Alignments for a candidate for leuB in Hippea alviniae EP5-r

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Hippea alviniae EP5-r

Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_022670320.1 G415_RS0104080 3-isopropylmalate dehydrogenase

Query= BRENDA::P93832
         (405 letters)



>NCBI__GCF_000420385.1:WP_022670320.1
          Length = 361

 Score =  400 bits (1028), Expect = e-116
 Identities = 210/356 (58%), Positives = 259/356 (72%), Gaps = 2/356 (0%)

Query: 42  RYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETIS 101
           ++ I +  GDGIGPEVV+    VL + GS  G EF + ++ IGG A+D    PLP+  + 
Sbjct: 3   KFKIAVAEGDGIGPEVVAEGLKVLDEVGSRFGHEFEYEKVYIGGCAVDKFEDPLPDSEVE 62

Query: 102 AAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLK 161
              + DA+  GA+GG KWDN  +  RPE G+L+IR  L  FANLRPA V  +LVDASTLK
Sbjct: 63  KILKCDALFFGAVGGPKWDNLPREKRPETGMLKIRKTLNAFANLRPAKVFDELVDASTLK 122

Query: 162 REVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETAR 221
            EV +G+D++VVRELTGGIYFG+P+GI   ENG + G NT +Y   EI+RI R+AFE AR
Sbjct: 123 PEVIKGIDILVVRELTGGIYFGQPKGI-VEENGVKKGINTMIYTEPEIERIVRLAFELAR 181

Query: 222 KRRGKLCSVDKANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIV 281
           +RR KL SVDKANVL+ S LWR  V  +A +YPDVE +H+ VDNAAMQLVRDPKQFD IV
Sbjct: 182 QRRKKLTSVDKANVLDVSQLWRDVVEKVAKDYPDVEYNHLLVDNAAMQLVRDPKQFDVIV 241

Query: 282 TNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILS 341
           T NIFGDILSDEASM+TGSIGMLPSAS+     G+FEPIHGSAPDIAG   ANP+A I S
Sbjct: 242 TGNIFGDILSDEASMLTGSIGMLPSASIGGE-VGMFEPIHGSAPDIAGLGIANPIAQIES 300

Query: 342 AAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKSV 397
           AAM+LKYG   +K A+ IE AV + L  G+RT DIYS GT+ V  ++MG+ + K+V
Sbjct: 301 AAMMLKYGFKLDKEAEAIEKAVDMILKMGYRTPDIYSEGTRKVNTQQMGDLIAKAV 356


Lambda     K      H
   0.316    0.134    0.374 

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: 448
Number of extensions: 16
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: 405
Length of database: 361
Length adjustment: 30
Effective length of query: 375
Effective length of database: 331
Effective search space:   124125
Effective search space used:   124125
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: 50 (23.9 bits)

Align candidate WP_022670320.1 G415_RS0104080 (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.682234.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-163  529.0   0.0   2.9e-163  528.8   0.0    1.0  1  NCBI__GCF_000420385.1:WP_022670320.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000420385.1:WP_022670320.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.8   0.0  2.9e-163  2.9e-163       1     348 [.       5     351 ..       5     352 .. 0.99

  Alignments for each domain:
  == domain 1  score: 528.8 bits;  conditional E-value: 2.9e-163
                             TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 
                                           kiav +GDgiGpevvae lkvL++v  rf++++e+e+  iGG a+d+  +Plp+  +++  + da+++gavGG
  NCBI__GCF_000420385.1:WP_022670320.1   5 KIAVAEGDGIGPEVVAEGLKVLDEVGSRFGHEFEYEKVYIGGCAVDKFEDPLPDSEVEKILKCDALFFGAVGG 77 
                                           79*********************************************************************** PP

                             TIGR00169  74 pkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkere 146
                                           pkWdnlpr++rPe+g+Lk+rk l+ fanLrPak+f++L+++s+lk+e++kg+D++vvreLtgGiYfG+pk++ 
  NCBI__GCF_000420385.1:WP_022670320.1  78 PKWDNLPREKRPETGMLKIRKTLNAFANLRPAKVFDELVDASTLKPEVIKGIDILVVRELTGGIYFGQPKGIV 150
                                           ************************************************************************* PP

                             TIGR00169 147 eaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyi 219
                                           e++  kk+++t+ Yt++eieri+r+afelar+rrkk+tsvDkanvL++s+lWr++ve++ak+yPdve +hl++
  NCBI__GCF_000420385.1:WP_022670320.1 151 EENGVKKGINTMIYTEPEIERIVRLAFELARQRRKKLTSVDKANVLDVSQLWRDVVEKVAKDYPDVEYNHLLV 223
                                           *888********************************************************************* PP

                             TIGR00169 220 DnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpi 292
                                           DnaamqLv++P+q+dv+vt+n+fGDilsDeas++tGs+G+LPsas++   +++fep+hgsapdiag gianpi
  NCBI__GCF_000420385.1:WP_022670320.1 224 DNAAMQLVRDPKQFDVIVTGNIFGDILSDEASMLTGSIGMLPSASIG-GEVGMFEPIHGSAPDIAGLGIANPI 295
                                           ***********************************************.56789******************** PP

                             TIGR00169 293 aailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                           a+i saa++l+y+++l+++aeaie+av+ +l+ g+rt+d++se+t +v t+++++ 
  NCBI__GCF_000420385.1:WP_022670320.1 296 AQIESAAMMLKYGFKLDKEAEAIEKAVDMILKMGYRTPDIYSEGTRKVNTQQMGDL 351
                                           *****************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (349 nodes)
Target sequences:                          1  (361 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: 22.50
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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