Alignments for a candidate for ilvE in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for ilvE in Pseudomonas fluorescens FW300-N1B4

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate Pf1N1B4_4476 Branched-chain amino acid aminotransferase (EC 2.6.1.42)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4476
          Length = 339

 Score =  671 bits (1730), Expect = 0.0
 Identities = 324/339 (95%), Positives = 332/339 (97%)

Query: 1   MGNESINWDKLGFDYIKTDKRYLSHWRDGAWDAGTLTDDNVLHISEGSTALHYGQQCFEG 60
           MGNESINWDKLGFDYIKTDKRYLSHWR+G WD GTLT+DNVLHISEGSTALHYGQQCFEG
Sbjct: 1   MGNESINWDKLGFDYIKTDKRYLSHWRNGEWDKGTLTEDNVLHISEGSTALHYGQQCFEG 60

Query: 61  LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPQVETEQFVEACKQVVRANERFIPPYGT 120
           LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPQV TEQFVEACK+VVRANERFIPPYGT
Sbjct: 61  LKAYRCKDGSINLFRPDQNAARMQRSCARLLMPQVSTEQFVEACKEVVRANERFIPPYGT 120

Query: 121 GGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISSFDRAAPQGT 180
           GGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISS+DRAAPQGT
Sbjct: 121 GGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYFKGGLTPHNFLISSYDRAAPQGT 180

Query: 181 GAAKVGGNYAASLMPGSQAKKASFADCIYLDPMTHSKIEEVGSANFFGITHDNTFVTPRS 240
           GAAKVGGNYAASLMPGSQAKKA FADCIYLDP+TH+KIEEVGSANFFGITHDN FVTP S
Sbjct: 181 GAAKVGGNYAASLMPGSQAKKAHFADCIYLDPLTHTKIEEVGSANFFGITHDNKFVTPNS 240

Query: 241 PSVLPGITRLSLIELAKSRLGLEVIEGDVFIDKLSDFKEAGACGTAAVITPIGGISYKDK 300
           PSVLPGITRLSLIELAK+RLGLEV+EGDVFIDKLSDFKEAGACGTAAVITPIGGISY DK
Sbjct: 241 PSVLPGITRLSLIELAKTRLGLEVVEGDVFIDKLSDFKEAGACGTAAVITPIGGISYNDK 300

Query: 301 LHVFHSETEVGPITQKLYKELTGVQTGDVEAPAGWIVKV 339
           LHVFHSETEVGPITQKLYKELTGVQTGDVEAPAGWIVKV
Sbjct: 301 LHVFHSETEVGPITQKLYKELTGVQTGDVEAPAGWIVKV 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: 574
Number of extensions: 14
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 Pf1N1B4_4476 (Branched-chain amino acid aminotransferase (EC 2.6.1.42))
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.13974.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.1e-142  460.7   0.0   1.2e-142  460.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4476  Branched-chain amino acid aminot


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4476  Branched-chain amino acid aminotransferase (EC 2.6.1.42)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.5   0.0  1.2e-142  1.2e-142       1     313 []      31     339 .]      31     339 .] 0.99

  Alignments for each domain:
  == domain 1  score: 460.5 bits;  conditional E-value: 1.2e-142
                                      TIGR01123   1 WdeaelaseaeleldegsavlhYgqevfeGlkayRtadGkillfRpdanakRlrrsaerlllPe 64 
                                                    Wd+++l++++ l+++egs++lhYgq++feGlkayR++dG+i+lfRpd+na+R++rs+ rll+P+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4476  31 WDKGTLTEDNVLHISEGSTALHYGQQCFEGLKAYRCKDGSINLFRPDQNAARMQRSCARLLMPQ 94 
                                                    **************************************************************** PP

                                      TIGR01123  65 leeelflealkqlvkadkdwvpkakseasLYlRPfliatednlGvkaakeylflvlasPvGaYf 128
                                                    +++e+f+ea+k++v+a+++++p+++++ +LYlRPf+i+++dn+Gv++a+e++f++++ PvGaYf
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4476  95 VSTEQFVEACKEVVRANERFIPPYGTGGALYLRPFVIGVGDNIGVRTAPEFIFSIFCIPVGAYF 158
                                                    **************************************************************** PP

                                      TIGR01123 129 kgglapvsifveteyvRaapkGtGavkvgGnYaasllaqkkaaeqglddvvyldpvekkkieev 192
                                                    kggl+p ++f+ + y+Raap+GtGa+kvgGnYaasl++ ++a++ +++d++yldp +++kieev
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4476 159 KGGLTP-HNFLISSYDRAAPQGTGAAKVGGNYAASLMPGSQAKKAHFADCIYLDPLTHTKIEEV 221
                                                    ******.99******************************************************* PP

                                      TIGR01123 193 GaaniflitkdgelvttplsesiLegvtresllelakd.lgleveereiaidelkaaveaGeiv 255
                                                    G+an+f+it+d ++++tp+s+s+L+g+tr sl+elak  lglev e+++ id+l++++eaG   
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4476 222 GSANFFGITHD-NKFVTPNSPSVLPGITRLSLIELAKTrLGLEVVEGDVFIDKLSDFKEAG--- 281
                                                    ***********.*************************99**********************... PP

                                      TIGR01123 256 facGtaavitPvgelkiegkevevkse.evGevtkklrdeltdiqyGkledkegWivev 313
                                                     acGtaavitP+g+++ ++k ++++se evG++t+kl++elt++q+G++e++ gWiv+v
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4476 282 -ACGTAAVITPIGGISYNDKLHVFHSEtEVGPITQKLYKELTGVQTGDVEAPAGWIVKV 339
                                                    .************************999*****************************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: 9.93
//
[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