Alignments for a candidate for leuB in Maridesulfovibrio zosterae DSM 11974

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Maridesulfovibrio zosterae DSM 11974

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_027722231.1 H589_RS0111950 3-isopropylmalate dehydrogenase

Query= BRENDA::Q9SA14
         (404 letters)



>NCBI__GCF_000425265.1:WP_027722231.1
          Length = 355

 Score =  441 bits (1134), Expect = e-128
 Identities = 225/354 (63%), Positives = 271/354 (76%), Gaps = 2/354 (0%)

Query: 46  ITLLPGDGIGPEVISVAKNVLQKAGFLQGLEFDFQEMPFGGAALDLVGVPLPEETSTAAK 105
           I ++PGDGIGPE++     VL       G  F+  E   GG A+D  GVPLP+ T  A K
Sbjct: 3   ICMMPGDGIGPEIMEQGIKVLNVIADRFGHNFETTEALIGGIAIDETGVPLPDATVKACK 62

Query: 106 QSDAILLGAIGGYKWDKNEKHLRPEMGLLNIRRDLNVFANLRPATVLPQLVDASTLKKE- 164
           ++DA+LLGA+GG KWD  +  +RPE GLL IR++L++FANLRPA + PQL DA  L+ + 
Sbjct: 63  EADAVLLGAVGGPKWDTIDPAIRPEKGLLGIRKELSLFANLRPAALFPQLKDACFLRPDI 122

Query: 165 VAQGVDMMIVRELTGGIYFGEPRGITINENGEEVGFNTEIYAAHEIDRIARVAFETARKR 224
           VA+G+D+M+VRELTGGIYFGEPRG T  ENGE +G+NT +Y  HE+ RIA+VAFE ARKR
Sbjct: 123 VAKGIDVMVVRELTGGIYFGEPRG-TKEENGERMGYNTMVYYEHEVRRIAKVAFEAARKR 181

Query: 225 RGKLCSVDKANVLDASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTN 284
           + +LCSVDKANVLD S +WR+ V  +A +YPDVELSHMYVDNAAMQLVRDP QFD IVT 
Sbjct: 182 KKRLCSVDKANVLDVSRVWREIVIEVAEDYPDVELSHMYVDNAAMQLVRDPSQFDVIVTG 241

Query: 285 NIFGDILSDEASMITGSIGMLPSASLGESGPGLFEPIHGSAPDIAGQDKANPLATILSAA 344
           N+FGDILSDEA++ITGSIGMLPSASLGES PGLFEPIHGSAPDIAGQ+KANPLATILS A
Sbjct: 242 NLFGDILSDEAAVITGSIGMLPSASLGESNPGLFEPIHGSAPDIAGQNKANPLATILSIA 301

Query: 345 MLLKYGLGEEKAAKMIEDAVVDALNKGFRTGDIYSPGNKLVGCKEMGEEVLKSV 398
           M+L+Y     + A  IE AV   L +G RTGDI   G  LVGC EMGE V+K++
Sbjct: 302 MMLRYSFNMTEEADCIEAAVEKTLAQGLRTGDIMDEGGTLVGCTEMGEAVIKNL 355


Lambda     K      H
   0.317    0.136    0.389 

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: 464
Number of extensions: 17
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: 404
Length of database: 355
Length adjustment: 30
Effective length of query: 374
Effective length of database: 325
Effective search space:   121550
Effective search space used:   121550
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: 50 (23.9 bits)

Align candidate WP_027722231.1 H589_RS0111950 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))

# 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/TIGR00169.hmm
# target sequence database:        /tmp/gapView.3482400.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00169  [M=349]
Accession:   TIGR00169
Description: leuB: 3-isopropylmalate dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.3e-169  549.7   0.0   1.5e-169  549.5   0.0    1.0  1  NCBI__GCF_000425265.1:WP_027722231.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000425265.1:WP_027722231.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  549.5   0.0  1.5e-169  1.5e-169       1     348 [.       2     350 ..       2     351 .. 0.99

  Alignments for each domain:
  == domain 1  score: 549.5 bits;  conditional E-value: 1.5e-169
                             TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 
                                           ki ++pGDgiGpe++++ +kvL+++++rf++++e+ ealiGG aid+tg Plp++t+kackeadavLlgavGG
  NCBI__GCF_000425265.1:WP_027722231.1   2 KICMMPGDGIGPEIMEQGIKVLNVIADRFGHNFETTEALIGGIAIDETGVPLPDATVKACKEADAVLLGAVGG 74 
                                           799********************************************************************** PP

                             TIGR00169  74 pkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepker 145
                                           pkWd+  + +rPekgLL +rkel lfanLrPa lf++L++++ l+++iv kg+D++vvreLtgGiYfGep+++
  NCBI__GCF_000425265.1:WP_027722231.1  75 PKWDTIDPAIRPEKGLLGIRKELSLFANLRPAALFPQLKDACFLRPDIVaKGIDVMVVRELTGGIYFGEPRGT 147
                                           ************************************************99*********************** PP

                             TIGR00169 146 eeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehly 218
                                           +e++ e+ +++t++Y+++e++ria+vafe+arkr+k+++svDkanvL++sr+Wr++v e+a++yPdvel+h+y
  NCBI__GCF_000425265.1:WP_027722231.1 148 KEENGERMGYNTMVYYEHEVRRIAKVAFEAARKRKKRLCSVDKANVLDVSRVWREIVIEVAEDYPDVELSHMY 220
                                           **888******************************************************************** PP

                             TIGR00169 219 iDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianp 291
                                           +DnaamqLv++P+q+dv+vt+nlfGDilsDea+vitGs+G+LPsasl+++  +lfep+hgsapdiag++ anp
  NCBI__GCF_000425265.1:WP_027722231.1 221 VDNAAMQLVRDPSQFDVIVTGNLFGDILSDEAAVITGSIGMLPSASLGESNPGLFEPIHGSAPDIAGQNKANP 293
                                           ************************************************************************* PP

                             TIGR00169 292 iaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                           +a+ils+a++lrys+n+ e+a+ ieaav+k+l++g rt d+++e++t v+++e++e 
  NCBI__GCF_000425265.1:WP_027722231.1 294 LATILSIAMMLRYSFNMTEEADCIEAAVEKTLAQGLRTGDIMDEGGTLVGCTEMGEA 350
                                           ******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (355 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: 14.74
//
[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