Alignments for a candidate for leuB in Desulforamulus ruminis DSM 2154

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Desulforamulus ruminis DSM 2154

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_013840436.1 DESRU_RS01895 3-isopropylmalate dehydrogenase

Query= SwissProt::P12010
         (366 letters)



>NCBI__GCF_000215085.1:WP_013840436.1
          Length = 356

 Score =  408 bits (1048), Expect = e-118
 Identities = 210/354 (59%), Positives = 267/354 (75%), Gaps = 3/354 (0%)

Query: 4   KLAVLPGDGIGPEVMDAAIRVLKTVLDNDGHEAVFENALIGGAAIDEAGTPLPEETLDIC 63
           K+A+LPGDGIGPE++  A+RVL+ V      E  FE ALIGGAA D  G PLPE TL++C
Sbjct: 3   KIALLPGDGIGPEIVPQAVRVLEAVGKKFNLEFQFETALIGGAAYDATGHPLPEATLELC 62

Query: 64  RRSDAILLGAVGGPKWDHNPASLRPEKG-LLGLRKEMGLFANLRPVKAYATLLNASPLKR 122
           RRSDAILLGAVGGPKWD+    LRPE+G LL LRKE+GL+ANLRP      L +AS LK 
Sbjct: 63  RRSDAILLGAVGGPKWDNLEPDLRPERGALLPLRKELGLYANLRPAAVNPALASASTLKE 122

Query: 123 ERVENVDLVIVRELTGGLYFGRPSERRGPGENE-VVDTLAYTREEIERIIEKAFQLAQIR 181
           E V  +D++I+RELTGGLYFG+      PG  +  V+TL Y+  EIER+    F++A+ R
Sbjct: 123 EIVSGLDIMIIRELTGGLYFGQKHREELPGGGQKAVETLEYSTGEIERVARLGFEMARKR 182

Query: 182 RKKLASVDKANVLESSRMWREIAEETAKKYPDVELSHMLVDSTSMQLIANPGQFDVIVTE 241
            K+L SVDKANVLESSR+WRE+ +E AK+YPDVEL+HM VD+ +MQL+ NP QFDV+VTE
Sbjct: 183 NKRLMSVDKANVLESSRLWREVVQELAKEYPDVELNHMYVDNCAMQLVRNPKQFDVMVTE 242

Query: 242 NMFGDILSDEASVITGSLGMLPSASLRSDRFGMYEPVHGSAPDIAGQGKANPLGTVLSAA 301
           NMFGDIL+D AS +TGS+GMLPSAS+  +   +YEP+HGSAPDIAG+  ANP+ T+LSAA
Sbjct: 243 NMFGDILTDLASQLTGSIGMLPSASIGGE-VALYEPIHGSAPDIAGKNLANPIATILSAA 301

Query: 302 LMLRYSFGLEKEAAAIEKAVDDVLQDGYCTGDLQVANGKVVSTIELTDRLIEKL 355
           +MLR SFGLE+ AA+IE AV  VL+ GY TGD+     K + T+E+T+ +++ L
Sbjct: 302 MMLRVSFGLEEPAASIEGAVAKVLEQGYRTGDIMQPGQKQLGTVEMTEAILKAL 355


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: 441
Number of extensions: 18
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: 356
Length adjustment: 29
Effective length of query: 337
Effective length of database: 327
Effective search space:   110199
Effective search space used:   110199
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_013840436.1 DESRU_RS01895 (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.1130435.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.1e-162  526.0   0.0   2.4e-162  525.8   0.0    1.0  1  NCBI__GCF_000215085.1:WP_013840436.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013840436.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  525.8   0.0  2.4e-162  2.4e-162       1     349 []       3     351 ..       3     351 .. 0.99

  Alignments for each domain:
  == domain 1  score: 525.8 bits;  conditional E-value: 2.4e-162
                             TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 
                                           kia+LpGDgiGpe+v +a++vL+av ++f+l+++fe+aliGGaa datg+Plpe+tl+ c+++da+LlgavGG
  NCBI__GCF_000215085.1:WP_013840436.1   3 KIALLPGDGIGPEIVPQAVRVLEAVGKKFNLEFQFETALIGGAAYDATGHPLPEATLELCRRSDAILLGAVGG 75 
                                           79*********************************************************************** PP

                             TIGR00169  74 pkWdnlprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepker 145
                                           pkWdnl +d rPe+ +LL+lrkel+l+anLrPa + ++L ++s+lkeeiv+g+D++++reLtgG+YfG+++ +
  NCBI__GCF_000215085.1:WP_013840436.1  76 PKWDNLEPDLRPERgALLPLRKELGLYANLRPAAVNPALASASTLKEEIVSGLDIMIIRELTGGLYFGQKHRE 148
                                           **************88*******************************************************99 PP

                             TIGR00169 146 eeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehly 218
                                           e  +  +ka++t +Y++ eier+ar++fe+arkr+k+++svDkanvLessrlWr++v+e+akeyPdvel+h+y
  NCBI__GCF_000215085.1:WP_013840436.1 149 ELPGGGQKAVETLEYSTGEIERVARLGFEMARKRNKRLMSVDKANVLESSRLWREVVQELAKEYPDVELNHMY 221
                                           99999******************************************************************** PP

                             TIGR00169 219 iDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianp 291
                                           +Dn+amqLv++P+q+dv+vt+n+fGDil D as +tGs+G+LPsas++   +al+ep+hgsapdiagk++anp
  NCBI__GCF_000215085.1:WP_013840436.1 222 VDNCAMQLVRNPKQFDVMVTENMFGDILTDLASQLTGSIGMLPSASIG-GEVALYEPIHGSAPDIAGKNLANP 293
                                           ************************************************.56789******************* PP

                             TIGR00169 292 iaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveeel 349
                                           ia+ilsaa++lr s++lee a+ ie av+kvle+g+rt d+++ + ++ +t e++e +
  NCBI__GCF_000215085.1:WP_013840436.1 294 IATILSAAMMLRVSFGLEEPAASIEGAVAKVLEQGYRTGDIMQPGQKQLGTVEMTEAI 351
                                           ******************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (356 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.76
//
[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 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