Alignments for a candidate for leuC in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuC in Saccharomonospora cyanea NA-134

Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_005454248.1 SACCYDRAFT_RS05155 3-isopropylmalate dehydratase large subunit

Query= SwissProt::Q7TXH6
         (473 letters)



>NCBI__GCF_000244975.1:WP_005454248.1
          Length = 471

 Score =  774 bits (1998), Expect = 0.0
 Identities = 375/465 (80%), Positives = 418/465 (89%)

Query: 9   RTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELTLATE 68
           RTLAEK+WD H V  G G  PDL+YIDLHLVHEVTSPQAFDGLRLAGR+VRRP+LT+ATE
Sbjct: 7   RTLAEKVWDAHTVRRGDGAEPDLLYIDLHLVHEVTSPQAFDGLRLAGRKVRRPDLTIATE 66

Query: 69  DHNVPTVDIDQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGPQLGLTQPG 128
           DHNVPTV I+ PIADPVSRTQVETLRRNC EFG+RLH MGD EQGIVHV+GPQLGLTQPG
Sbjct: 67  DHNVPTVGIELPIADPVSRTQVETLRRNCEEFGVRLHPMGDDEQGIVHVIGPQLGLTQPG 126

Query: 129 MTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGRLPDGVSAK 188
           MT+VCGDSHTSTHGAFGA+A GIGTSEVEHVLATQTLPLRPFKTMAVNV+G L  GV+AK
Sbjct: 127 MTVVCGDSHTSTHGAFGAMAFGIGTSEVEHVLATQTLPLRPFKTMAVNVEGELRPGVTAK 186

Query: 189 DIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMVAPDETTYA 248
           DIILA+IAKIGTGGGQG+V+EYRGSAIESLSME RMTICNMSIEAGARAGM+APDETT+A
Sbjct: 187 DIILAVIAKIGTGGGQGYVLEYRGSAIESLSMEARMTICNMSIEAGARAGMIAPDETTFA 246

Query: 249 FLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTNPGQGVPLA 308
           +L+ RPHAP GA+WD A+  W+ LRTD  AVFD EV+L+A+ L+PFVTWGTNPGQG+PLA
Sbjct: 247 YLKDRPHAPKGAEWDAAVAEWRELRTDDDAVFDAEVHLNASELTPFVTWGTNPGQGLPLA 306

Query: 309 AAVPDPQLMTDDAERQAAEKALAYMDLRPGTAMREIAVDAVFVGSCTNGRIEDLRVVAEV 368
            +VPDP+ + D+ ER AAEKAL+YMDL PGT +R+IAVD VF+GSCTNGR+EDLR  AEV
Sbjct: 307 ESVPDPERIADENERLAAEKALSYMDLEPGTPLRDIAVDTVFLGSCTNGRLEDLRAAAEV 366

Query: 369 LRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGMNPDQLASG 428
           LRGRKVADGVRML+VPGSMRVR  AEAEGL E+FT+AGA+WR AGCSMCLGMNPDQL  G
Sbjct: 367 LRGRKVADGVRMLVVPGSMRVRQAAEAEGLHEVFTEAGAEWRAAGCSMCLGMNPDQLKPG 426

Query: 429 ERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLSSPADLN 473
           ER A+TSNRNFEGRQG GGRTHLVSP VAAATAVRGTL+SP DL+
Sbjct: 427 ERSASTSNRNFEGRQGKGGRTHLVSPLVAAATAVRGTLASPEDLD 471


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: 878
Number of extensions: 25
Number of successful extensions: 1
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: 471
Length adjustment: 33
Effective length of query: 440
Effective length of database: 438
Effective search space:   192720
Effective search space used:   192720
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_005454248.1 SACCYDRAFT_RS05155 (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.15460.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.5e-230  749.9   0.0   5.7e-230  749.6   0.0    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005454248.1  SACCYDRAFT_RS05155 3-isopropylma


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005454248.1  SACCYDRAFT_RS05155 3-isopropylmalate dehydratase large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  749.6   0.0  5.7e-230  5.7e-230       3     460 ..       7     464 ..       5     469 .. 0.99

  Alignments for each domain:
  == domain 1  score: 749.6 bits;  conditional E-value: 5.7e-230
                                 TIGR00170   3 ktlyeklfdahvvkeaen.etdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr 70 
                                               +tl ek++dah v+++++ e+dllyid+hlvhevtspqaf+glr agrkvrr+d t+at dhn++t+  
  lcl|NCBI__GCF_000244975.1:WP_005454248.1   7 RTLAEKVWDAHTVRRGDGaEPDLLYIDLHLVHEVTSPQAFDGLRLAGRKVRRPDLTIATEDHNVPTVGI 75 
                                               9************998763899*********************************************** PP

                                 TIGR00170  71 dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafga 139
                                               ++ i + +++ qv++l +n++efgv+l+ + + eqgivhv+gp+ glt pg+t+vcgdsht+thgafga
  lcl|NCBI__GCF_000244975.1:WP_005454248.1  76 ELPIADPVSRTQVETLRRNCEEFGVRLHPMGDDEQGIVHVIGPQLGLTQPGMTVVCGDSHTSTHGAFGA 144
                                               ********************************************************************* PP

                                 TIGR00170 140 lafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageai 208
                                               +afgigtsevehvlatqtl     kt+ ++veg+l +g+takdiila+i kig+ gg gyv+e+ g ai
  lcl|NCBI__GCF_000244975.1:WP_005454248.1 145 MAFGIGTSEVEHVLATQTLPLRPFKTMAVNVEGELRPGVTAKDIILAVIAKIGTGGGQGYVLEYRGSAI 213
                                               ********************************************************************* PP

                                 TIGR00170 209 rdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvv 277
                                               ++lsme+rmt+cnm+ieaga+ag+iapdettf+y+kdr++apkg+e++ ava+w+ l+td++a+fd +v
  lcl|NCBI__GCF_000244975.1:WP_005454248.1 214 ESLSMEARMTICNMSIEAGARAGMIAPDETTFAYLKDRPHAPKGAEWDAAVAEWRELRTDDDAVFDAEV 282
                                               ********************************************************************* PP

                                 TIGR00170 278 tleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigs 346
                                                l+a++++p vtwgtnpgq l++ e+vpdp+ +ad+ e+  aekal+y+ lepgt+l+di+vd vf+gs
  lcl|NCBI__GCF_000244975.1:WP_005454248.1 283 HLNASELTPFVTWGTNPGQGLPLAESVPDPERIADENERLAAEKALSYMDLEPGTPLRDIAVDTVFLGS 351
                                               ********************************************************************* PP

                                 TIGR00170 347 ctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmn 415
                                               ctn+r+edlraaaev++g+kvad+v+ +lvvpgs  v++ ae+egl ++f eag+ewr agcs+clgmn
  lcl|NCBI__GCF_000244975.1:WP_005454248.1 352 CTNGRLEDLRAAAEVLRGRKVADGVR-MLVVPGSMRVRQAAEAEGLHEVFTEAGAEWRAAGCSMCLGMN 419
                                               **************************.9***************************************** PP

                                 TIGR00170 416 ndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkf 460
                                               +d+l+++er astsnrnfegrqgkg+rthlvsp +aaa+av g +
  lcl|NCBI__GCF_000244975.1:WP_005454248.1 420 PDQLKPGERSASTSNRNFEGRQGKGGRTHLVSPLVAAATAVRGTL 464
                                               ******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (471 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: 00:00:00.04
# Mc/sec: 5.44
//
[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