (734), Expect = 4e-82
 Identities = 152/347 (43%), Positives = 218/347 (62%), Gaps = 6/347 (1%)

Query: 13  TKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPAAMVYHYGQTVFE 72
           T++ KP+ N + FG + TDHMF+MDY  D  W DPRI+PY P  M P AM  HYGQ++FE
Sbjct: 15  TEQFKPEGN-VGFGSLRTDHMFLMDYR-DGEWRDPRIVPYGPFEMAPGAMALHYGQSIFE 72

Query: 73  GLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQLVAIDKDWIPNAE 132
           G KA++ ED  +  FR  KN ER+N+S D +CIP IDE+  ++ +  L+ +D+ W P  E
Sbjct: 73  GAKAFMHEDGEIYTFRINKNAERMNRSADIVCIPNIDEQMQIDAINALIDVDRLWFPMQE 132

Query: 133 GTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGI-KPVKIAVESEFVRAVKG 191
           G  LYIRPFI ATE  L V+ S  Y   ++LSP G+YY  G+ K +++ +   + RAV G
Sbjct: 133 GACLYIRPFIFATEDRLSVSPSTRYTFCVVLSPSGAYYAAGVNKGIRLLISKTYHRAVSG 192

Query: 192 GTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIFFKI-NGEIVTP 250
           GTG +K AGNYA+SL+A + A + G SQVL+LD    + IEE G+MN F  + +G ++ P
Sbjct: 193 GTGASKAAGNYAASLRAGKAAAQFGASQVLYLDA-NNQQIEEAGAMNHFHILKDGTVIIP 251

Query: 251 MLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFGTGTAAVISPV 310
               +IL+ IT  S++ L +  G +V +  + +D+ I   + G + EA G GTAAV+S V
Sbjct: 252 TFTDTILKSITSQSIMELGELLGCEVRQETVMLDKFIADIESGEIIEAGGFGTAAVVSAV 311

Query: 311 GELIWQD-ETLSINNGETGEIAKKLYDTITGIQKGAVADEFGWTTEV 356
           G  I++D   +++ NGE GE  +++Y   T IQKG +    GW   V
Sbjct: 312 GSYIFEDGRVVTVGNGEVGEHIQRIYKLYTDIQKGHIQGPDGWVKRV 358


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: 361
Number of extensions: 16
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: 363
Length adjustment: 29
Effective length of query: 334
Effective length of database: 334
Effective search space:   111556
Effective search space used:   111556
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 7026697 Shewana3_3830 (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.carbon/TIGR01123.hmm
# target sequence database:        /tmp/gapView.15062.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.2e-101  324.9   0.1   2.6e-101  324.7   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7026697  Shewana3_3830 branched-chain ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7026697  Shewana3_3830 branched-chain amino acid aminotransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.7   0.1  2.6e-101  2.6e-101       1     313 []      44     358 ..      44     358 .. 0.96

  Alignments for each domain:
  == domain 1  score: 324.7 bits;  conditional E-value: 2.6e-101
                         TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealkql 77 
                                       W ++++++++++e+++g+++lhYgq +feG ka+ ++dG+i++fR ++na+R++rsa+++ +P+++e++ ++a++ l
  lcl|FitnessBrowser__ANA3:7026697  44 WRDPRIVPYGPFEMAPGAMALHYGQSIFEGAKAFMHEDGEIYTFRINKNAERMNRSADIVCIPNIDEQMQIDAINAL 120
                                       99*************************************************************************** PP

                         TIGR01123  78 vkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglap.vsifveteyvRaapkGtGa 153
                                       + +d+ w p ++ +a LY+RPf++ated l v ++++y+f+v++sP GaY++ g+++ ++ ++++ y Ra+ +GtGa
  lcl|FitnessBrowser__ANA3:7026697 121 IDVDRLWFPMQE-GACLYIRPFIFATEDRLSVSPSTRYTFCVVLSPSGAYYAAGVNKgIRLLISKTYHRAVSGGTGA 196
                                       *********777.*****************************************99978999*************** PP

                         TIGR01123 154 vkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresllelakd 230
                                        k +GnYaasl+a k aa+ g ++v+yld++++ +iee+Ga+n f i+kdg+++++  ++ iL+++t +s++el + 
  lcl|FitnessBrowser__ANA3:7026697 197 SKAAGNYAASLRAGKAAAQFGASQVLYLDANNQ-QIEEAGAMNHFHILKDGTVIIPTFTDTILKSITSQSIMELGEL 272
                                       ******************************998.9****************************************** PP

                         TIGR01123 231 lgleveereiaidelkaaveaGei..vfacGtaavitPvge.lkiegkevevkseevGevtkklrdeltdiqyGkle 304
                                       lg ev+ + + +d++ a  e+Gei  + + Gtaav++ vg+ +  +g+ v+v ++evGe  +++++  tdiq G+++
  lcl|FitnessBrowser__ANA3:7026697 273 LGCEVRQETVMLDKFIADIESGEIieAGGFGTAAVVSAVGSyIFEDGRVVTVGNGEVGEHIQRIYKLYTDIQKGHIQ 349
                                       ***********************96566679********9835566788899999********************** PP

                         TIGR01123 305 dkegWivev 313
                                       ++ gW+ +v
  lcl|FitnessBrowser__ANA3:7026697 350 GPDGWVKRV 358
                                       *****9876 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.58
//
[ok]

This GapMind analysis is from Sep 17 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:

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:

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:

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:

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