GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Marivita geojedonensis DPG-138

Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate WP_085635863.1 MGEO_RS06350 citramalate synthase

Query= curated2:Q8TYB1
         (499 letters)



>NCBI__GCF_002115805.1:WP_085635863.1
          Length = 539

 Score =  212 bits (539), Expect = 3e-59
 Identities = 166/525 (31%), Positives = 260/525 (49%), Gaps = 39/525 (7%)

Query: 4   RVRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIAG 63
           R+ ++DTTLRDG+QT GV  +  EK  I   LD  G+D IE G+P A+  +      +  
Sbjct: 5   RLTLYDTTLRDGQQTQGVQFSTPEKHRIVEALDALGIDYIEGGWPGANPTDSAFFDEVGH 64

Query: 64  EELDAEICGLA----RCVKGD--IDAAIDADVDCVHVFIATSDIHLRYKLEMSREEALER 117
                   G+     R  + D  + A ++A    V +   T D H+   L ++ EE +E 
Sbjct: 65  TRATVTAFGMTKRAGRSAENDDVLAAVMNAGTKSVCLVGKTHDFHVTAALGITLEENVEH 124

Query: 118 AIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMTPP 174
               V +         F AE   D  + + DY L    A  EAGA  + + DT G   P 
Sbjct: 125 IRASVAHIVSQKREALFDAEHFFDGYKANPDYALTCLHAAYEAGARWIVLCDTNGGALPS 184

Query: 175 EMYRLTAEVVDAVDVP---VSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGIGERAGNA 231
           E+ R+T E V A  +P   V +H HND  MAVA +LAAV+AGA Q+  T+NG+GER GNA
Sbjct: 185 EVGRIT-EAVIASGIPGTHVGIHTHNDTEMAVATTLAAVDAGARQIQGTLNGLGERCGNA 243

Query: 232 SLEQVV--MALKALY--DIELDVRTEML---VELSRLVERLTGVVVPPNTPIVGENAFAH 284
           +L  ++  + LK  Y    E  V  E L     +SR+++ +   V    +  VG +AFAH
Sbjct: 244 NLTSLIPTLLLKEPYASTYETGVTLEALEGMTRISRMLDEILNRVPLKQSAYVGSSAFAH 303

Query: 285 ESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEVTEEQ--LD 342
           ++G+H+  ++K   TYE I P  VG+RR I +   AG+  ++++L E GIEV ++   L 
Sbjct: 304 KAGLHASAILKNPTTYEHIDPALVGNRRVIPMSNQAGQSNLRRRLAEAGIEVPDKDPALA 363

Query: 343 EIVRRVKELGDKGKR--VTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFTPTAS- 399
            I+ R+K    +G      +   E +ARD +G +PE     +         NK+    S 
Sbjct: 364 RILDRIKAREAEGYSYDTAQASFELLARDELGMLPEFFEVKRYRVTVERRKNKYNKMISH 423

Query: 400 ---VRVYLDGEEHEAAST----GVGSVDAAIRALREAI-EELGM------DVELKEYRLE 445
              V V   G+E + + +     +G+    + AL +A+ ++LG       D+ L ++++ 
Sbjct: 424 SEAVVVVKVGDEKKLSVSESMDELGNDRGPVNALSKALAKDLGPYQHMIDDLRLVDFKVR 483

Query: 446 AITGGTDALAEVTVRLEDEDGNVTTARGAAEDIVMASVKAFVRGV 490
              GGT+A+  V +  ED  G   +  G + +I+ AS +A +  V
Sbjct: 484 ITQGGTEAVTRVIIDSEDGQGRRWSTVGVSANIIDASFEALLDAV 528


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: 622
Number of extensions: 30
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: 539
Length adjustment: 35
Effective length of query: 464
Effective length of database: 504
Effective search space:   233856
Effective search space used:   233856
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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