Alignments for a candidate for ilvE in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Sphingomonas koreensis DSMZ 15582

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate Ga0059261_3811 Ga0059261_3811 branched-chain amino acid aminotransferase, group II

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



>FitnessBrowser__Korea:Ga0059261_3811
          Length = 362

 Score =  462 bits (1188), Expect = e-135
 Identities = 220/354 (62%), Positives = 266/354 (75%), Gaps = 1/354 (0%)

Query: 7   FSLEPNPNALDAATRDALMRDPAFGRVFTDHMVTITWREGQGWQDAKVTARKPFSIDPAC 66
           F  E NPN + A+ R AL+ +P FG++FTDHM  + W + +GW DAKV AR P S+DPA 
Sbjct: 6   FEFEANPNPVPASERAALLENPGFGKLFTDHMAMVRWSDTKGWHDAKVVARGPLSLDPAT 65

Query: 67  SVLHYGQEIFEGMKAYRGADGAVTLFRPLENARRFQASAKRMAMPALPESLFLEAIEQLV 126
           +VLHY QEIFEG+KAYR  D    LFRPLENARRF+ SA+RMAMP LP+ LFL +IE LV
Sbjct: 66  AVLHYAQEIFEGLKAYRTGDEGTALFRPLENARRFRESAQRMAMPELPDDLFLGSIEALV 125

Query: 127 RIDQAWVPH-GSGSLYLRPFMFANEVFLGIKPASEFIFCVIACPVGPYFKGGDKAVSVWV 185
           + D+ W+P    GSLYLRPFMFA+EVFLG+KPASE+++ VIA P G YFKGG  AV++WV
Sbjct: 126 KADREWIPQIEGGSLYLRPFMFASEVFLGVKPASEYLYLVIASPAGAYFKGGAPAVTIWV 185

Query: 186 SENYTRAAPGGTGEAKCGGNYAGSLVAQNEATANGCDQVVFLDAAEHRWVEELGGMNIFF 245
           S++YTRAAPGGTG AKCGGNYA SLVAQ EA   GCDQVVFLDA E RWVEELGGMN+FF
Sbjct: 186 SDHYTRAAPGGTGAAKCGGNYASSLVAQAEAIREGCDQVVFLDAVERRWVEELGGMNLFF 245

Query: 246 VMDDGTLVTPPLSGSILPGITRASVIELAREMGMVVEERRYSYPEWEADAKSGRLAEAFV 305
           V DDG++VTPPL G+ILPGITR S++ LARE G+ V E  Y+  +W+ADA SG+L E F 
Sbjct: 246 VFDDGSMVTPPLGGTILPGITRESILTLAREQGITVREEPYAIDQWKADAGSGKLVETFA 305

Query: 306 CGTAATLVAIGEVRSARTRFAIGNGTAGNTVKVLRDRLVEIQRNQAAGPAGWVH 359
           CGTAA +  +G+V+S    F IG+G  G   + L+ RL  IQR QA    GWVH
Sbjct: 306 CGTAAVVTPVGKVKSRDGEFTIGSGGPGQVTEALKARLTAIQRGQAPDIHGWVH 359


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: 497
Number of extensions: 21
Number of successful extensions: 2
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: 362
Length adjustment: 29
Effective length of query: 334
Effective length of database: 333
Effective search space:   111222
Effective search space used:   111222
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 Ga0059261_3811 Ga0059261_3811 (branched-chain amino acid aminotransferase, group II)
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.42368.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.6e-128  411.5   0.0   1.1e-127  411.3   0.0    1.0  1  FitnessBrowser__Korea:Ga0059261_3811  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Korea:Ga0059261_3811  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.3   0.0  1.1e-127  1.1e-127       1     311 [.      48     359 ..      48     361 .. 0.99

  Alignments for each domain:
  == domain 1  score: 411.3 bits;  conditional E-value: 1.1e-127
                             TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflea 73 
                                           W++a++++ ++l+ld+++avlhY+qe+feGlkayRt d    lfRp +na+R+r+sa+r+++Pel+++lfl +
  FitnessBrowser__Korea:Ga0059261_3811  48 WHDAKVVARGPLSLDPATAVLHYAQEIFEGLKAYRTGDEGTALFRPLENARRFRESAQRMAMPELPDDLFLGS 120
                                           ************************************************************************* PP

                             TIGR01123  74 lkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRa 146
                                           ++ lvkad++w+p+ + + sLYlRPf++a e  lGvk+a+eyl+lv+asP+GaYfkgg   v+i+v+++y+Ra
  FitnessBrowser__Korea:Ga0059261_3811 121 IEALVKADREWIPQIE-GGSLYLRPFMFASEVFLGVKPASEYLYLVIASPAGAYFKGGAPAVTIWVSDHYTRA 192
                                           *************999.99****************************************************** PP

                             TIGR01123 147 apkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegv 219
                                           ap+GtGa+k+gGnYa+sl aq++a ++g+d+vv+ld+ve++ +ee+G++n+f++ +dg++vt+pl + iL+g+
  FitnessBrowser__Korea:Ga0059261_3811 193 APGGTGAAKCGGNYASSLVAQAEAIREGCDQVVFLDAVERRWVEELGGMNLFFVFDDGSMVTPPLGGTILPGI 265
                                           ************************************************************************* PP

                             TIGR01123 220 tresllelakdlgleveereiaidelkaaveaGei..vfacGtaavitPvgelkiegkevevkseevGevtkk 290
                                           tres+l+la++ g++v+e+  aid++ka + +G++   facGtaav+tPvg++k  + e+++ s+ +G+vt++
  FitnessBrowser__Korea:Ga0059261_3811 266 TRESILTLAREQGITVREEPYAIDQWKADAGSGKLveTFACGTAAVVTPVGKVKSRDGEFTIGSGGPGQVTEA 338
                                           *********************************99888*********************************** PP

                             TIGR01123 291 lrdeltdiqyGkledkegWiv 311
                                           l+  lt iq+G++ d +gW+ 
  FitnessBrowser__Korea:Ga0059261_3811 339 LKARLTAIQRGQAPDIHGWVH 359
                                           *******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (362 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: 29.85
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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