Alignments for a candidate for leuD in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuD in Shewanella oneidensis MR-1

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate 203314 SO4233 3-isopropylmalate dehydratase, small subunit (NCBI ptt file)

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__MR1:203314
          Length = 201

 Score =  244 bits (623), Expect = 8e-70
 Identities = 120/200 (60%), Positives = 145/200 (72%), Gaps = 1/200 (0%)

Query: 3   EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPEFV 62
           + FT HTGL V +D+AN+DTD IIPKQFL KVTR GFG HLF+DWR+LD+ G  PNPEF 
Sbjct: 2   QPFTCHTGLAVMIDSANIDTDQIIPKQFLSKVTRDGFGVHLFHDWRYLDDAGDVPNPEFT 61

Query: 63  LNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPV 122
           LN P Y GASILLA+ENFGCGSSREHAPWAL D+G + +IAPSFADIFYGNS NN LLPV
Sbjct: 62  LNKPRYNGASILLAQENFGCGSSREHAPWALADFGLRAIIAPSFADIFYGNSINNGLLPV 121

Query: 123 TLSDAQVDELFALVKANPGIKFEVDL-EAQVVKAGDKTYSFKIDDFRRHCMLNGLDSIGL 181
            LS  +V +L   V +  G +  VDL   QV       +SF + +  RH +LNGLD+IGL
Sbjct: 122 KLSANEVRQLMDEVASEEGAQITVDLTTCQVTSPSGAQFSFSLAESARHKLLNGLDAIGL 181

Query: 182 TLQHEDAIAAYENKQPAFMR 201
           TL H   I+ YE++ P++ R
Sbjct: 182 TLSHGAQISEYESQIPSWRR 201


Lambda     K      H
   0.321    0.138    0.416 

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: 166
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: 201
Length of database: 201
Length adjustment: 21
Effective length of query: 180
Effective length of database: 180
Effective search space:    32400
Effective search space used:    32400
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 203314 SO4233 (3-isopropylmalate dehydratase, small subunit (NCBI ptt file))
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.1373.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    5.8e-86  273.2   0.0    6.5e-86  273.0   0.0    1.0  1  lcl|FitnessBrowser__MR1:203314  SO4233 3-isopropylmalate dehydra


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203314  SO4233 3-isopropylmalate dehydratase, small subunit (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  273.0   0.0   6.5e-86   6.5e-86       1     188 []       1     189 [.       1     189 [. 0.99

  Alignments for each domain:
  == domain 1  score: 273.0 bits;  conditional E-value: 6.5e-86
                       TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasillarenf 79 
                                     m++f  +tGl+v +d an+dtd+iipkqfl k++r Gfg hlf++wryld+ G+ pnpef ln p+y+gasilla+enf
  lcl|FitnessBrowser__MR1:203314   1 MQPFTCHTGLAVMIDSANIDTDQIIPKQFLSKVTRDGFGVHLFHDWRYLDDAGDVPNPEFTLNKPRYNGASILLAQENF 79 
                                     89***************************************************************************** PP

                       TIGR00171  80 GcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvdleaqkvkdsegk 157
                                     GcGssrehapwal+d+G++ iiapsfadify+ns++ngllp++ls +ev++l+  v+ ++g ++tvdl + +v++  g 
  lcl|FitnessBrowser__MR1:203314  80 GCGSSREHAPWALADFGLRAIIAPSFADIFYGNSINNGLLPVKLSANEVRQLMDEVAsEEGAQITVDLTTCQVTSPSGA 158
                                     ********************************************************9899******************* PP

                       TIGR00171 158 vysfeidefrkhcllnGldeigltlqkedei 188
                                     + sf + e  +h llnGld igltl +  +i
  lcl|FitnessBrowser__MR1:203314 159 QFSFSLAESARHKLLNGLDAIGLTLSHGAQI 189
                                     *************************997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (201 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: 00:00:00.00
# Mc/sec: 4.79
//
[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