GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Marinobacter adhaerens HP15

Align Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized)
to candidate GFF555 HP15_538 2-isopropylmalate synthase

Query= curated2:Q8TYM1
         (509 letters)



>FitnessBrowser__Marino:GFF555
          Length = 516

 Score =  377 bits (969), Expect = e-109
 Identities = 210/501 (41%), Positives = 306/501 (61%), Gaps = 16/501 (3%)

Query: 12  DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71
           D + IFDTTLRDGEQ+PG  +   EKLRIA+ L+++ VD IEAGFA AS+G+ +A++ IA
Sbjct: 5   DHLVIFDTTLRDGEQSPGATMNKAEKLRIAKALEKLRVDVIEAGFAIASQGDFEAVKAIA 64

Query: 72  REELDAEVCSMARMVKGDVDAAVE----AEADAVHIVVPTSEVHVKKKLRMDREEVLERA 127
               D+ +CS+AR +  D+D A E    A+   +H  + TS +H+K KL+M  +EV+E+A
Sbjct: 65  ESIKDSTICSLARALDKDIDRAAEAIRPAQRGRIHTFIATSPIHMKHKLQMQPDEVIEQA 124

Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187
              V+ AR H   VE S ED  R+EL++L  + +A ++AGA  +   DTVG   PE    
Sbjct: 125 VRSVKRARSHVDDVEFSCEDAGRSELDFLCRIIEAAIDAGASTINIPDTVGYAIPEQFGE 184

Query: 188 AVKKLRERV--GEDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245
            +++L  R+   +  I SVHCH+D G+A +N++AAV  GARQV  T+NG+GERAGNAALE
Sbjct: 185 TIRQLLNRIPNADKAIFSVHCHNDLGLAVSNSLAAVSQGARQVECTINGLGERAGNAALE 244

Query: 246 EVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302
           E+V+ +   ++L+ +DT I  + +   S+LV  +TG  V PNKA+VG NAF HESGIH D
Sbjct: 245 EIVMAVRTRQDLFHIDTRIDAQHIVPASRLVSTITGFPVQPNKAIVGANAFAHESGIHQD 304

Query: 303 GILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDE-QLLEILRRLK 360
           G+LK   TYE +  + VG H    VLGKH G +  R +L ++G+  + E +L E   R K
Sbjct: 305 GVLKHRETYEIMRAQDVGWHTNSLVLGKHSGRNAFRTRLLELGIQFETETELNEAFTRFK 364

Query: 361 RLGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEA 420
            L D    I + DL+AIA D   +  +    +      +    +P A++ + +DG   + 
Sbjct: 365 ALADLKHEIFDEDLQAIASDTRQKEEDGRYGLVCMQVCSETGVVPKANLTLSVDGKEHKV 424

Query: 421 ASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVH 480
            + G GPVDAT KA+E +L D G + +L  Y    +T GTDA   V V+L     G IV+
Sbjct: 425 EAEGSGPVDATFKAIE-SLVDSGCNLQL--YSVNNITSGTDAQGEVTVRLE--RGGRIVN 479

Query: 481 SGSSREDIVVASLEAFIDGIN 501
              +  DI++AS +A+I+ +N
Sbjct: 480 GVGADTDIIIASAKAYIEALN 500


Lambda     K      H
   0.315    0.134    0.367 

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: 620
Number of extensions: 38
Number of successful extensions: 8
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: 509
Length of database: 516
Length adjustment: 35
Effective length of query: 474
Effective length of database: 481
Effective search space:   227994
Effective search space used:   227994
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: 52 (24.6 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