Alignments for a candidate for leuC in Rhodobacter sphaeroides ATCC 17029

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Rhodobacter sphaeroides ATCC 17029

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_011841723.1 RSPH17029_RS12730 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000015985.1:WP_011841723.1
          Length = 475

 Score =  633 bits (1632), Expect = 0.0
 Identities = 309/464 (66%), Positives = 378/464 (81%), Gaps = 2/464 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TLY+K++D HVV+++E+ T LLYIDRHLVHEVTSPQAF+GLR  GR VR P KT A  D
Sbjct: 5   RTLYDKIWDDHVVHQSEDGTCLLYIDRHLVHEVTSPQAFEGLRMTGRKVRAPEKTIAVPD 64

Query: 63  HNV-STQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPG 121
           HNV +T+ +D     E +RIQ++ L +N ++FG+  Y ++   QGIVH++GPEQG TLPG
Sbjct: 65  HNVPTTEGRDTKIDNEESRIQVEALDRNARDFGINYYPVSDIRQGIVHIVGPEQGWTLPG 124

Query: 122 MTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAK 181
           MT+VCGDSHTATHGAFGALA GIGTSEVEHVLATQTL Q ++K MK+E+ G   PG+TAK
Sbjct: 125 MTVVCGDSHTATHGAFGALAHGIGTSEVEHVLATQTLIQKKSKNMKVEITGSLRPGVTAK 184

Query: 182 DIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFN 241
           DI L++IG TG+AGGTG+V+E+CG+AIR+LSMEGRMT+CNMAIE GA+AGL+APDE TF 
Sbjct: 185 DITLSVIGLTGTAGGTGYVIEYCGQAIRELSMEGRMTVCNMAIEGGARAGLIAPDEKTFA 244

Query: 242 YVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVN 301
           YV GR HAPKG  ++ A+AYWKTL TD+GA FD VVT++ E+I+P VTWGT+P  V+ + 
Sbjct: 245 YVMGRPHAPKGAAWEAALAYWKTLFTDKGAQFDKVVTIRGEDIAPVVTWGTSPEDVLPIT 304

Query: 302 DNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEI 361
             +P P  F      A A ++L YMGL PG  LT++ ID VFIGSCTN RIEDLRAAAEI
Sbjct: 305 ATVPAPEDFTGGKVEA-ARRSLEYMGLTPGQKLTDIKIDTVFIGSCTNGRIEDLRAAAEI 363

Query: 362 AKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421
            KG+KVAPG++A+VVPGSG V+AQAE EGL +IFI+AGFEWRL GCSMCLAMN D+L+PG
Sbjct: 364 LKGKKVAPGMRAMVVPGSGLVRAQAEEEGLAQIFIDAGFEWRLAGCSMCLAMNPDQLSPG 423

Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           ERCASTSNRNFEGRQGR GRTHLVSP MAAAAA+TGH  D+R++
Sbjct: 424 ERCASTSNRNFEGRQGRNGRTHLVSPGMAAAAAITGHLTDVRDL 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: 860
Number of extensions: 32
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: 466
Length of database: 475
Length adjustment: 33
Effective length of query: 433
Effective length of database: 442
Effective search space:   191386
Effective search space used:   191386
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 WP_011841723.1 RSPH17029_RS12730 (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.9837.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.9e-248  808.9   0.1   6.9e-248  808.7   0.1    1.0  1  lcl|NCBI__GCF_000015985.1:WP_011841723.1  RSPH17029_RS12730 3-isopropylmal


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015985.1:WP_011841723.1  RSPH17029_RS12730 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  808.7   0.1  6.9e-248  6.9e-248       2     466 .]       4     467 ..       3     467 .. 0.99

  Alignments for each domain:
  == domain 1  score: 808.7 bits;  conditional E-value: 6.9e-248
                                 TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnist.es 69 
                                               ++tly+k++d hvv+++e++t llyidrhlvhevtspqafeglr +grkvr ++kt+a  dhn++t e 
  lcl|NCBI__GCF_000015985.1:WP_011841723.1   4 PRTLYDKIWDDHVVHQSEDGTCLLYIDRHLVHEVTSPQAFEGLRMTGRKVRAPEKTIAVPDHNVPTtEG 72 
                                               8***************************************************************97267 PP

                                 TIGR00170  70 rdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafg 138
                                               rd++i +e++++qv++l++n+++fg++++ +s+ +qgivh+vgpe+g tlpg+t+vcgdshtathgafg
  lcl|NCBI__GCF_000015985.1:WP_011841723.1  73 RDTKIDNEESRIQVEALDRNARDFGINYYPVSDIRQGIVHIVGPEQGWTLPGMTVVCGDSHTATHGAFG 141
                                               9******************************************************************** PP

                                 TIGR00170 139 alafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefagea 207
                                               ala gigtsevehvlatqtl+q+++k++k+e+ g l +g+takdi l +ig++g+aggtgyv+e++g+a
  lcl|NCBI__GCF_000015985.1:WP_011841723.1 142 ALAHGIGTSEVEHVLATQTLIQKKSKNMKVEITGSLRPGVTAKDITLSVIGLTGTAGGTGYVIEYCGQA 210
                                               ********************************************************************* PP

                                 TIGR00170 208 irdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkv 276
                                               ir+lsme+rmtvcnmaie ga+agliapde tf+yv +r++apkg+ +e a+aywktl td+ga+fdkv
  lcl|NCBI__GCF_000015985.1:WP_011841723.1 211 IRELSMEGRMTVCNMAIEGGARAGLIAPDEKTFAYVMGRPHAPKGAAWEAALAYWKTLFTDKGAQFDKV 279
                                               ********************************************************************* PP

                                 TIGR00170 277 vtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfig 345
                                               vt+ ++di+p vtwgt+p++vl+++ +vp+p++++   + + a ++l+y+gl+pg+kl+dik+d vfig
  lcl|NCBI__GCF_000015985.1:WP_011841723.1 280 VTIRGEDIAPVVTWGTSPEDVLPITATVPAPEDFTGG-KVEAARRSLEYMGLTPGQKLTDIKIDTVFIG 347
                                               **********************************986.456789************************* PP

                                 TIGR00170 346 sctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgm 414
                                               sctn+riedlraaae++kgkkva++++ a+vvpgsglv++qae+egl +if++agfewr agcs+cl+m
  lcl|NCBI__GCF_000015985.1:WP_011841723.1 348 SCTNGRIEDLRAAAEILKGKKVAPGMR-AMVVPGSGLVRAQAEEEGLAQIFIDAGFEWRLAGCSMCLAM 415
                                               ***************************.***************************************** PP

                                 TIGR00170 415 nndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466
                                               n+d+l+++ercastsnrnfegrqg+++rthlvsp maaaaa++g++ d+r+l
  lcl|NCBI__GCF_000015985.1:WP_011841723.1 416 NPDQLSPGERCASTSNRNFEGRQGRNGRTHLVSPGMAAAAAITGHLTDVRDL 467
                                               **************************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (475 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.42
//
[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