Alignments for a candidate for leuC in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Halorhodospira halophila SL1

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_011814598.1 HHAL_RS09140 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>NCBI__GCF_000015585.1:WP_011814598.1
          Length = 466

 Score =  600 bits (1547), Expect = e-176
 Identities = 294/462 (63%), Positives = 360/462 (77%), Gaps = 1/462 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+KL+D+HVV E ++ + LLYIDR L+HEVTSPQAF+GLR  GR   +     A  D
Sbjct: 4   KTLYDKLWDSHVVTEYDDGSALLYIDRQLLHEVTSPQAFEGLRLAGRQPWRVASNLAVTD 63

Query: 63  HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
           HNV T  +       ++R+Q++ L +NCK+F V  + +  P QGIVHV+GPEQG TLPGM
Sbjct: 64  HNVPTTDRSQPVEDPVSRVQIETLDRNCKDFQVIEFGIRDPRQGIVHVVGPEQGTTLPGM 123

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
           T+VCGDSHT+THGA GALAFG+GTSEVEHVLATQTL Q +A+TM I + G+   G+TAKD
Sbjct: 124 TLVCGDSHTSTHGALGALAFGVGTSEVEHVLATQTLVQKKARTMLIRIDGQLGRGVTAKD 183

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           I+LAIIG+ G+AGGTG+ +E+ GEAIR LSMEGRMT+CNM+IE GA+ G+VA D+TT  Y
Sbjct: 184 IILAIIGRIGTAGGTGYALEYGGEAIRSLSMEGRMTICNMSIEAGARTGMVAVDDTTIEY 243

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           V+GR +AP+G  +D AVA W+ L +DE A FD VV L A+EI PQVTWGT+P  V SVN 
Sbjct: 244 VRGRPNAPEGALWDQAVASWRHLVSDEDAAFDRVVELHADEIEPQVTWGTSPEMVASVNR 303

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
            +PDPA  +D V   +  +AL YMGL+PG PLT++ +DK+FIGSCTN+RIEDLR AA + 
Sbjct: 304 RVPDPAEESDAVRARAMGRALEYMGLEPGTPLTDIPMDKIFIGSCTNARIEDLREAAAVV 363

Query: 363 KGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421
            GR+VA  + QALVVPGSG VK QAE EGLD++F++AGFEWR PGCSMCL MN DRL PG
Sbjct: 364 HGRRVAENIRQALVVPGSGVVKQQAEGEGLDRVFLDAGFEWREPGCSMCLGMNPDRLEPG 423

Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           ERCASTSNRNFEGRQG+GGRTHL SPAM AAAA+ GHF DIR
Sbjct: 424 ERCASTSNRNFEGRQGQGGRTHLASPAMVAAAAIHGHFVDIR 465


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: 771
Number of extensions: 24
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: 466
Length of database: 466
Length adjustment: 33
Effective length of query: 433
Effective length of database: 433
Effective search space:   187489
Effective search space used:   187489
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_011814598.1 HHAL_RS09140 (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.510360.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.3e-236  768.9   0.0   9.8e-236  768.6   0.0    1.0  1  NCBI__GCF_000015585.1:WP_011814598.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015585.1:WP_011814598.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  768.6   0.0  9.8e-236  9.8e-236       2     465 ..       3     466 .]       2     466 .] 1.00

  Alignments for each domain:
  == domain 1  score: 768.6 bits;  conditional E-value: 9.8e-236
                             TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdvei 74 
                                            ktly+kl+d+hvv e ++++ llyidr l+hevtspqafeglr agr+  rv + la  dhn++t+ r   +
  NCBI__GCF_000015585.1:WP_011814598.1   3 GKTLYDKLWDSHVVTEYDDGSALLYIDRQLLHEVTSPQAFEGLRLAGRQPWRVASNLAVTDHNVPTTDRSQPV 75 
                                           59*********************************************************************** PP

                             TIGR00170  75 keekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigts 147
                                            + ++++q+++l++n+k+f v  f++++ +qgivhvvgpe+g tlpg+t+vcgdsht+thga+galafg+gts
  NCBI__GCF_000015585.1:WP_011814598.1  76 EDPVSRVQIETLDRNCKDFQVIEFGIRDPRQGIVHVVGPEQGTTLPGMTLVCGDSHTSTHGALGALAFGVGTS 148
                                           ************************************************************************* PP

                             TIGR00170 148 evehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvc 220
                                           evehvlatqtl+q++a+t+ i+++g+l +g+takdiilaiig+ig+aggtgy +e+ geair+lsme+rmt+c
  NCBI__GCF_000015585.1:WP_011814598.1 149 EVEHVLATQTLVQKKARTMLIRIDGQLGRGVTAKDIILAIIGRIGTAGGTGYALEYGGEAIRSLSMEGRMTIC 221
                                           ************************************************************************* PP

                             TIGR00170 221 nmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtn 293
                                           nm+ieaga++g++a d+tt+eyv++r+ ap g+ +++ava w+ l +de+a fd+vv l+a++i pqvtwgt+
  NCBI__GCF_000015585.1:WP_011814598.1 222 NMSIEAGARTGMVAVDDTTIEYVRGRPNAPEGALWDQAVASWRHLVSDEDAAFDRVVELHADEIEPQVTWGTS 294
                                           ************************************************************************* PP

                             TIGR00170 294 pgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkk 366
                                           p++v svn  vpdp++ +d v+ + + +al+y+glepgt+l+di +dk+figsctn+riedlr+aa+vv+g++
  NCBI__GCF_000015585.1:WP_011814598.1 295 PEMVASVNRRVPDPAEESDAVRARAMGRALEYMGLEPGTPLTDIPMDKIFIGSCTNARIEDLREAAAVVHGRR 367
                                           ************************************************************************* PP

                             TIGR00170 367 vadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgk 439
                                           va+n+++alvvpgsg vk+qae egld++fl+agfewre+gcs+clgmn+d+l+++ercastsnrnfegrqg+
  NCBI__GCF_000015585.1:WP_011814598.1 368 VAENIRQALVVPGSGVVKQQAEGEGLDRVFLDAGFEWREPGCSMCLGMNPDRLEPGERCASTSNRNFEGRQGQ 440
                                           ************************************************************************* PP

                             TIGR00170 440 garthlvspamaaaaavagkfvdire 465
                                           g+rthl spam aaaa++g+fvdire
  NCBI__GCF_000015585.1:WP_011814598.1 441 GGRTHLASPAMVAAAAIHGHFVDIRE 466
                                           ************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (466 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: 00:00:00.01
# Mc/sec: 21.20
//
[ok]

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