Alignments for a candidate for ilvE in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Pedobacter sp. GW460-11-11-14-LB5

Align Branched-chain-amino-acid aminotransferase 2; BCAT 2; Vegetative protein 85; VEG85; EC 2.6.1.42 (characterized)
to candidate CA265_RS22650 CA265_RS22650 branched chain amino acid aminotransferase

Query= SwissProt::P39576
         (363 letters)



>FitnessBrowser__Pedo557:CA265_RS22650
          Length = 354

 Score =  309 bits (791), Expect = 8e-89
 Identities = 149/352 (42%), Positives = 228/352 (64%), Gaps = 7/352 (1%)

Query: 4   QTIRVELTS---TKKPKPDPNQLSFGRVFTDHMFVMDYAADKGWYDPRIIPYQPLSMDPA 60
           +T+ +++T    T+    D +QL FG+VFTDHMF  DY  D  W + +I+PY P+ M PA
Sbjct: 3   ETLDIKITKADQTRLTVTDFSQLPFGKVFTDHMFTADYE-DGEWKNLQILPYGPIPMSPA 61

Query: 61  AMVYHYGQTVFEGLKAYVSEDDHVLLFRPEKNMERLNQSNDRLCIPQIDEEQVLEGLKQL 120
               HYGQ +FEGLKAY   D  + +FR +KN ER N+S  R+ +P I EE  ++GL  L
Sbjct: 62  ISALHYGQAIFEGLKAYRQPDGKISVFRADKNFERFNKSAARMSMPGIPEEIFMQGLAAL 121

Query: 121 VAIDKDWIPNAEGTSLYIRPFIIATEPFLGVAASHTYKLLIILSPVGSYYKEGIKPVKIA 180
           + +D+ W+PN E  +LYIRP + A +P+LGV AS TYK  ++ +P G YY   +K   + 
Sbjct: 122 INVDEKWVPNQEDYALYIRPVMFAMDPYLGVKASDTYKFALLTTPTGPYYSSALK---VK 178

Query: 181 VESEFVRAVKGGTGNAKTAGNYASSLKAQQVAEEKGFSQVLWLDGIEKKYIEEVGSMNIF 240
           +E+EF RA +GG G AKTAGNYA SL   + A+++G+ Q++W D +  ++IEE G+ N+ 
Sbjct: 179 IETEFTRADEGGVGFAKTAGNYARSLYPFEQAKKEGYDQLIWTDSVTHEFIEEAGTANLL 238

Query: 241 FKINGEIVTPMLNGSILEGITRNSVIALLKHWGLQVSERKIAIDEVIQAHKDGILEEAFG 300
           F ING++VTP +  ++L+G+TR+++I L K  G++V ER++++ EVI+  ++G L EAF 
Sbjct: 239 FVINGKLVTPSVRSTVLDGVTRDTIIKLAKDAGVEVEERRVSVKEVIEGIENGSLTEAFA 298

Query: 301 TGTAAVISPVGELIWQDETLSINNGETGEIAKKLYDTITGIQKGAVADEFGW 352
            GTAA ++ VGE+ +  +   + +  T  I+  +   +  I+ G   DEFGW
Sbjct: 299 AGTAATVTHVGEMGYNGQIYKLTDPSTRHISNGIAKKLNDIRYGLAPDEFGW 350


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: 388
Number of extensions: 18
Number of successful extensions: 3
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 CA265_RS22650 CA265_RS22650 (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.carbon/TIGR01123.hmm
# target sequence database:        /tmp/gapView.1984.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   7.1e-103  329.8   0.0     8e-103  329.6   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS22650  CA265_RS22650 branched chain ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS22650  CA265_RS22650 branched chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.6   0.0    8e-103    8e-103       1     309 [.      45     350 ..      45     354 .] 0.99

  Alignments for each domain:
  == domain 1  score: 329.6 bits;  conditional E-value: 8e-103
                                  TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleee 68 
                                                W++ ++ +++++ ++++ ++lhYgq++feGlkayR+ dGki +fR+d+n +R+++sa r+++P ++ee
  lcl|FitnessBrowser__Pedo557:CA265_RS22650  45 WKNLQILPYGPIPMSPAISALHYGQAIFEGLKAYRQPDGKISVFRADKNFERFNKSAARMSMPGIPEE 112
                                                999***************************************************************** PP

                                  TIGR01123  69 lflealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvs 136
                                                +f++ l+ l+++d++wvp+++ + +LY+RP+++a++++lGvka+ +y f +l++P G+Y+ + l++  
  lcl|FitnessBrowser__Pedo557:CA265_RS22650 113 IFMQGLAALINVDEKWVPNQE-DYALYIRPVMFAMDPYLGVKASDTYKFALLTTPTGPYYSSALKV-- 177
                                                ******************888.9**************************************99988.. PP

                                  TIGR01123 137 ifveteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdg 204
                                                  +ete++Ra ++G+G++k++GnYa sl + ++a+++g+d+ ++ d+v+++ iee+G+an++++++ g
  lcl|FitnessBrowser__Pedo557:CA265_RS22650 178 -KIETEFTRADEGGVGFAKTAGNYARSLYPFEQAKKEGYDQLIWTDSVTHEFIEEAGTANLLFVIN-G 243
                                                .79**************************************************************9.8 PP

                                  TIGR01123 205 elvttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgel 270
                                                +lvt++    +L+gvtr+ +++lakd+g+eveer++++ e+ +  e+G++  +fa+Gtaa +t vge+
  lcl|FitnessBrowser__Pedo557:CA265_RS22650 244 KLVTPSVRSTVLDGVTRDTIIKLAKDAGVEVEERRVSVKEVIEGIENGSLteAFAAGTAATVTHVGEM 311
                                                ************************************************9999**************** PP

                                  TIGR01123 271 kiegkevevkseevGevtkklrdeltdiqyGkledkegW 309
                                                  +g+ +++++  + ++++ + ++l di yG + d++gW
  lcl|FitnessBrowser__Pedo557:CA265_RS22650 312 GYNGQIYKLTDPSTRHISNGIAKKLNDIRYGLAPDEFGW 350
                                                *************************************** 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.66
//
[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:

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

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 catabolism of small carbon sources