Alignments for a candidate for leuB in Thermus aquaticus YT-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuB in Thermus aquaticus YT-1

Align 3-isopropylmalate/3-methylmalate dehydrogenase; 3-isopropylmalate dehydrogenase; 3-IPM-DH; IMDH; IPMDH; Beta-IPM dehydrogenase; D-malate dehydrogenase [decarboxylating]; EC 1.1.1.85; EC 1.1.1.n5; EC 1.1.1.83 (characterized)
to candidate WP_053767817.1 BVI061214_RS07200 NADP-dependent isocitrate dehydrogenase

Query= SwissProt::Q58130
         (333 letters)



>NCBI__GCF_001280255.1:WP_053767817.1
          Length = 426

 Score =  154 bits (388), Expect = 5e-42
 Identities = 124/367 (33%), Positives = 176/367 (47%), Gaps = 63/367 (17%)

Query: 7   IEGDGIGKEVVPATIQVLEAT-----GLPFEFVYAE--AGDEVYKRTGKA--LPEETIET 57
           IEGDG G ++  A   VL+A      G     V+ E  AG++  +  G+   LPEET+E 
Sbjct: 33  IEGDGTGPDIWRAAQPVLDAAVAKAYGGQRRIVWVELYAGEKANQVYGEPIWLPEETLEF 92

Query: 58  ALDCDAVLFGA----AGETAADVIVKLRHILDTYANIRPVKAYKGVKC--LRPD-IDYVI 110
             +    + G      G     + V LR  LD YA +RPV+ ++GV      P+ ++ VI
Sbjct: 93  IREYLVAIKGPLTTPVGGGIRSINVALRQELDLYACVRPVRWFQGVPSPVKHPELVNMVI 152

Query: 111 VRENTEGLYKGIE-----AEIDEGITIATRVITEKACERIFRFAFNLARERKKMGKEG-- 163
            RENTE +Y GIE      E+ + +    R    KA  +I RF        K + KEG  
Sbjct: 153 FRENTEDIYAGIEWPAGSEEVKKVLDFLKREFP-KAYAKI-RFPETSGLGLKPISKEGTE 210

Query: 164 ----------------KVTCAHKANVLKLTDGLFKKIFYKVAEEY--------------- 192
                            VT  HK N++K T+G F++  Y +A E                
Sbjct: 211 RLVEAAIEYAIKEDLPSVTLVHKGNIMKFTEGAFREWGYALAREKYGATPLDGGPWHVLK 270

Query: 193 -----DDIKAEDYYIDAMNMYIITKPQVFDVVVTSNLFGDILSDGAAGTVGGLGLAPSAN 247
                 +I  +D   D     I+ +P  + V+ T NL GD +SD  A  VGG+G+AP AN
Sbjct: 271 NPRTGREIVIKDMIADNFLQQILLRPDEYSVIATMNLNGDYISDALAAQVGGIGIAPGAN 330

Query: 248 IGDE--HGLFEPVHGSAPDIAGKKIANPTATILSAVLMLRYLGEYEAADKVEKALEEVLA 305
           I  +  H +FE  HG+AP  AG+   NP++ ILS  +MLRYLG  EAAD + +A+E  ++
Sbjct: 331 INYKTGHAVFEATHGTAPKYAGQDKVNPSSVILSGEMMLRYLGWNEAADLIIRAMERTIS 390

Query: 306 LGLTTPD 312
            GL T D
Sbjct: 391 KGLVTYD 397


Lambda     K      H
   0.318    0.138    0.390 

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: 342
Number of extensions: 22
Number of successful extensions: 6
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: 333
Length of database: 426
Length adjustment: 30
Effective length of query: 303
Effective length of database: 396
Effective search space:   119988
Effective search space used:   119988
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)

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 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