GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Marinobacter adhaerens HP15

Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate GFF3491 HP15_3433 aconitate hydratase 1

Query= curated2:Q9WYC7
         (418 letters)



>FitnessBrowser__Marino:GFF3491
          Length = 919

 Score =  114 bits (286), Expect = 9e-30
 Identities = 128/496 (25%), Positives = 199/496 (40%), Gaps = 111/496 (22%)

Query: 21  GEIVLARVDIAMAQDGTGPLMINEFRELGF---KEVKVPKAFLFIDHASPSPRKELSNSQ 77
           G + LA +  A+   G  P MIN    +       V V K   F D +S      +   +
Sbjct: 100 GVVDLAAMREAVQAAGKDPAMINPLSPVDLVIDHSVMVDK---FGDASSFKDNVAIEMER 156

Query: 78  KMMREFGKEMGVKVFD------AGDGISHQILAE-------------KYVKPGDLVAGAD 118
              R      G + FD       G GI HQ+  E             K +   D + G D
Sbjct: 157 NQERYEFLRWGQQAFDNFRVVPPGTGICHQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTD 216

Query: 119 SHTCTAGGLGAFGTGMGSTDVAIIFGLGQNW-FKVPETIKVVVNGKLQDGVYAKDIILEI 177
           SHT    GLG  G G+G  +      LGQ     +PE +   + GKL++G+ A D++L +
Sbjct: 217 SHTTMINGLGILGWGVGGIEAEAAM-LGQPVSMLIPEVVGFKITGKLREGITATDLVLTV 275

Query: 178 ARILGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFLKKMG 237
             +L   G   K +EF+G  +++M V DR TI+NMA E GA  G  P DE+T ++++  G
Sbjct: 276 TEMLRKKGVVGKFVEFYGDGLKDMPVADRATIANMAPEYGATCGFFPVDEQTIKYMRLTG 335

Query: 238 REEDFREL------------KADPDAVYETEIEIDATTLEPLVSLP-------------- 271
           REE+  EL            +   + VY   +E+D   +E  ++ P              
Sbjct: 336 REEEQLELVEAYAKAQGLWREPGHEPVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKS 395

Query: 272 ---------------------------------HYVDNVRKVSEVEKEKIKIDQ-----V 293
                                             Y  +  +  E+  EK ++D       
Sbjct: 396 SFELLMETAEGPAENREANLESEGGQTAVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIA 455

Query: 294 FIGTCTNGRLQDLEIALKILEKH------GKHPDVRLIVGPASRKVYMDALEKGIIKKFV 347
            I +CTN     + +A  ++ +          P V+  + P S KV  D L+ G  +  +
Sbjct: 456 AITSCTNTSNPSVMMAAGLIAQKAVQKGLSTKPWVKTSLAPGS-KVVTDYLKVGGFQDDL 514

Query: 348 E-LGAAVIPPGCGPCVGIHMGVLGDG-ERVLS----------TQNRNFKGRMGNPNAEIY 395
           + LG  ++  GC  C+G + G L D  E+ +S          + NRNF+GR+       +
Sbjct: 515 DKLGFNLVGYGCTTCIG-NSGPLPDAVEKAISDGDLTVASVLSGNRNFEGRVHPLVKTNW 573

Query: 396 LASPATAAATAVTGYI 411
           LASP    A A+ G +
Sbjct: 574 LASPPLVVAYALAGNV 589


Lambda     K      H
   0.318    0.137    0.395 

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: 858
Number of extensions: 44
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 418
Length of database: 919
Length adjustment: 37
Effective length of query: 381
Effective length of database: 882
Effective search space:   336042
Effective search space used:   336042
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: 53 (25.0 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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:

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:

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:

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