Alignments for a candidate for leuA in Desulfitobacterium hafniense DCB-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Desulfitobacterium hafniense DCB-2

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate WP_011461751.1 DHAF_RS05075 2-isopropylmalate synthase

Query= SwissProt::P42455
         (616 letters)



>NCBI__GCF_000021925.1:WP_011461751.1
          Length = 557

 Score =  491 bits (1263), Expect = e-143
 Identities = 257/549 (46%), Positives = 365/549 (66%), Gaps = 26/549 (4%)

Query: 58  WPDKK-ITVAPQWCAVDLRDGNQALIDPMSPERKRRMFELLVQMGFKEIEVGFPSASQTD 116
           W +K+ IT  P WC+VDLRDGNQAL+ PMS E K   + +L+++GFKEIEVGFP+AS+T+
Sbjct: 21  WAEKEYITTPPTWCSVDLRDGNQALVVPMSLEEKLEYYHMLLKIGFKEIEVGFPAASETE 80

Query: 117 FDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGAKNVIVHFYNSTSILQRNVVF 176
           + F+R +IE+ +IP+DVTIQVL Q+R+H+I +TF+A  G K  +VH YNSTS+ QR  VF
Sbjct: 81  YAFLRTLIEQNLIPEDVTIQVLTQSRDHIIEKTFKALVGVKKAVVHLYNSTSVAQREQVF 140

Query: 177 RMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFTGTEVEYAKEVVDAVVEVMDP 236
           +M + ++ ++A   A L+K  A +  + N++++YSPESFTGTE+E+A E+ + V++V +P
Sbjct: 141 KMSREEIVEIAVSGARLLKKYAAE-TEGNFQFEYSPESFTGTEMEFALEICNQVLDVFEP 199

Query: 237 TPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSIILSLHPHNDRGTGVGAAELGY 296
           TPEN +IINLP+TV +  P+VYA  IE+M  +L  RD++ILSLHPHNDRGT V  AELG 
Sbjct: 200 TPENKVIINLPATVSLSMPHVYASQIEYMSEHLKYRDNVILSLHPHNDRGTAVADAELGL 259

Query: 297 MAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLDFTDIRQIRSTVEYCNQLRVP 356
           +AG  RIEG LFGNGERTGNV +VTLALN+ + GVDP L+F  + +I +  E   +++V 
Sbjct: 260 LAGGQRIEGTLFGNGERTGNVDIVTLALNLFSHGVDPGLNFASMLEITAKYEALTRMKVH 319

Query: 357 ERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASSTEVSWEQLRDTE-WEVPYLPI 415
           +R PYGG LVF AFSGSHQDA+ KG                + W +  +   W VPYL I
Sbjct: 320 DRQPYGGKLVFAAFSGSHQDAITKG----------------IKWREEHECHYWNVPYLLI 363

Query: 416 DPKDVGRDYEA-VIRVNSQSGKGGVAYIMKTDHGLQIPRSMQVEFSTVVQNVTDAEGGEV 474
           DP+D+GR+YE  VIR+NSQSGKGG+AY+++  + L +P  M+  F   V+NV+D    E+
Sbjct: 364 DPQDIGREYEGDVIRINSQSGKGGIAYMLEQHYALDLPAKMREAFGYKVKNVSDNLHKEL 423

Query: 475 NSKAMWDIFATEYLERTAPVEQIALRVENAQTENEDASITAELIHNGKDVTVDGRGNGPL 534
             + + DIF  EY+    P++ +     N    ++D   T  L   G+   + G G+G L
Sbjct: 424 MPEEIKDIFFKEYVNIENPIKFLNFHFLN----HDDFQTTVTLEFKGEIQELSGEGDGRL 479

Query: 535 AAYANALE-KLGIDVEIQEYNQHARTSGDDAEAAAYV-LAEVNGRKVWGVGIAGSITYAS 592
            A +NAL+ +LG+      Y +HA   G  ++A +YV +   +G   WG GI   I  +S
Sbjct: 480 DAISNALQARLGLSYSNLIYKEHALELGSKSQAVSYVGVTGPDGVIHWGCGIHTDIFTSS 539

Query: 593 LKAVTSAVN 601
           +KA+ SA+N
Sbjct: 540 VKALISAIN 548


Lambda     K      H
   0.316    0.133    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: 840
Number of extensions: 34
Number of successful extensions: 7
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: 616
Length of database: 557
Length adjustment: 37
Effective length of query: 579
Effective length of database: 520
Effective search space:   301080
Effective search space used:   301080
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: 53 (25.0 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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