Aligments for a candidate for ilvE in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for ilvE in Pseudomonas simiae WCS417

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate GFF3433 PS417_17565 branched-chain amino acid aminotransferase

Query= reanno::pseudo5_N2C3_1:AO356_22970
         (339 letters)



>lcl|FitnessBrowser__WCS417:GFF3433 PS417_17565 branched-chain amino
           acid aminotransferase
          Length = 339

 Score =  631 bits (1628), Expect = 0.0
 Identities = 302/339 (89%), Positives = 319/339 (94%)

Query: 1   MGNESINWDKLGFDYIKTDKRYLSHWRDGAWDAGTLTDDNVLHISEGSTALHYGQQCFEG 60
           MGNESINWDKLGFDYIKTDKR+L  W++G W AGTLTDDNVLHISEGSTALHYGQQCFEG
Sbjct: 1   MGNESINWDKLGFDYIKTDKRFLQVWKNGEWQAGTLTDDNVLHISEGSTALHYGQQCFEG 60

Query: 61  LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPQVETEQFVEACKQVVRANERFIPPYGT 120
           LKAYRCKDGSINLFRPDQNAARMQRSCARLLMP V TE F++ACKQVV+ANE FIPPYG+
Sbjct: 61  LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPHVPTEVFIDACKQVVKANEHFIPPYGS 120

Query: 121 GGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISSFDRAAPQGT 180
           GGALYLRPFVIG GDNIGVRTAPEFIFS+FCIPVGAYFKGGL PHNF IS+FDRAAPQGT
Sbjct: 121 GGALYLRPFVIGTGDNIGVRTAPEFIFSVFCIPVGAYFKGGLVPHNFQISTFDRAAPQGT 180

Query: 181 GAAKVGGNYAASLMPGSQAKKASFADCIYLDPMTHSKIEEVGSANFFGITHDNTFVTPRS 240
           GAAKVGGNYAASLMPGS+AKK+ FAD IYLDPMTHSKIEEVGSANFFGITHDN F+TP+S
Sbjct: 181 GAAKVGGNYAASLMPGSEAKKSGFADAIYLDPMTHSKIEEVGSANFFGITHDNKFITPKS 240

Query: 241 PSVLPGITRLSLIELAKSRLGLEVIEGDVFIDKLSDFKEAGACGTAAVITPIGGISYKDK 300
           PSVLPGITRLSLIELAK+RLGLEV+EG+VFIDKL  FKEAGACGTAAVI+PIGGI Y  K
Sbjct: 241 PSVLPGITRLSLIELAKTRLGLEVVEGEVFIDKLDQFKEAGACGTAAVISPIGGIQYNGK 300

Query: 301 LHVFHSETEVGPITQKLYKELTGVQTGDVEAPAGWIVKV 339
           LHVFHSETEVGPITQKLYKELTGVQTGDVEAP GWIVKV
Sbjct: 301 LHVFHSETEVGPITQKLYKELTGVQTGDVEAPQGWIVKV 339


Lambda     K      H
   0.320    0.138    0.422 

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: 535
Number of extensions: 10
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: 339
Length of database: 339
Length adjustment: 28
Effective length of query: 311
Effective length of database: 311
Effective search space:    96721
Effective search space used:    96721
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: 49 (23.5 bits)

Align candidate GFF3433 PS417_17565 (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.1115.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.2e-142  460.5   0.0   1.4e-142  460.3   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF3433  PS417_17565 branched-chain amino


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3433  PS417_17565 branched-chain amino acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.3   0.0  1.4e-142  1.4e-142       1     313 []      31     339 .]      31     339 .] 0.99

  Alignments for each domain:
  == domain 1  score: 460.3 bits;  conditional E-value: 1.4e-142
                           TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealk 75 
                                         W++++l+ ++ l+++egs++lhYgq++feGlkayR++dG+i+lfRpd+na+R++rs+ rll+P++++e+f++a+k
  lcl|FitnessBrowser__WCS417:GFF3433  31 WQAGTLTDDNVLHISEGSTALHYGQQCFEGLKAYRCKDGSINLFRPDQNAARMQRSCARLLMPHVPTEVFIDACK 105
                                         *************************************************************************** PP

                           TIGR01123  76 qlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkG 150
                                         q+vka+++++p+++s+ +LYlRPf+i+t+dn+Gv++a+e++f+v++ PvGaYfkggl p ++f  + ++Raap+G
  lcl|FitnessBrowser__WCS417:GFF3433 106 QVVKANEHFIPPYGSGGALYLRPFVIGTGDNIGVRTAPEFIFSVFCIPVGAYFKGGLVP-HNFQISTFDRAAPQG 179
                                         ***********************************************************.8998899******** PP

                           TIGR01123 151 tGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresll 225
                                         tGa+kvgGnYaasl++ ++a+++g++d++yldp+++ kieevG+an+f+it+d ++++tp+s+s+L+g+tr sl+
  lcl|FitnessBrowser__WCS417:GFF3433 180 TGAAKVGGNYAASLMPGSEAKKSGFADAIYLDPMTHSKIEEVGSANFFGITHD-NKFITPKSPSVLPGITRLSLI 253
                                         *****************************************************.********************* PP

                           TIGR01123 226 elakd.lgleveereiaidelkaaveaGeivfacGtaavitPvgelkiegkevevkse.evGevtkklrdeltdi 298
                                         elak  lglev e+e+ id+l++++eaG    acGtaavi+P+g+++ +gk ++++se evG++t+kl++elt++
  lcl|FitnessBrowser__WCS417:GFF3433 254 ELAKTrLGLEVVEGEVFIDKLDQFKEAG----ACGTAAVISPIGGIQYNGKLHVFHSEtEVGPITQKLYKELTGV 324
                                         ****99**********************....*************************99**************** PP

                           TIGR01123 299 qyGkledkegWivev 313
                                         q+G++e+++gWiv+v
  lcl|FitnessBrowser__WCS417:GFF3433 325 QTGDVEAPQGWIVKV 339
                                         *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (313 nodes)
Target sequences:                          1  (339 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: 12.23
//
[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, 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