Alignments for a candidate for leuD in Pedobacter sp. GW460-11-11-14-LB5

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuD in Pedobacter sp. GW460-11-11-14-LB5

Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate CA265_RS15840 CA265_RS15840 3-isopropylmalate dehydratase small subunit

Query= uniprot:A0A1X9Z766
         (195 letters)



>FitnessBrowser__Pedo557:CA265_RS15840
          Length = 195

 Score =  394 bits (1012), Expect = e-115
 Identities = 195/195 (100%), Positives = 195/195 (100%)

Query: 1   MKKFTKLTSAVVPLNIENIDTDQIIPARFLKATTREGFGENLFRDWRYENDNQPKADFVM 60
           MKKFTKLTSAVVPLNIENIDTDQIIPARFLKATTREGFGENLFRDWRYENDNQPKADFVM
Sbjct: 1   MKKFTKLTSAVVPLNIENIDTDQIIPARFLKATTREGFGENLFRDWRYENDNQPKADFVM 60

Query: 61  NNPTYSGQVLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPIQV 120
           NNPTYSGQVLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPIQV
Sbjct: 61  NNPTYSGQVLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPIQV 120

Query: 121 SDEFLAQIFKAVDNNPKSALEVDLENQTVTIVETGAQESFEINPYKKSCLINGYDDIDFI 180
           SDEFLAQIFKAVDNNPKSALEVDLENQTVTIVETGAQESFEINPYKKSCLINGYDDIDFI
Sbjct: 121 SDEFLAQIFKAVDNNPKSALEVDLENQTVTIVETGAQESFEINPYKKSCLINGYDDIDFI 180

Query: 181 LNQKQLIEEFEEGRR 195
           LNQKQLIEEFEEGRR
Sbjct: 181 LNQKQLIEEFEEGRR 195


Lambda     K      H
   0.318    0.135    0.393 

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: 281
Number of extensions: 7
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: 195
Length of database: 195
Length adjustment: 20
Effective length of query: 175
Effective length of database: 175
Effective search space:    30625
Effective search space used:    30625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 44 (21.6 bits)

Align candidate CA265_RS15840 CA265_RS15840 (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.2841.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
      4e-69  218.3   0.4    4.5e-69  218.1   0.4    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS15840  CA265_RS15840 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS15840  CA265_RS15840 3-isopropylmalate dehydratase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.1   0.4   4.5e-69   4.5e-69       1     186 [.       1     185 [.       1     187 [. 0.95

  Alignments for each domain:
  == domain 1  score: 218.1 bits;  conditional E-value: 4.5e-69
                                  TIGR00171   1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyq 68 
                                                mk+f klt  vvpl+  n+dtd+iip +flk+ +r Gfg++lf +wry  e+ ++p+++fv+n p+y 
  lcl|FitnessBrowser__Pedo557:CA265_RS15840   1 MKKFTKLTSAVVPLNIENIDTDQIIPARFLKATTREGFGENLFRDWRY--ENDNQPKADFVMNNPTYS 66 
                                                899*********************************************..66668************9 PP

                                  TIGR00171  69 gasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk 136
                                                g ++l+a++nfGcGssreha wa++d Gf  +i+  fadif +n+++ngllpi++s+e + ++++ v 
  lcl|FitnessBrowser__Pedo557:CA265_RS15840  67 G-QVLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPIQVSDEFLAQIFKAVD 133
                                                8.79***************************************************************9 PP

                                  TIGR00171 137 .nkglkltvdleaqkvkdse.gkvysfeidefrkhcllnGldeigltlqked 186
                                                 n+   l+vdle+q+v+  e g + sfei++++k cl+nG+d+i + l++++
  lcl|FitnessBrowser__Pedo557:CA265_RS15840 134 nNPKSALEVDLENQTVTIVEtGAQESFEINPYKKSCLINGYDDIDFILNQKQ 185
                                                778889**********9877369**********************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (188 nodes)
Target sequences:                          1  (195 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: 7.69
//
[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