Alignments for a candidate for leuA in Herbaspirillum seropedicae SmR1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Herbaspirillum seropedicae SmR1

Align 2-isopropylmalate synthase; Alpha-IPM synthase; Alpha-isopropylmalate synthase; EC 2.3.3.13 (characterized)
to candidate HSERO_RS04700 HSERO_RS04700 2-isopropylmalate synthase

Query= SwissProt::P42455
         (616 letters)



>FitnessBrowser__HerbieS:HSERO_RS04700
          Length = 575

 Score =  499 bits (1284), Expect = e-145
 Identities = 272/576 (47%), Positives = 357/576 (61%), Gaps = 42/576 (7%)

Query: 48  VEDISLPDRTWPDKKITVAPQWCAVDLRDGNQALIDPMSPERKRRMFELLVQMGFKEIEV 107
           +  + LPDR WP + +  AP W + DLRDGNQAL +PM+ ERK R+F  LV++GFKEIEV
Sbjct: 12  IAPVDLPDRRWPSRTLRQAPTWLSTDLRDGNQALFEPMNRERKLRLFHELVRIGFKEIEV 71

Query: 108 GFPSASQTDFDFVREIIEKGMIPDDVTIQVLVQAREHLIRRTFEACEGAKNVIVHFYNST 167
           GFP+AS+ DF+ VR +I++ +IPDDVT  V+ Q R  LI  T ++  GA+ VIVHFYN+ 
Sbjct: 72  GFPAASRIDFETVRHLIDEHLIPDDVTPMVMTQLRADLITETVKSVAGARRVIVHFYNAI 131

Query: 168 SILQRNVVFRMDKVQVKKLATDAAELIKTIAQDYPDTNWRWQYSPESFTGTEVEYAKEVV 227
           +   R +VF M   Q+  L  D   L + +   +P+T W  QYSPE+F   E+E + EV 
Sbjct: 132 APAWREIVFGMSVPQIITLVEDHIALFRRLTAVHPETEWILQYSPETFCMAELEVSLEVC 191

Query: 228 DAVVEVMDPTPENPMIINLPSTVEMITPNVYADSIEWMHRNLNRRDSIILSLHPHNDRGT 287
           +A +   D  P   MIINLP+TVE+ TPNV+AD IEWM R L RR+ +ILS+HPHNDRGT
Sbjct: 192 NAAIRAWDAGPRRRMIINLPTTVEVSTPNVFADQIEWMDRRLERREHLILSVHPHNDRGT 251

Query: 288 GVGAAELGYMAGADRIEGCLFGNGERTGNVCLVTLALNMLTQGVDPQLDFTDIRQIRSTV 347
            V  AE   +AGA R+EGCLFGNGER+GNV +VTLALN+ TQG+ P LDF+DI  +    
Sbjct: 252 AVACAEQAMLAGAQRVEGCLFGNGERSGNVDVVTLALNLYTQGIAPGLDFSDIAALARVA 311

Query: 348 EYCNQLRVPERHPYGGDLVFTAFSGSHQDAVNKGLDAMAAKVQPGASSTEVSWEQLRDTE 407
           E C  L +  RHPY GDLVFTAFSGSHQDA+ KG  A                 Q  D  
Sbjct: 312 EECTALPIHPRHPYVGDLVFTAFSGSHQDAIAKGFAA-----------------QRPDAP 354

Query: 408 WEVPYLPIDPKDVGRDYEAVIRVNSQSGKGGVAYIMKTDHGLQIPRSMQVEFSTVVQNVT 467
           W VPYLPIDP D+GR Y++++RVNSQSGKGG+A++++ DH + +PR MQVEFS +VQ + 
Sbjct: 355 WRVPYLPIDPTDLGRTYDSIVRVNSQSGKGGIAFLLQRDHHITMPRRMQVEFSAIVQALA 414

Query: 468 DAEGGEVNSKAMWDIFATEYL----------ERT--APV---EQIALRVENAQTENEDAS 512
           DA   E+ S+ +WD+F   YL          +RT  AP     +   R        +   
Sbjct: 415 DASETELTSEHLWDVFERTYLAPVQASPDFSDRTSLAPALEQRRFIYRSHCLHPHPDGER 474

Query: 513 ITAELIHNGKDV-TVDGRGNGPLAAYANALEKLGIDVEIQEYNQHARTSGDDAEAAAYVL 571
           I  EL     +V TV+G GNGP+AA   A   LG+ + I  Y + +   G  A+A A  +
Sbjct: 475 IVLELADTEGNVRTVEGSGNGPIAATVAA---LGLALRIDSYEERSLGVGVGADAQALAI 531

Query: 572 AE-----VNGRKVWGVGIAGSITYASLKAVTSAVNR 602
            E     V G + +GVG   +IT AS+ AV SA +R
Sbjct: 532 VEAALPTVPGSR-FGVGRHENITTASIMAVLSAASR 566


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: 903
Number of extensions: 39
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: 616
Length of database: 575
Length adjustment: 37
Effective length of query: 579
Effective length of database: 538
Effective search space:   311502
Effective search space used:   311502
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 09 2024. The underlying query database was built on Apr 09 2024.

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

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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