Alignments for a candidate for leuC in Amycolatopsis halophila YIM 93223

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Amycolatopsis halophila YIM 93223

Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_034273535.1 AMYHA_RS20130 3-isopropylmalate dehydratase large subunit

Query= SwissProt::Q7TXH6
         (473 letters)



>NCBI__GCF_000504245.1:WP_034273535.1
          Length = 485

 Score =  740 bits (1910), Expect = 0.0
 Identities = 366/481 (76%), Positives = 407/481 (84%), Gaps = 11/481 (2%)

Query: 1   MALQTGEPRTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRR 60
           M   TG  RTLAEK+WD H+V  G G  PD++YIDLHLVHEVTSPQAFDGLRLAGR VRR
Sbjct: 1   MTATTG--RTLAEKVWDAHVVRRGDGAEPDVLYIDLHLVHEVTSPQAFDGLRLAGRPVRR 58

Query: 61  PELTLATEDHNVPTVDIDQP---------IADPVSRTQVETLRRNCAEFGIRLHSMGDIE 111
           P+LT+ATEDHNVPT     P         I DPVSRTQV TLR+NC EFG+RLH MGD E
Sbjct: 59  PDLTIATEDHNVPTTWTLDPSRKSADIEAIEDPVSRTQVSTLRKNCEEFGVRLHPMGDAE 118

Query: 112 QGIVHVVGPQLGLTQPGMTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFK 171
           QGIVHV+GPQLGLTQPGMT+VCGDSHTSTHGAFGA+A GIGTSEVEHVLATQTLPLRPFK
Sbjct: 119 QGIVHVIGPQLGLTQPGMTVVCGDSHTSTHGAFGAMAFGIGTSEVEHVLATQTLPLRPFK 178

Query: 172 TMAVNVDGRLPDGVSAKDIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSI 231
           TMAVNV G+L  GV+AKDIILA+IAKIGTGGGQG+V+EYRG AIESLSME RMTICNMSI
Sbjct: 179 TMAVNVTGKLRPGVTAKDIILAVIAKIGTGGGQGYVLEYRGEAIESLSMEARMTICNMSI 238

Query: 232 EAGARAGMVAPDETTYAFLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASL 291
           EAGARAGM+APDETT+ +L+GRPHAP GA WD A+  W+ L TD  A FDTEV ++A  L
Sbjct: 239 EAGARAGMIAPDETTFEYLKGRPHAPQGADWDEAVAAWRALPTDDDAEFDTEVEINADEL 298

Query: 292 SPFVTWGTNPGQGVPLAAAVPDPQLMTDDAERQAAEKALAYMDLRPGTAMREIAVDAVFV 351
           +PFVTWGTNPGQG+PL+ +VPDP+ + D+  R +AEKALAYMDL+PGT +REIAVD VF+
Sbjct: 299 TPFVTWGTNPGQGLPLSESVPDPEQIADETARYSAEKALAYMDLKPGTPLREIAVDTVFL 358

Query: 352 GSCTNGRIEDLRVVAEVLRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQ 411
           GSCTNGRIEDLR  A+VL G KVADGVRML+VPGSMRVR  AE EGL ++F DAGA+WRQ
Sbjct: 359 GSCTNGRIEDLRAAADVLAGHKVADGVRMLVVPGSMRVRKLAEEEGLDKVFLDAGAEWRQ 418

Query: 412 AGCSMCLGMNPDQLASGERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLSSPAD 471
           AGCSMCLGMNPDQL  GER A+TSNRNFEGRQG GGRTHLVSP VAAATAVRGTLSSP D
Sbjct: 419 AGCSMCLGMNPDQLTPGERSASTSNRNFEGRQGKGGRTHLVSPLVAAATAVRGTLSSPED 478

Query: 472 L 472
           L
Sbjct: 479 L 479


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: 857
Number of extensions: 22
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: 473
Length of database: 485
Length adjustment: 34
Effective length of query: 439
Effective length of database: 451
Effective search space:   197989
Effective search space used:   197989
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_034273535.1 AMYHA_RS20130 (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.2918229.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-230  750.1   0.0   5.1e-230  749.8   0.0    1.0  1  NCBI__GCF_000504245.1:WP_034273535.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000504245.1:WP_034273535.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  749.8   0.0  5.1e-230  5.1e-230       2     460 ..       6     473 ..       5     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 749.8 bits;  conditional E-value: 5.1e-230
                             TIGR00170   2 aktlyeklfdahvvkeaen.etdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr... 70 
                                            +tl ek++dahvv+++++ e+d+lyid+hlvhevtspqaf+glr agr+vrr+d t+at dhn++t+     
  NCBI__GCF_000504245.1:WP_034273535.1   6 GRTLAEKVWDAHVVRRGDGaEPDVLYIDLHLVHEVTSPQAFDGLRLAGRPVRRPDLTIATEDHNVPTTWTldp 78 
                                           59************998763799********************************************977788 PP

                             TIGR00170  71 .....dveik.eekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgaf 137
                                                d+e+  + +++ qv +l kn++efgv+l+ + +aeqgivhv+gp+ glt pg+t+vcgdsht+thgaf
  NCBI__GCF_000504245.1:WP_034273535.1  79 srksaDIEAIeDPVSRTQVSTLRKNCEEFGVRLHPMGDAEQGIVHVIGPQLGLTQPGMTVVCGDSHTSTHGAF 151
                                           889999987615699********************************************************** PP

                             TIGR00170 138 galafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageaird 210
                                           ga+afgigtsevehvlatqtl     kt+ ++v gkl +g+takdiila+i kig+ gg gyv+e+ geai++
  NCBI__GCF_000504245.1:WP_034273535.1 152 GAMAFGIGTSEVEHVLATQTLPLRPFKTMAVNVTGKLRPGVTAKDIILAVIAKIGTGGGQGYVLEYRGEAIES 224
                                           ************************************************************************* PP

                             TIGR00170 211 lsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakd 283
                                           lsme+rmt+cnm+ieaga+ag+iapdettfey+k+r++ap+g+++++ava w++l td++a+fd++v ++a++
  NCBI__GCF_000504245.1:WP_034273535.1 225 LSMEARMTICNMSIEAGARAGMIAPDETTFEYLKGRPHAPQGADWDEAVAAWRALPTDDDAEFDTEVEINADE 297
                                           ************************************************************************* PP

                             TIGR00170 284 ispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlr 356
                                           ++p vtwgtnpgq l+++e+vpdp+++ad+  + saekalay+ l+pgt+l++i+vd vf+gsctn+riedlr
  NCBI__GCF_000504245.1:WP_034273535.1 298 LTPFVTWGTNPGQGLPLSESVPDPEQIADETARYSAEKALAYMDLKPGTPLREIAVDTVFLGSCTNGRIEDLR 370
                                           ************************************************************************* PP

                             TIGR00170 357 aaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercasts 429
                                           aaa+v+ g+kvad+v+ +lvvpgs  v+k ae+egldk+fl+ag+ewr+agcs+clgmn+d+l ++er asts
  NCBI__GCF_000504245.1:WP_034273535.1 371 AAADVLAGHKVADGVR-MLVVPGSMRVRKLAEEEGLDKVFLDAGAEWRQAGCSMCLGMNPDQLTPGERSASTS 442
                                           ****************.9******************************************************* PP

                             TIGR00170 430 nrnfegrqgkgarthlvspamaaaaavagkf 460
                                           nrnfegrqgkg+rthlvsp +aaa+av g +
  NCBI__GCF_000504245.1:WP_034273535.1 443 NRNFEGRQGKGGRTHLVSPLVAAATAVRGTL 473
                                           ***************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (485 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: 00:00:00.00
# Mc/sec: 30.21
//
[ok]

This GapMind analysis is from Jul 26 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