Alignments for a candidate for leuD in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuD in Pseudomonas fluorescens GW456-L13

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate PfGW456L13_3947 3-isopropylmalate dehydratase small subunit (EC 4.2.1.33)

Query= uniprot:Q845W4
         (216 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3947
          Length = 214

 Score =  320 bits (819), Expect = 2e-92
 Identities = 152/210 (72%), Positives = 173/210 (82%)

Query: 1   MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60
           M+ FT HTG+VAPLDR NVDTD IIPKQFLKSIKRTGFGPN FDEWRYLD G+P QDNSK
Sbjct: 1   MKAFTQHTGLVAPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPYQDNSK 60

Query: 61  RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120
           RPLN DFVLN  RYQGAS+L+ R+NFGCGSSREHAPWAL++YGFR+IIAPS+ADIFFNN 
Sbjct: 61  RPLNKDFVLNAERYQGASVLLARENFGCGSSREHAPWALEEYGFRSIIAPSYADIFFNNS 120

Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180
           FKNGLLPI+L++ +VD L  +  A  GYQL +DL+AQ V  PDG+   FEI AFRK+CLL
Sbjct: 121 FKNGLLPIILSDAEVDELFQQVEANPGYQLQVDLQAQTVTRPDGKVLSFEIDAFRKHCLL 180

Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWL 210
           NG DDIGLTL+  D I  FEA+  A QPWL
Sbjct: 181 NGLDDIGLTLQDGDAIAAFEAKHRASQPWL 210


Lambda     K      H
   0.322    0.141    0.437 

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: 230
Number of extensions: 4
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: 216
Length of database: 214
Length adjustment: 22
Effective length of query: 194
Effective length of database: 192
Effective search space:    37248
Effective search space used:    37248
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: 45 (21.9 bits)

Align candidate PfGW456L13_3947 (3-isopropylmalate dehydratase small subunit (EC 4.2.1.33))
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

# 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/TIGR00171.hmm
# target sequence database:        /tmp/gapView.20673.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00171  [M=188]
Accession:   TIGR00171
Description: leuD: 3-isopropylmalate dehydratase, small subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    2.7e-94  300.4   0.0    3.4e-94  300.1   0.0    1.1  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3947  3-isopropylmalate dehydratase sm


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3947  3-isopropylmalate dehydratase small subunit (EC 4.2.1.33)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.1   0.0   3.4e-94   3.4e-94       1     188 []       1     196 [.       1     196 [. 0.94

  Alignments for each domain:
  == domain 1  score: 300.1 bits;  conditional E-value: 3.4e-94
                                               TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryld..... 50 
                                                             mk f ++tGlv+pld+anvdtd+iipkqflk ikrtGfg +lf ewryld     
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3947   1 MKAFTQHTGLVAPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDvgqpy 55 
                                                             899*********************************************9833332 PP

                                               TIGR00171  51 .ekGkep.npefvlnvpqyqgasillarenfGcGssrehapwalkdyGfkviiap 103
                                                              ++ k p n +fvln ++yqgas+llarenfGcGssrehapwal++yGf++iiap
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3947  56 qDNSKRPlNKDFVLNAERYQGASVLLARENFGCGSSREHAPWALEEYGFRSIIAP 110
                                                             2233333489********************************************* PP

                                               TIGR00171 104 sfadifynnsfkngllpirlseeeveellalvk.nkglkltvdleaqkvkdsegk 157
                                                             s+adif+nnsfkngllpi ls++ev+el+++v+ n+g +l+vdl+aq+v+  +gk
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3947 111 SYADIFFNNSFKNGLLPIILSDAEVDELFQQVEaNPGYQLQVDLQAQTVTRPDGK 165
                                                             ********************************99********************* PP

                                               TIGR00171 158 vysfeidefrkhcllnGldeigltlqkedei 188
                                                             v sfeid+frkhcllnGld+igltlq  d+i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3947 166 VLSFEIDAFRKHCLLNGLDDIGLTLQDGDAI 196
                                                             **************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (214 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 5.43
//
[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