Alignments for a candidate for leuC in Haloglycomyces albus DSM 45210

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Haloglycomyces albus DSM 45210

Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_025272325.1 HALAL_RS0101595 3-isopropylmalate dehydratase large subunit

Query= SwissProt::Q7TXH6
         (473 letters)



>NCBI__GCF_000527155.1:WP_025272325.1
          Length = 462

 Score =  686 bits (1770), Expect = 0.0
 Identities = 332/463 (71%), Positives = 386/463 (83%), Gaps = 2/463 (0%)

Query: 10  TLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELTLATED 69
           TLAEKIW DH+V S  G  PDL+YIDLHL+HEVTSPQAFDGLR  GRRVRR +LT+ATED
Sbjct: 2   TLAEKIWADHVVSSAAG-QPDLLYIDLHLLHEVTSPQAFDGLRQEGRRVRRTDLTIATED 60

Query: 70  HNVPTVDIDQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGPQLGLTQPGM 129
           HN PT ++   I+DP SR QV+TLR NC EFG+RLH +GD EQG+VHVVGPQLGLTQPG 
Sbjct: 61  HNTPTDNLFT-ISDPTSRKQVDTLRANCEEFGVRLHPLGDEEQGVVHVVGPQLGLTQPGT 119

Query: 130 TIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGRLPDGVSAKD 189
           T+VCGDSHTSTHGAFGA+A GIGTSEVEHVLATQTLP    KTMAV V+G LPDGVS KD
Sbjct: 120 TVVCGDSHTSTHGAFGAVAFGIGTSEVEHVLATQTLPQSTPKTMAVTVNGSLPDGVSPKD 179

Query: 190 IILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMVAPDETTYAF 249
           +ILA+IA+ GTGGG+GH++EYRG AIE +SMEGRMT+CNMSIE GA+AG++APDETT+A+
Sbjct: 180 LILAVIARAGTGGGKGHIVEYRGQAIEEMSMEGRMTVCNMSIEWGAKAGLIAPDETTFAY 239

Query: 250 LRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTNPGQGVPLAA 309
           L+ +P+AP G  WD A+ YW+ L TD  A FD E+ +DA  LSP+VTWGTNPGQG PL +
Sbjct: 240 LKDKPNAPQGTDWDAAVEYWRGLHTDADAEFDHEIVIDATELSPYVTWGTNPGQGAPLNS 299

Query: 310 AVPDPQLMTDDAERQAAEKALAYMDLRPGTAMREIAVDAVFVGSCTNGRIEDLRVVAEVL 369
            VP P+   D  ER+A  KAL YMDL  G  +R++ V+ VF+GSCTNGRIEDLR  A ++
Sbjct: 300 TVPSPEDFDDADEREATRKALDYMDLTAGQVLRDVGVNVVFLGSCTNGRIEDLRTAAAMI 359

Query: 370 RGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGMNPDQLASGE 429
            GR VADGVRML+VPGS RVRAQAE+EGL ++FT AGA+WR AGCSMCLGMNPDQL++GE
Sbjct: 360 EGRSVADGVRMLVVPGSARVRAQAESEGLDQVFTKAGAEWRFAGCSMCLGMNPDQLSAGE 419

Query: 430 RCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLSSPADL 472
           R A+TSNRNFEGRQG GGRTHLVSPAVAAATAVRGTLSSPADL
Sbjct: 420 RAASTSNRNFEGRQGKGGRTHLVSPAVAAATAVRGTLSSPADL 462


Lambda     K      H
   0.319    0.135    0.402 

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: 806
Number of extensions: 26
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: 473
Length of database: 462
Length adjustment: 33
Effective length of query: 440
Effective length of database: 429
Effective search space:   188760
Effective search space used:   188760
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate WP_025272325.1 HALAL_RS0101595 (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.1431250.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-222  723.7   0.0   4.9e-222  723.5   0.0    1.0  1  NCBI__GCF_000527155.1:WP_025272325.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000527155.1:WP_025272325.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  723.5   0.0  4.9e-222  4.9e-222       4     460 ..       2     456 ..       1     461 [. 0.99

  Alignments for each domain:
  == domain 1  score: 723.5 bits;  conditional E-value: 4.9e-222
                             TIGR00170   4 tlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveike 76 
                                           tl ek++  hvv  a +++dllyid+hl+hevtspqaf+glr++gr+vrr+d t+at dhn +t++  ++i +
  NCBI__GCF_000527155.1:WP_025272325.1   2 TLAEKIWADHVVSSAAGQPDLLYIDLHLLHEVTSPQAFDGLRQEGRRVRRTDLTIATEDHNTPTDNL-FTISD 73 
                                           899**************************************************************99.9**** PP

                             TIGR00170  77 ekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsev 149
                                            +++ qv +l  n++efgv+l+ l ++eqg+vhvvgp+ glt pg+t+vcgdsht+thgafga+afgigtsev
  NCBI__GCF_000527155.1:WP_025272325.1  74 PTSRKQVDTLRANCEEFGVRLHPLGDEEQGVVHVVGPQLGLTQPGTTVVCGDSHTSTHGAFGAVAFGIGTSEV 146
                                           ************************************************************************* PP

                             TIGR00170 150 ehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnm 222
                                           ehvlatqtl q+ +kt+ ++v+g l +g++ kd+ila+i + g+ gg g++ve+ g+ai+++sme+rmtvcnm
  NCBI__GCF_000527155.1:WP_025272325.1 147 EHVLATQTLPQSTPKTMAVTVNGSLPDGVSPKDLILAVIARAGTGGGKGHIVEYRGQAIEEMSMEGRMTVCNM 219
                                           ************************************************************************* PP

                             TIGR00170 223 aieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpg 295
                                           +ie gakagliapdettf+y+kd++ ap+g +++ av+yw+ l+td +a+fd++++++a+++sp vtwgtnpg
  NCBI__GCF_000527155.1:WP_025272325.1 220 SIEWGAKAGLIAPDETTFAYLKDKPNAPQGTDWDAAVEYWRGLHTDADAEFDHEIVIDATELSPYVTWGTNPG 292
                                           ************************************************************************* PP

                             TIGR00170 296 qvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkva 368
                                           q  ++n++vp+p+++ d +e++ + kal+y+ l++g+ l+d+ v+ vf+gsctn+riedlr+aa+++ g+ va
  NCBI__GCF_000527155.1:WP_025272325.1 293 QGAPLNSTVPSPEDFDDADEREATRKALDYMDLTAGQVLRDVGVNVVFLGSCTNGRIEDLRTAAAMIEGRSVA 365
                                           ************************************************************************* PP

                             TIGR00170 369 dnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkga 441
                                           d+v+ +lvvpgs  v++qae egld++f +ag+ewr agcs+clgmn+d+l+++er astsnrnfegrqgkg+
  NCBI__GCF_000527155.1:WP_025272325.1 366 DGVR-MLVVPGSARVRAQAESEGLDQVFTKAGAEWRFAGCSMCLGMNPDQLSAGERAASTSNRNFEGRQGKGG 437
                                           ****.9******************************************************************* PP

                             TIGR00170 442 rthlvspamaaaaavagkf 460
                                           rthlvspa+aaa+av g +
  NCBI__GCF_000527155.1:WP_025272325.1 438 RTHLVSPAVAAATAVRGTL 456
                                           ***************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (462 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: 26.73
//
[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 2024 update 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 original 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