Alignments for a candidate for ilvE in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvE in Pseudomonas putida KT2440

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate PP_3511 PP_3511 Branched-chain-amino-acid aminotransferase

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



>FitnessBrowser__Putida:PP_3511
          Length = 339

 Score =  585 bits (1507), Expect = e-172
 Identities = 283/339 (83%), Positives = 308/339 (90%), Gaps = 1/339 (0%)

Query: 1   MGNESINWDKLGFDYIKTDKRYLSHWRDGAWDAGTLTDDNVLHISEGSTALHYGQQCFEG 60
           M NESINWDKLGFDYIKTDKRYLS WR+G WD GTLT+DNVLHISEGSTALHYGQQCFEG
Sbjct: 1   MSNESINWDKLGFDYIKTDKRYLSVWRNGEWDKGTLTEDNVLHISEGSTALHYGQQCFEG 60

Query: 61  LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPQVETEQFVEACKQVVRANERFIPPYGT 120
           LKAYRCKDGSINLFRPDQNAARMQRSCARLLMP V T+ F+EACKQVV+ANE+F+PP+G 
Sbjct: 61  LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPHVPTDVFIEACKQVVKANEKFVPPHGK 120

Query: 121 GGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISSFDRAAPQGT 180
           G ALYLRPFVIG GDNIGVRTAPEFIFS+F IPVG+YFKGG+ PHNF ISSFDRAAPQGT
Sbjct: 121 G-ALYLRPFVIGTGDNIGVRTAPEFIFSVFAIPVGSYFKGGMKPHNFQISSFDRAAPQGT 179

Query: 181 GAAKVGGNYAASLMPGSQAKKASFADCIYLDPMTHSKIEEVGSANFFGITHDNTFVTPRS 240
           GAAKVGGNYAASL PG++AKKA+FAD IYLDP+TH+KIEEVGSANFFGIT +N FVTP+S
Sbjct: 180 GAAKVGGNYAASLQPGAEAKKANFADAIYLDPLTHTKIEEVGSANFFGITANNEFVTPKS 239

Query: 241 PSVLPGITRLSLIELAKSRLGLEVIEGDVFIDKLSDFKEAGACGTAAVITPIGGISYKDK 300
            SVLPGITRLSL+ELA+SRLG+ VIEGDV I KL  F EAGACGTAAVITPIGGI Y  K
Sbjct: 240 ASVLPGITRLSLMELAQSRLGMTVIEGDVEISKLDRFVEAGACGTAAVITPIGGIEYNGK 299

Query: 301 LHVFHSETEVGPITQKLYKELTGVQTGDVEAPAGWIVKV 339
           LHVFH   +VGP+TQKLY ELTG+Q+GDVEAPAGWIVKV
Sbjct: 300 LHVFHDLEKVGPVTQKLYNELTGIQSGDVEAPAGWIVKV 338


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: 505
Number of extensions: 16
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: 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 PP_3511 PP_3511 (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.aa/TIGR01123.hmm
# target sequence database:        /tmp/gapView.4112.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.4e-138  447.1   0.0   1.6e-138  447.0   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3511  PP_3511 Branched-chain-amino-aci


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3511  PP_3511 Branched-chain-amino-acid aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.0   0.0  1.6e-138  1.6e-138       1     313 []      31     338 ..      31     338 .. 0.99

  Alignments for each domain:
  == domain 1  score: 447.0 bits;  conditional E-value: 1.6e-138
                           TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPeleeelflealk 75 
                                         Wd+++l++++ l+++egs++lhYgq++feGlkayR++dG+i+lfRpd+na+R++rs+ rll+P++++++f+ea+k
  lcl|FitnessBrowser__Putida:PP_3511  31 WDKGTLTEDNVLHISEGSTALHYGQQCFEGLKAYRCKDGSINLFRPDQNAARMQRSCARLLMPHVPTDVFIEACK 105
                                         *************************************************************************** PP

                           TIGR01123  76 qlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYfkgglapvsifveteyvRaapkG 150
                                         q+vka++++vp+++ + +LYlRPf+i+t+dn+Gv++a+e++f+v+a PvG+Yfkgg++p ++f  + ++Raap+G
  lcl|FitnessBrowser__Putida:PP_3511 106 QVVKANEKFVPPHG-KGALYLRPFVIGTGDNIGVRTAPEFIFSVFAIPVGSYFKGGMKP-HNFQISSFDRAAPQG 178
                                         ***********998.999*****************************************.999999********* PP

                           TIGR01123 151 tGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieevGaaniflitkdgelvttplsesiLegvtresll 225
                                         tGa+kvgGnYaasl++ ++a++ +++d++yldp +++kieevG+an+f+it + + ++tp+s s+L+g+tr sl+
  lcl|FitnessBrowser__Putida:PP_3511 179 TGAAKVGGNYAASLQPGAEAKKANFADAIYLDPLTHTKIEEVGSANFFGITAN-NEFVTPKSASVLPGITRLSLM 252
                                         ****************************************************8.99******************* PP

                           TIGR01123 226 elakd.lgleveereiaidelkaaveaGeivfacGtaavitPvgelkiegkevevkse.evGevtkklrdeltdi 298
                                         ela++ lg++v e++++i +l+++veaG    acGtaavitP+g+++ +gk +++++  +vG+vt+kl++elt+i
  lcl|FitnessBrowser__Putida:PP_3511 253 ELAQSrLGMTVIEGDVEISKLDRFVEAG----ACGTAAVITPIGGIEYNGKLHVFHDLeKVGPVTQKLYNELTGI 323
                                         *****9**********************....***********************99769*************** PP

                           TIGR01123 299 qyGkledkegWivev 313
                                         q G++e++ gWiv+v
  lcl|FitnessBrowser__Putida:PP_3511 324 QSGDVEAPAGWIVKV 338
                                         *************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.93
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis