Alignments for a candidate for leuC in Nitriliruptor alkaliphilus DSM 45188

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Nitriliruptor alkaliphilus DSM 45188

Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_052666348.1 NITAL_RS11510 3-isopropylmalate dehydratase large subunit

Query= SwissProt::Q7TXH6
         (473 letters)



>NCBI__GCF_000969705.1:WP_052666348.1
          Length = 474

 Score =  583 bits (1504), Expect = e-171
 Identities = 286/464 (61%), Positives = 350/464 (75%), Gaps = 5/464 (1%)

Query: 8   PRTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELTLAT 67
           P+T+ EKIWD H+V SGG   PDL+Y+DLHLVHEVTSPQAF GLR AGR VRRP+LTLAT
Sbjct: 4   PKTIVEKIWDRHVVRSGGD-EPDLLYVDLHLVHEVTSPQAFSGLRAAGRAVRRPDLTLAT 62

Query: 68  EDHNVPT----VDIDQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGPQLG 123
            DHNVPT    V  + P+AD +S  Q++ +R N AEFGI+L  MG   QGIVH++GP+LG
Sbjct: 63  MDHNVPTDPRQVSGELPMADELSVAQMDAMRDNAAEFGIKLFEMGSRNQGIVHIIGPELG 122

Query: 124 LTQPGMTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGRLPD 183
           +TQPG  IVCGDSHT+THGAFGALA GIGTSEVEHVLATQTLP    KT+A+ V+G LP 
Sbjct: 123 ITQPGSVIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLPQARPKTLAIEVEGALPA 182

Query: 184 GVSAKDIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMVAPD 243
           G +AKD+IL ++  IG  GG G VIEYRG AI  LSME RMT+CNMSIE GARAG++APD
Sbjct: 183 GTTAKDLILHILGVIGVDGGVGQVIEYRGQAIRDLSMEARMTVCNMSIEGGARAGLIAPD 242

Query: 244 ETTYAFLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTNPGQ 303
           ETT+A+L+ RP+AP GA WD A+  W+ L TD GA FD  V + AA + P VTWGT P Q
Sbjct: 243 ETTFAYLKDRPYAPKGADWDAAVEDWRSLVTDEGATFDRTVTIQAADVVPTVTWGTTPAQ 302

Query: 304 GVPLAAAVPDPQLMTDDAERQAAEKALAYMDLRPGTAMREIAVDAVFVGSCTNGRIEDLR 363
            VP+   VP  +   D+   +   ++L YM L+ G  + ++ VD VF+GSCTNGRIEDLR
Sbjct: 303 SVPVTGTVPRVEDAPDEGTARQYRRSLDYMGLQGGERIADLTVDKVFIGSCTNGRIEDLR 362

Query: 364 VVAEVLRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGMNPD 423
            VAE+++G++ ADGV +++VPGS  V+  AEAEG+ ++  +AG  WR  GCSMCLGMNPD
Sbjct: 363 AVAEIVKGKRKADGVEVMVVPGSGLVKEAAEAEGIADVLIEAGFDWRAPGCSMCLGMNPD 422

Query: 424 QLASGERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLS 467
           QLA  ERCA+TSNRNFEGRQG  GRTHLVSPA+AAA A+ G L+
Sbjct: 423 QLAPEERCASTSNRNFEGRQGFKGRTHLVSPAMAAAAALTGRLT 466


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: 750
Number of extensions: 28
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: 474
Length adjustment: 33
Effective length of query: 440
Effective length of database: 441
Effective search space:   194040
Effective search space used:   194040
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_052666348.1 NITAL_RS11510 (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.30231.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.6e-229  746.6   0.1   5.3e-229  746.4   0.1    1.0  1  lcl|NCBI__GCF_000969705.1:WP_052666348.1  NITAL_RS11510 3-isopropylmalate 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000969705.1:WP_052666348.1  NITAL_RS11510 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  746.4   0.1  5.3e-229  5.3e-229       2     465 ..       4     470 ..       3     471 .. 0.99

  Alignments for each domain:
  == domain 1  score: 746.4 bits;  conditional E-value: 5.3e-229
                                 TIGR00170   2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr 70 
                                               +kt++ek++d hvv+ + +e+dlly+d+hlvhevtspqaf glraagr vrr+d tlat+dhn++t+ r
  lcl|NCBI__GCF_000969705.1:WP_052666348.1   4 PKTIVEKIWDRHVVRSGGDEPDLLYVDLHLVHEVTSPQAFSGLRAAGRAVRRPDLTLATMDHNVPTDPR 72 
                                               89*****************************************************************99 PP

                                 TIGR00170  71 ....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathg 135
                                                   ++ + +e +  q+ ++  n+ efg+klf++ s +qgivh++gpe g+t pg  ivcgdshtathg
  lcl|NCBI__GCF_000969705.1:WP_052666348.1  73 qvsgELPMADELSVAQMDAMRDNAAEFGIKLFEMGSRNQGIVHIIGPELGITQPGSVIVCGDSHTATHG 141
                                               666667789************************************************************ PP

                                 TIGR00170 136 afgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefa 204
                                               afgalafgigtsevehvlatqtl qar+ktl ieveg l  g takd+il i+g igv gg g+v+e+ 
  lcl|NCBI__GCF_000969705.1:WP_052666348.1 142 AFGALAFGIGTSEVEHVLATQTLPQARPKTLAIEVEGALPAGTTAKDLILHILGVIGVDGGVGQVIEYR 210
                                               ********************************************************************* PP

                                 TIGR00170 205 geairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakf 273
                                               g+airdlsme+rmtvcnm+ie ga+agliapdettf+y+kdr+yapkg++++ av+ w++l tdega+f
  lcl|NCBI__GCF_000969705.1:WP_052666348.1 211 GQAIRDLSMEARMTVCNMSIEGGARAGLIAPDETTFAYLKDRPYAPKGADWDAAVEDWRSLVTDEGATF 279
                                               ********************************************************************* PP

                                 TIGR00170 274 dkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkv 342
                                               d++vt++a d++p+vtwgt+p q ++v+++vp  ++  d+   ++  ++l+y+gl+ g ++ d+ vdkv
  lcl|NCBI__GCF_000969705.1:WP_052666348.1 280 DRTVTIQAADVVPTVTWGTTPAQSVPVTGTVPRVEDAPDEGTARQYRRSLDYMGLQGGERIADLTVDKV 348
                                               ********************************************************************* PP

                                 TIGR00170 343 figsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslc 411
                                               figsctn+riedlra ae+vkgk++ad+v+ ++vvpgsglvk+ ae+eg+  +++eagf+wr +gcs+c
  lcl|NCBI__GCF_000969705.1:WP_052666348.1 349 FIGSCTNGRIEDLRAVAEIVKGKRKADGVE-VMVVPGSGLVKEAAEAEGIADVLIEAGFDWRAPGCSMC 416
                                               ******************************.************************************** PP

                                 TIGR00170 412 lgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465
                                               lgmn+d+l + ercastsnrnfegrqg ++rthlvspamaaaaa++g++ d+r 
  lcl|NCBI__GCF_000969705.1:WP_052666348.1 417 LGMNPDQLAPEERCASTSNRNFEGRQGFKGRTHLVSPAMAAAAALTGRLTDVRT 470
                                               ****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (474 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: 11.40
//
[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