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 (EC 2.6.1.42) (characterized)
to candidate CA265_RS15785 CA265_RS15785 branched-chain-amino-acid transaminase

Query= reanno::psRCH2:GFF445
         (307 letters)



>FitnessBrowser__Pedo557:CA265_RS15785
          Length = 296

 Score =  196 bits (497), Expect = 7e-55
 Identities = 113/297 (38%), Positives = 168/297 (56%), Gaps = 6/297 (2%)

Query: 1   MSMADRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTD 60
           M   + + +I+ DG+  +  +++T +   +LHYG   FEG+RAY T +G  IF+  AH D
Sbjct: 1   MKYYNSNTIIYLDGQFEKAVNSSTDLYGQSLHYGYAAFEGIRAYKTHNGNRIFKAAAHFD 60

Query: 61  RLFDSAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHV 120
           RL  S  + N+P P+ K+E+  AT   ++ N L+ AYIRP+VF          SG  V +
Sbjct: 61  RLERSCQLANIPFPWDKQELIAATYKLLQLNKLKDAYIRPLVFCHPNMKLNEPSG--VSI 118

Query: 121 IVAAWHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGA 180
           ++ AW W AY G++ L+L +    S + R +       AK +G Y+NS+LA   A   G 
Sbjct: 119 LICAWEWDAYSGNKLLKLTV----SDYERPNPKSIPMEAKLSGNYVNSILATTAANIKGY 174

Query: 181 DEALMLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKR 240
           DEAL+LD  G+VAE SG NIF+ KDG ++TP +   L GITR TV  L     ++ +EK+
Sbjct: 175 DEALLLDMHGFVAEASGANIFLEKDGKLFTPSLGNILPGITRATVKELCTVLDIECIEKK 234

Query: 241 ITRDEVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTGKTD 297
           +T +++  AD AF  GTA E+  I  +D        R  I   +Q+AY +LV  K +
Sbjct: 235 LTIEDLKNADSAFLCGTATEIAGIASIDDIVYRPIWRESIGYTIQRAYKNLVLEKVN 291


Lambda     K      H
   0.319    0.135    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: 205
Number of extensions: 5
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: 307
Length of database: 296
Length adjustment: 27
Effective length of query: 280
Effective length of database: 269
Effective search space:    75320
Effective search space used:    75320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate CA265_RS15785 CA265_RS15785 (branched-chain-amino-acid transaminase)
to HMM TIGR01122 (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/TIGR01122.hmm
# target sequence database:        /tmp/gapView.2526.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01122  [M=298]
Accession:   TIGR01122
Description: ilvE_I: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
    7.2e-79  251.0   0.0    8.3e-79  250.8   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS15785  CA265_RS15785 branched-chain-ami


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15785  CA265_RS15785 branched-chain-amino-acid transaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.8   0.0   8.3e-79   8.3e-79       1     288 [.      11     290 ..      11     295 .. 0.97

  Alignments for each domain:
  == domain 1  score: 250.8 bits;  conditional E-value: 8.3e-79
                                  TIGR01122   1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyske 68 
                                                +ldG++ +  ++ + +  ++lhYG + feGiRaY+t++g +if++  h++Rl  s +  +++ p+ k+
  lcl|FitnessBrowser__Pedo557:CA265_RS15785  11 YLDGQFEKAVNSSTDLYGQSLHYGYAAFEGIRAYKTHNGNRIFKAAAHFDRLERSCQLANIPFPWDKQ 78 
                                                89****************************************************************** PP

                                  TIGR01122  69 elvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvs 136
                                                el+ +t ++l+ n+lk+aYiRplv+  + +++l+++++  v+++i awew ay g+    k +k +vs
  lcl|FitnessBrowser__Pedo557:CA265_RS15785  79 ELIAATYKLLQLNKLKDAYIRPLVF-CHPNMKLNEPSG--VSILICAWEWDAYSGN----KLLKLTVS 139
                                                *************************.7899****9666..99*************6....7899**** PP

                                  TIGR01122 137 sfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpv 204
                                                 ++r +++sip +ak +gnY+ns+la + a+ +Gydea+lLd +G+vae sG nif+ kdg+l+tP++
  lcl|FitnessBrowser__Pedo557:CA265_RS15785 140 DYERPNPKSIPMEAKLSGNYVNSILATTAANIKGYDEALLLDMHGFVAEASGANIFLEKDGKLFTPSL 207
                                                ******************************************************************** PP

                                  TIGR01122 205 sesiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpv 272
                                                  +iL gitr +v +l + l ie  e++++ e+l  aD +fl Gta e++ i ++D++      r ++
  lcl|FitnessBrowser__Pedo557:CA265_RS15785 208 -GNILPGITRATVKELCTVLDIECIEKKLTIEDLKNADSAFLCGTATEIAGIASIDDIVYRPIWRESI 274
                                                .66***************************************************************** PP

                                  TIGR01122 273 tkklqeaffdlvegkt 288
                                                  ++q a+++lv +k+
  lcl|FitnessBrowser__Pedo557:CA265_RS15785 275 GYTIQRAYKNLVLEKV 290
                                                ***********98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (296 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: 7.92
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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, or view the source code.

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