Alignments for a candidate for leuC in Rhodospirillum rubrum ATCC 11170

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Rhodospirillum rubrum ATCC 11170

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate YP_426277.1 Rru_A1189 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000013085.1:YP_426277.1
          Length = 472

 Score =  635 bits (1639), Expect = 0.0
 Identities = 310/463 (66%), Positives = 374/463 (80%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTL+ K++ +H+V   ++ T L+YIDRHLVHEVTSPQAF+GLR  GR VR+P +T A  D
Sbjct: 5   KTLFNKIWQSHLVDVQDDGTCLIYIDRHLVHEVTSPQAFEGLRMTGRKVRRPEQTLAVAD 64

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           HNV T  +      E +RIQ++ L  N  EFGV   +++   QGIVH++GPEQG TLPG 
Sbjct: 65  HNVPTTDRSKGIADEESRIQVEALGSNTAEFGVPYLEMDDIRQGIVHIVGPEQGFTLPGA 124

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
           TIVCGDSHT+THGAFGALAFGIGTSEVEHVLATQTL Q  AK M + + G   PG++AKD
Sbjct: 125 TIVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLLQKPAKDMLVRIDGALRPGVSAKD 184

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           IVLA+IG+ G+AGGTGHV+EF GEAIR LSMEGRMT+CNM IE GA+AGL+APDE TF Y
Sbjct: 185 IVLAVIGRIGTAGGTGHVIEFAGEAIRGLSMEGRMTVCNMTIEGGARAGLIAPDEVTFEY 244

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           +KGR  APKG  ++ A++YWKTL+TDEGA +DTV+ + A  I PQVTWGT+P  V++++ 
Sbjct: 245 LKGRPFAPKGAAWEAAISYWKTLKTDEGAVYDTVIEMDAGAIEPQVTWGTSPENVVALSG 304

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
            +PDPA+ ADP  RA+ E+ALAYM LKPG+P+TEVAIDKVFIGSCTN RIEDLRAAA IA
Sbjct: 305 RVPDPAAEADPGRRAAIERALAYMDLKPGMPMTEVAIDKVFIGSCTNGRIEDLRAAAAIA 364

Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422
           KGRKVA  V A+VVPGSG VK QAE+EGLD+IF+EAGFEWR PGCSMCLAMN D+L PGE
Sbjct: 365 KGRKVAATVNAIVVPGSGLVKEQAESEGLDQIFLEAGFEWREPGCSMCLAMNADKLAPGE 424

Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           RCASTSNRNFEGRQG+GGRTHLVSPA+A A+A+TG   D +++
Sbjct: 425 RCASTSNRNFEGRQGKGGRTHLVSPAVAVASAITGKLTDAQSL 467


Lambda     K      H
   0.317    0.134    0.396 

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: 817
Number of extensions: 37
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: 466
Length of database: 472
Length adjustment: 33
Effective length of query: 433
Effective length of database: 439
Effective search space:   190087
Effective search space used:   190087
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: 51 (24.3 bits)

Align candidate YP_426277.1 Rru_A1189 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large 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/TIGR00170.hmm
# target sequence database:        /tmp/gapView.6706.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00170  [M=466]
Accession:   TIGR00170
Description: leuC: 3-isopropylmalate dehydratase, large 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   4.7e-243  792.8   0.1   5.5e-243  792.5   0.1    1.0  1  lcl|NCBI__GCF_000013085.1:YP_426277.1  Rru_A1189 3-isopropylmalate dehy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000013085.1:YP_426277.1  Rru_A1189 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  792.5   0.1  5.5e-243  5.5e-243       2     464 ..       4     465 ..       3     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 792.5 bits;  conditional E-value: 5.5e-243
                              TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 
                                            +ktl++k++++h+v  ++++t l+yidrhlvhevtspqafeglr +grkvrr+++tla  dhn++t+ r   
  lcl|NCBI__GCF_000013085.1:YP_426277.1   4 PKTLFNKIWQSHLVDVQDDGTCLIYIDRHLVHEVTSPQAFEGLRMTGRKVRRPEQTLAVADHNVPTTDRSKG 75 
                                            89********************************************************************** PP

                              TIGR00170  74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgig 145
                                            i +e++++qv++l  n+ efgv+++++++ +qgivh+vgpe+g+tlpg tivcgdsht+thgafgalafgig
  lcl|NCBI__GCF_000013085.1:YP_426277.1  76 IADEESRIQVEALGSNTAEFGVPYLEMDDIRQGIVHIVGPEQGFTLPGATIVCGDSHTSTHGAFGALAFGIG 147
                                            ************************************************************************ PP

                              TIGR00170 146 tsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeerm 217
                                            tsevehvlatqtl q+ ak + ++++g l +g++akdi+la+ig+ig+aggtg+v+efageair lsme+rm
  lcl|NCBI__GCF_000013085.1:YP_426277.1 148 TSEVEHVLATQTLLQKPAKDMLVRIDGALRPGVSAKDIVLAVIGRIGTAGGTGHVIEFAGEAIRGLSMEGRM 219
                                            ************************************************************************ PP

                              TIGR00170 218 tvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvt 289
                                            tvcnm+ie ga+agliapde+tfey+k+r++apkg+ +e a++ywktlktdega++d+v+ ++a  i pqvt
  lcl|NCBI__GCF_000013085.1:YP_426277.1 220 TVCNMTIEGGARAGLIAPDEVTFEYLKGRPFAPKGAAWEAAISYWKTLKTDEGAVYDTVIEMDAGAIEPQVT 291
                                            ************************************************************************ PP

                              TIGR00170 290 wgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaev 361
                                            wgt+p++v+++++ vpdp+  adp ++a +e+alay+ l+pg++++++++dkvfigsctn+riedlraaa++
  lcl|NCBI__GCF_000013085.1:YP_426277.1 292 WGTSPENVVALSGRVPDPAAEADPGRRAAIERALAYMDLKPGMPMTEVAIDKVFIGSCTNGRIEDLRAAAAI 363
                                            ************************************************************************ PP

                              TIGR00170 362 vkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnf 433
                                            +kg+kva +v+ a+vvpgsglvk+qae egld+ifleagfewre+gcs+cl+mn d+l ++ercastsnrnf
  lcl|NCBI__GCF_000013085.1:YP_426277.1 364 AKGRKVAATVN-AIVVPGSGLVKEQAESEGLDQIFLEAGFEWREPGCSMCLAMNADKLAPGERCASTSNRNF 434
                                            ***********.************************************************************ PP

                              TIGR00170 434 egrqgkgarthlvspamaaaaavagkfvdir 464
                                            egrqgkg+rthlvspa+a a+a++gk+ d +
  lcl|NCBI__GCF_000013085.1:YP_426277.1 435 EGRQGKGGRTHLVSPAVAVASAITGKLTDAQ 465
                                            ***************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (472 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.62
//
[ok]

This GapMind analysis is from Apr 10 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