Alignments for a candidate for leuB in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Desulfitobacterium hafniense DCB-2

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_005816724.1 DHAF_RS12335 3-isopropylmalate dehydrogenase

Query= SwissProt::P12010
         (366 letters)



>NCBI__GCF_000021925.1:WP_005816724.1
          Length = 352

 Score =  398 bits (1022), Expect = e-115
 Identities = 210/353 (59%), Positives = 258/353 (73%), Gaps = 4/353 (1%)

Query: 4   KLAVLPGDGIGPEVMDAAIRVLKTVLDNDGHEAVFENALIGGAAIDEAGTPLPEETLDIC 63
           K+AVLPGDGIG E++  A+RVLK VL     E  F++  IGGAAI+  G  LP+ETL  C
Sbjct: 3   KIAVLPGDGIGQEIIPQAVRVLKAVLAETDAEFEFQDYPIGGAAIELVGKALPDETLQGC 62

Query: 64  RRSDAILLGAVGGPKWDHNPASLRPEKG-LLGLRKEMGLFANLRPVKAYATLLNASPLKR 122
           R +DA+LLGAVGG +WDH PAS RPE   LLGLRK +  +AN+RPV+   +LL  S LK 
Sbjct: 63  READAVLLGAVGGHQWDHLPASERPETAALLGLRKGLNFYANIRPVRMIPSLLATSTLKE 122

Query: 123 ERVENVDLVIVRELTGGLYFGRPSERRGPGENEVVDTLAYTREEIERIIEKAFQLAQIRR 182
             ++ VD+V++RELTGG+YFG       P      D + Y+ EEI RI+ + F+ A +R 
Sbjct: 123 NVLDGVDMVVIRELTGGVYFGEKGRSDNP--RSAYDKMTYSEEEIRRILIQGFETAMLRS 180

Query: 183 KKLASVDKANVLESSRMWREIAEETAKKYPDVELSHMLVDSTSMQLIANPGQFDVIVTEN 242
           KKL SVDKANVLE+SR+WREIA E AK+YP+VEL+HM VD+ +MQL+ NP QFDVIVTEN
Sbjct: 181 KKLCSVDKANVLETSRLWREIANELAKEYPEVELTHMYVDNAAMQLVRNPKQFDVIVTEN 240

Query: 243 MFGDILSDEASVITGSLGMLPSASLRSDRFGMYEPVHGSAPDIAGQGKANPLGTVLSAAL 302
           MFGDIL+D AS++ GS+GML SASL S   GMYEP HGSAPDIAG+  ANPL T+LSAAL
Sbjct: 241 MFGDILTDLASMLGGSIGMLSSASL-SGTQGMYEPAHGSAPDIAGKNLANPLATILSAAL 299

Query: 303 MLRYSFGLEKEAAAIEKAVDDVLQDGYCTGDLQVANGKVVSTIELTDRLIEKL 355
           MLRYSFG+E EA  IE AV+ VL+ GY TGDL  A  KVV TIE+ D ++  L
Sbjct: 300 MLRYSFGMEAEALRIESAVEKVLEQGYRTGDLAQAGDKVVGTIEMGDAVLAAL 352


Lambda     K      H
   0.316    0.135    0.379 

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: 417
Number of extensions: 20
Number of successful extensions: 4
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: 366
Length of database: 352
Length adjustment: 29
Effective length of query: 337
Effective length of database: 323
Effective search space:   108851
Effective search space used:   108851
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_005816724.1 DHAF_RS12335 (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.26000.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.7e-152  492.0   0.0   5.4e-152  491.8   0.0    1.0  1  lcl|NCBI__GCF_000021925.1:WP_005816724.1  DHAF_RS12335 3-isopropylmalate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021925.1:WP_005816724.1  DHAF_RS12335 3-isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  491.8   0.0  5.4e-152  5.4e-152       1     348 [.       3     347 ..       3     348 .. 0.98

  Alignments for each domain:
  == domain 1  score: 491.8 bits;  conditional E-value: 5.4e-152
                                 TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 
                                               kiavLpGDgiG+e++ +a++vLkav  +++ ++ef+++ iGGaai+ +g+ lp+etl++c+eadavLlg
  lcl|NCBI__GCF_000021925.1:WP_005816724.1   3 KIAVLPGDGIGQEIIPQAVRVLKAVLAETDAEFEFQDYPIGGAAIELVGKALPDETLQGCREADAVLLG 71 
                                               79******************************************************************* PP

                                 TIGR00169  70 avGGpkWdnlprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGi 137
                                               avGG +Wd+lp++ rPe+ +LL lrk l+++an+rP+++++sL+++s+lke++ +gvD+vv+reLtgG+
  lcl|NCBI__GCF_000021925.1:WP_005816724.1  72 AVGGHQWDHLPASERPETaALLGLRKGLNFYANIRPVRMIPSLLATSTLKENVLDGVDMVVIRELTGGV 140
                                               *****************989************************************************* PP

                                 TIGR00169 138 YfGepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206
                                               YfGe+  +++    ++a+d ++Y++eei+ri  ++fe+a+ r kk++svDkanvLe+srlWr++++e+a
  lcl|NCBI__GCF_000021925.1:WP_005816724.1 141 YFGEKGRSDN---PRSAYDKMTYSEEEIRRILIQGFETAMLRSKKLCSVDKANVLETSRLWREIANELA 206
                                               ***9766655...89****************************************************** PP

                                 TIGR00169 207 keyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275
                                               keyP+vel h+y+DnaamqLv++P+q+dv+vt+n+fGDil D as++ Gs+G+L sasls  +++++ep
  lcl|NCBI__GCF_000021925.1:WP_005816724.1 207 KEYPEVELTHMYVDNAAMQLVRNPKQFDVIVTENMFGDILTDLASMLGGSIGMLSSASLS-GTQGMYEP 274
                                               ************************************************************.78899*** PP

                                 TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344
                                               +hgsapdiagk++anp+a+ilsaal+lrys+++e +a +ie+av+kvle+g+rt dla+ + + v+t e
  lcl|NCBI__GCF_000021925.1:WP_005816724.1 275 AHGSAPDIAGKNLANPLATILSAALMLRYSFGMEAEALRIESAVEKVLEQGYRTGDLAQAGDKVVGTIE 343
                                               *************************************************************99999999 PP

                                 TIGR00169 345 veee 348
                                               +++ 
  lcl|NCBI__GCF_000021925.1:WP_005816724.1 344 MGDA 347
                                               9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (352 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.21
//
[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