Alignments for a candidate for leuD in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuD in Herbaspirillum seropedicae SmR1

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate HSERO_RS16505 HSERO_RS16505 3-isopropylmalate dehydratase small subunit

Query= uniprot:Q845W4
         (216 letters)



>FitnessBrowser__HerbieS:HSERO_RS16505
          Length = 215

 Score =  361 bits (926), Expect = e-105
 Identities = 171/215 (79%), Positives = 189/215 (87%), Gaps = 1/215 (0%)

Query: 1   MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60
           M KF VH G+VAPLDR NVDTDAIIPKQFLKSIKR+GFGPN FDEWRYLDHGEPG DNSK
Sbjct: 1   MNKFIVHEGLVAPLDRANVDTDAIIPKQFLKSIKRSGFGPNLFDEWRYLDHGEPGMDNSK 60

Query: 61  RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120
           RPLNPDFVLNQ RYQG+SIL++RKNFGCGSSREHAPWAL Q+GFRA+IAPSFADIFFNNC
Sbjct: 61  RPLNPDFVLNQERYQGSSILLSRKNFGCGSSREHAPWALDQFGFRAVIAPSFADIFFNNC 120

Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDG-RDYPFEITAFRKYCL 179
           +KNGLLPIVLTEQQVDHL NE  AF GY+L IDLE Q+V T +G + YPFEI+ FRKYCL
Sbjct: 121 YKNGLLPIVLTEQQVDHLFNEVKAFPGYRLVIDLEKQIVSTTNGSQTYPFEISEFRKYCL 180

Query: 180 LNGFDDIGLTLRHADKIRQFEAERLAKQPWLNNKL 214
           LNGFDDIGLTLR AD IR +E + L +QPWL+N +
Sbjct: 181 LNGFDDIGLTLRKADTIRAYEEKHLHEQPWLSNTI 215


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: 233
Number of extensions: 2
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: 215
Length adjustment: 22
Effective length of query: 194
Effective length of database: 193
Effective search space:    37442
Effective search space used:    37442
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 HSERO_RS16505 HSERO_RS16505 (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.3754602.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
    1.9e-85  271.5   0.0    2.2e-85  271.3   0.0    1.0  1  FitnessBrowser__HerbieS:HSERO_RS16505  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__HerbieS:HSERO_RS16505  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.3   0.0   2.2e-85   2.2e-85       1     188 []       1     197 [.       1     197 [. 0.94

  Alignments for each domain:
  == domain 1  score: 271.3 bits;  conditional E-value: 2.2e-85
                              TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewrylde..kGkep.....npefvlnvp 65 
                                            m++f+ ++Glv+pld+anvdtdaiipkqflk ikr Gfg +lf ewryld+   G ++     np+fvln++
  FitnessBrowser__HerbieS:HSERO_RS16505   1 MNKFIVHEGLVAPLDRANVDTDAIIPKQFLKSIKRSGFGPNLFDEWRYLDHgePGMDNskrplNPDFVLNQE 72 
                                            899*********************************************9852234332222359******** PP

                              TIGR00171  66 qyqgasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk. 136
                                            +yqg+sill+r+nfGcGssrehapwal+++Gf+ +iapsfadif+nn++kngllpi l+e++v++l++ vk 
  FitnessBrowser__HerbieS:HSERO_RS16505  73 RYQGSSILLSRKNFGCGSSREHAPWALDQFGFRAVIAPSFADIFFNNCYKNGLLPIVLTEQQVDHLFNEVKa 144
                                            **********************************************************************98 PP

                              TIGR00171 137 nkglkltvdleaqkvkdseg.kvysfeidefrkhcllnGldeigltlqkedei 188
                                             +g +l +dle+q v +++g ++y fei efrk cllnG+d+igltl+k d+i
  FitnessBrowser__HerbieS:HSERO_RS16505 145 FPGYRLVIDLEKQIVSTTNGsQTYPFEISEFRKYCLLNGFDDIGLTLRKADTI 197
                                            9******************98899*************************9987 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: 9.94
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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