Alignments for a candidate for leuB in Halorhodospira halophila SL1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Halorhodospira halophila SL1

Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_011814596.1 HHAL_RS09130 3-isopropylmalate dehydrogenase

Query= SwissProt::Q56268
         (358 letters)



>NCBI__GCF_000015585.1:WP_011814596.1
          Length = 356

 Score =  429 bits (1102), Expect = e-125
 Identities = 226/355 (63%), Positives = 274/355 (77%), Gaps = 3/355 (0%)

Query: 2   KKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQL 61
           +KI +  GDGIGPEI A AR+VL+A+++   +G       +GGA  DA+  PLP  +L+L
Sbjct: 3   QKILLLPGDGIGPEITAEARRVLEALNKRYGVGCEMETAPIGGAGYDAAGQPLPDETLRL 62

Query: 62  AMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRP 121
           A  ADAV+LGAVGGP++DA P   RPE+GLL +R  L L+ NLRPA ++PQL  AS LR 
Sbjct: 63  AREADAVLLGAVGGPQYDALPRDVRPERGLLAIRSELGLFGNLRPAILYPQLAGASALRE 122

Query: 122 ELVRDVDILVVRELTGDIYFGQPRGLEVID-GKRRGFNTMVYDEDEIRRIAHVAFRAAQG 180
           ++V  +DIL+VRELTG IYFGQPRG+  +D G+R+GFNT VY E EI RIA +AF AA+ 
Sbjct: 123 DVVAGLDILIVRELTGGIYFGQPRGIRTLDSGERQGFNTEVYSESEIERIARLAFAAAEQ 182

Query: 181 RRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLT 240
           R+ ++CSVDKANVLE++ LWREVV  VA DYP V LSHMYVDNAAMQL+RAP QFDV++T
Sbjct: 183 RQGRVCSVDKANVLESSELWREVVERVAADYPGVELSHMYVDNAAMQLVRAPKQFDVVVT 242

Query: 241 GNMFGDILSDEASQLTGSIGMLPSASLGE-GRAMYEPIHGSAPDIAGQDKANPLATILSV 299
           GN+FGDILSD A+QLTGSIGMLPSASL E G+ +YEP+HGSAPDIAGQDKANPLATILSV
Sbjct: 243 GNLFGDILSDCAAQLTGSIGMLPSASLDEHGKGLYEPVHGSAPDIAGQDKANPLATILSV 302

Query: 300 AMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354
           AMMLR+SL A   A RVEAAV  VL++GLRT D+     PV GT+ MG AV   L
Sbjct: 303 AMMLRYSLGAGEAADRVEAAVGAVLEEGLRTPDLQGGNRPV-GTREMGEAVAGRL 356


Lambda     K      H
   0.320    0.137    0.396 

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: 420
Number of extensions: 14
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: 358
Length of database: 356
Length adjustment: 29
Effective length of query: 329
Effective length of database: 327
Effective search space:   107583
Effective search space used:   107583
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: 49 (23.5 bits)

Align candidate WP_011814596.1 HHAL_RS09130 (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.3565365.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-156  506.2   0.0   2.6e-156  506.0   0.0    1.0  1  NCBI__GCF_000015585.1:WP_011814596.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015585.1:WP_011814596.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  506.0   0.0  2.6e-156  2.6e-156       1     348 [.       4     351 ..       4     352 .. 0.99

  Alignments for each domain:
  == domain 1  score: 506.0 bits;  conditional E-value: 2.6e-156
                             TIGR00169   1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 
                                           ki +LpGDgiGpe++aea +vL+a+++r+++  e+e+a iGGa  da g+Plp+etl+ ++eadavLlgavGG
  NCBI__GCF_000015585.1:WP_011814596.1   4 KILLLPGDGIGPEITAEARRVLEALNKRYGVGCEMETAPIGGAGYDAAGQPLPDETLRLAREADAVLLGAVGG 76 
                                           799********************************************************************** PP

                             TIGR00169  74 pkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkere 146
                                           p++d+lprdvrPe+gLL++r el+lf nLrPa l+++L  +s+l+e++v g+D+++vreLtgGiYfG+p++++
  NCBI__GCF_000015585.1:WP_011814596.1  77 PQYDALPRDVRPERGLLAIRSELGLFGNLRPAILYPQLAGASALREDVVAGLDILIVRELTGGIYFGQPRGIR 149
                                           ************************************************************************9 PP

                             TIGR00169 147 eaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehly 218
                                             ++ e+++++te+Y+++eieriar+af +a++r+ +v+svDkanvLess+lWr++ve +a +yP vel+h+y
  NCBI__GCF_000015585.1:WP_011814596.1 150 TLDSgERQGFNTEVYSESEIERIARLAFAAAEQRQGRVCSVDKANVLESSELWREVVERVAADYPGVELSHMY 222
                                           98888******************************************************************** PP

                             TIGR00169 219 iDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianp 291
                                           +DnaamqLv++P+q+dvvvt+nlfGDilsD a+ +tGs+G+LPsasl ++g++l+epvhgsapdiag++ anp
  NCBI__GCF_000015585.1:WP_011814596.1 223 VDNAAMQLVRAPKQFDVVVTGNLFGDILSDCAAQLTGSIGMLPSASLDEHGKGLYEPVHGSAPDIAGQDKANP 295
                                           ************************************************************************* PP

                             TIGR00169 292 iaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348
                                           +a+ils+a++lrysl++ eaa+++eaav  vleeg rt+dl++ +   v+t+e++e 
  NCBI__GCF_000015585.1:WP_011814596.1 296 LATILSVAMMLRYSLGAGEAADRVEAAVGAVLEEGLRTPDLQGGN-RPVGTREMGEA 351
                                           *****************************************9998.99*****9986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.63
//
[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