GapMind for catabolism of small carbon sources

 

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.carbon/TIGR01123.hmm
# target sequence database:        /tmp/gapView.485925.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 25.76
//
[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