Aligments for a candidate for leuD in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Aligments for a candidate for leuD in Pseudomonas stutzeri RCH2

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate GFF2540 Psest_2590 3-isopropylmalate dehydratase, small subunit

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__psRCH2:GFF2540
          Length = 215

 Score =  260 bits (664), Expect = 1e-74
 Identities = 128/197 (64%), Positives = 154/197 (78%), Gaps = 8/197 (4%)

Query: 5   FTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLD------EKGQQP- 57
           FTQHTGLV PLD ANVDTD IIPKQFL+ + RTGFG +LF++WR+LD      +  Q+P 
Sbjct: 4   FTQHTGLVCPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPNQDCSQRPV 63

Query: 58  NPEFVLNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNN 117
           N +FVLNFP Y+GAS+LLARENFGCGSSREHAPWAL +YGF+ +IAPSFADIFY NSF N
Sbjct: 64  NKDFVLNFPRYRGASVLLARENFGCGSSREHAPWALEEYGFRTIIAPSFADIFYNNSFKN 123

Query: 118 QLLPVTLSDAQVDELFALVKANPGIKFEVDLEAQVVKAGD-KTYSFKIDDFRRHCMLNGL 176
            LLP+ L + +VDELFA  +A+ G +  VDL AQVV   D K YSF++D FR+HC+LNGL
Sbjct: 124 GLLPIVLKEEEVDELFAQAEASEGYQLTVDLAAQVVTRPDGKQYSFEVDAFRKHCLLNGL 183

Query: 177 DSIGLTLQHEDAIAAYE 193
           D IGLTLQ  +AI  +E
Sbjct: 184 DDIGLTLQDAEAIKTFE 200


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: 187
Number of extensions: 7
Number of successful extensions: 3
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: 215
Length adjustment: 21
Effective length of query: 180
Effective length of database: 194
Effective search space:    34920
Effective search space used:    34920
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 GFF2540 Psest_2590 (3-isopropylmalate dehydratase, small subunit)
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.14196.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    4.3e-93  296.4   0.0    5.1e-93  296.2   0.0    1.1  1  lcl|FitnessBrowser__psRCH2:GFF2540  Psest_2590 3-isopropylmalate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2540  Psest_2590 3-isopropylmalate dehydratase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.2   0.0   5.1e-93   5.1e-93       1     188 []       1     196 [.       1     196 [. 0.94

  Alignments for each domain:
  == domain 1  score: 296.2 bits;  conditional E-value: 5.1e-93
                           TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkep.......npefvlnvpqyq 68 
                                         mk f ++tGlv pld+anvdtd+iipkqflk ikrtGfg +lf ewryld+   ++       n +fvln+p+y+
  lcl|FitnessBrowser__psRCH2:GFF2540   1 MKAFTQHTGLVCPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPNQdcsqrpvNKDFVLNFPRYR 75 
                                         899**********************************************9643222122223488********** PP

                           TIGR00171  69 gasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkl 142
                                         gas+llarenfGcGssrehapwal++yGf++iiapsfadifynnsfkngllpi l+eeev+el+a+ +  +g +l
  lcl|FitnessBrowser__psRCH2:GFF2540  76 GASVLLARENFGCGSSREHAPWALEEYGFRTIIAPSFADIFYNNSFKNGLLPIVLKEEEVDELFAQAEaSEGYQL 150
                                         ******************************************************************9989***** PP

                           TIGR00171 143 tvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188
                                         tvdl aq v+  +gk+ysfe+d+frkhcllnGld+igltlq  ++i
  lcl|FitnessBrowser__psRCH2:GFF2540 151 TVDLAAQVVTRPDGKQYSFEVDAFRKHCLLNGLDDIGLTLQDAEAI 196
                                         *****************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (215 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: 8.92
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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, or see 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