Alignments for a candidate for ilvE in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Cupriavidus basilensis 4G11

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate RR42_RS25890 RR42_RS25890 branched-chain amino acid aminotransferase

Query= reanno::Cup4G11:RR42_RS25890
         (363 letters)



>FitnessBrowser__Cup4G11:RR42_RS25890
          Length = 363

 Score =  736 bits (1899), Expect = 0.0
 Identities = 363/363 (100%), Positives = 363/363 (100%)

Query: 1   MTQQTTFSLEPNPNALDAATRDALMRDPAFGRVFTDHMVTITWREGQGWQDAKVTARKPF 60
           MTQQTTFSLEPNPNALDAATRDALMRDPAFGRVFTDHMVTITWREGQGWQDAKVTARKPF
Sbjct: 1   MTQQTTFSLEPNPNALDAATRDALMRDPAFGRVFTDHMVTITWREGQGWQDAKVTARKPF 60

Query: 61  SIDPACSVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESLFLE 120
           SIDPACSVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESLFLE
Sbjct: 61  SIDPACSVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESLFLE 120

Query: 121 AIEQLVRIDQAWVPHGSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKA 180
           AIEQLVRIDQAWVPHGSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKA
Sbjct: 121 AIEQLVRIDQAWVPHGSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKA 180

Query: 181 VSVWVSENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGG 240
           VSVWVSENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGG
Sbjct: 181 VSVWVSENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGG 240

Query: 241 MNIFFVMDDGTLVTPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRL 300
           MNIFFVMDDGTLVTPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRL
Sbjct: 241 MNIFFVMDDGTLVTPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRL 300

Query: 301 AEAFVCGTAATLVAIGEVRSARTRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVHH 360
           AEAFVCGTAATLVAIGEVRSARTRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVHH
Sbjct: 301 AEAFVCGTAATLVAIGEVRSARTRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVHH 360

Query: 361 VAL 363
           VAL
Sbjct: 361 VAL 363


Lambda     K      H
   0.321    0.135    0.415 

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: 647
Number of extensions: 11
Number of successful extensions: 1
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate RR42_RS25890 RR42_RS25890 (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.17176.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.9e-124  399.3   0.0   5.8e-124  399.1   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS25890  RR42_RS25890 branched-chain amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS25890  RR42_RS25890 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.1   0.0  5.8e-124  5.8e-124       1     313 []      49     361 ..      49     361 .. 0.99

  Alignments for each domain:
  == domain 1  score: 399.1 bits;  conditional E-value: 5.8e-124
                                 TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeel 69 
                                               W++a++++ +++++d++ +vlhYgqe+feG+kayR adG ++lfRp +na+R++ sa+r+++P l+e l
  lcl|FitnessBrowser__Cup4G11:RR42_RS25890  49 WQDAKVTARKPFSIDPACSVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESL 117
                                               ********************************************************************* PP

                                 TIGR01123  70 flealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsif 138
                                               flea++qlv++d++wvp  ++  sLYlRPf++a e  lG+k+a+e++f+v+a+PvG+Yfkgg + vs++
  lcl|FitnessBrowser__Cup4G11:RR42_RS25890 118 FLEAIEQLVRIDQAWVP--HGSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKAVSVW 184
                                               *****************..5579********************************************** PP

                                 TIGR01123 139 veteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelv 207
                                               v+++y+Raap+GtG +k+gGnYa sl aq++a+++g+d+vv+ld++e++ +ee+G++nif++++dg+lv
  lcl|FitnessBrowser__Cup4G11:RR42_RS25890 185 VSENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGGMNIFFVMDDGTLV 253
                                               ********************************************************************* PP

                                 TIGR01123 208 ttplsesiLegvtresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkieg 274
                                               t+pls+siL+g+tr+s++ela+++g+ veer+ +  e++a +++G +  +f cGtaa +  +ge++   
  lcl|FitnessBrowser__Cup4G11:RR42_RS25890 254 TPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRLaeAFVCGTAATLVAIGEVRSAR 322
                                               *********************************************98889******************* PP

                                 TIGR01123 275 kevevkseevGevtkklrdeltdiqyGkledkegWivev 313
                                               + + + ++  G+  k lrd l++iq+ +++++ gW+ +v
  lcl|FitnessBrowser__Cup4G11:RR42_RS25890 323 TRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVHHV 361
                                               ***********************************9765 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 12.80
//
[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