Alignments for a candidate for leuA in Magnetospirillum magneticum AMB-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for leuA in Magnetospirillum magneticum AMB-1

Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_011384529.1 AMB_RS10755 citramalate synthase

Query= curated2:Q8TYB1
         (499 letters)



>NCBI__GCF_000009985.1:WP_011384529.1
          Length = 546

 Score =  224 bits (571), Expect = 6e-63
 Identities = 179/548 (32%), Positives = 263/548 (47%), Gaps = 52/548 (9%)

Query: 1   MPDRVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGE---FEA 57
           M +RV ++DTTLRDG QT GV  +  +KV IAR+LD  G+D +E G+P A+  +   F  
Sbjct: 1   MAERVYLYDTTLRDGAQTQGVDFSAADKVRIARELDRIGIDYVEGGWPGANPTDDAFFAD 60

Query: 58  VRAIAGEELDAEICGLARCV--KGDIDAAIDADVDC---VHVFIATS-DIHLRYKLEMSR 111
             A     L A   G+ R      D D  ++A +     V   +  S D  +   L +  
Sbjct: 61  PPAFKRSRLTA--FGMTRRAGRSADNDPGLNALLVTPARVATMVGKSWDFQVTVALGIEL 118

Query: 112 EEALERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTV 168
           +E L    + V++A      V F AE   D  + +  Y L   KA  +AGA  V + DT 
Sbjct: 119 DENLRMVADSVQHARTKVEEVMFDAEHFFDGYKANPAYALAAAKAAYDAGARWVVLCDTN 178

Query: 169 GVMTPPEMYRLTAEVVDAVDVPVS---VHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIG 225
           G   P EM R+  EV+    +P S   VHCHND   AVANSLAAVEAG  Q+  T+NG+G
Sbjct: 179 GGTLPHEMRRIVGEVIKG-GIPGSHLGVHCHNDSDTAVANSLAAVEAGVRQIQGTLNGLG 237

Query: 226 ERAGNASLEQVVMALKALYDIELDVRTE---MLVELSRLVERLTGVVVPPNTPIVGENAF 282
           ER GNA+L  ++ AL      +  +  E    LV +SR ++ +         P VG++AF
Sbjct: 238 ERCGNANLISIIPALMLKMGFDTGIAPEDLKNLVSVSRALDEVLDRTPNRGQPYVGKSAF 297

Query: 283 AHESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQLD 342
           AH+ G+H   V K  + YE + P  VG+ R IV+   AGR  +  +L E+GI++   + +
Sbjct: 298 AHKGGLHVSAVAKDPKCYEHVDPASVGNMRHIVMSDQAGRSNLVARLTEIGIDLDSVKRE 357

Query: 343 EIVRRV------------KELGDKGKRVTED---------DLEAIARDVVGEVPESEAAV 381
            +VR V             +L D  KR+  +           E + R  +GEVPE  A  
Sbjct: 358 SLVRVVDQMQVTFDAREATDLVDLVKRLEHEGYAYDQAAASFELLVRRALGEVPEYFALE 417

Query: 382 KLEEIAVMTGNKF-----TPTASVRVYLDGEEHEAASTGVGSV---DAAIRALREAIEEL 433
           +   I     N          A+V+V + G E+     G G V   D A+R +   +   
Sbjct: 418 RYRVIDERRRNAHGEWITLSEATVKVEVGGTEYMEVGEGTGPVHAFDVALRKVLTRVYPA 477

Query: 434 GMDVELKEYRLEAI--TGGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGVN 491
              +ELK+YR+     T GT A   VT+  ED+ G+  T  G   +++ AS++A    + 
Sbjct: 478 LTALELKDYRVRITESTVGTAAKTRVTIESEDDKGHRWTTVGVHTNVLEASLEALQDSIT 537

Query: 492 RLARRRRD 499
            +  R +D
Sbjct: 538 FMLFRFKD 545


Lambda     K      H
   0.315    0.133    0.364 

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: 632
Number of extensions: 34
Number of successful extensions: 5
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: 499
Length of database: 546
Length adjustment: 35
Effective length of query: 464
Effective length of database: 511
Effective search space:   237104
Effective search space used:   237104
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 (21.5 bits)
S2: 52 (24.6 bits)

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

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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