GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Shewanella oneidensis MR-1

Align acetolactate synthase isozyme 2 large subunit; EC 2.2.1.6 (characterized)
to candidate 202370 SO3262 acetolactate synthase isozyme I, large subunit (NCBI ptt file)

Query= CharProtDB::CH_003896
         (548 letters)



>FitnessBrowser__MR1:202370
          Length = 581

 Score =  323 bits (828), Expect = 1e-92
 Identities = 202/562 (35%), Positives = 294/562 (52%), Gaps = 28/562 (4%)

Query: 4   AQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATGK 63
           A  ++  L  QG+     YPGG I P+ DA    GV     R+EQGA  AA+   + T  
Sbjct: 10  ADAIIEFLAHQGIKAFHNYPGGTIAPLLDACKRFGVTVYTSRNEQGAGYAALAQGKLTQL 69

Query: 64  TGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSA------PFIGTDAFQEVDVLGL 117
            G+   TSGPG TN++T +ADA  D IP++  TGQV          +    FQEVD   L
Sbjct: 70  PGIVAVTSGPGVTNVLTPVADAYFDGIPMLVFTGQVGTGDLTGQKRVRQSGFQEVDTPSL 129

Query: 118 SLACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVEN 177
               TK  F  ++ EEL  I+  A+ +A  GR GPV +D+P D+Q ++         V  
Sbjct: 130 MKPITKGQFQPKNSEELYAILPIAWQLALEGRKGPVSIDLPMDVQRSAAIKS---IKVPE 186

Query: 178 EVTFPHAEVE------QARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTL 231
            VT+P    E      +    +  +QKP++  G G+     V A+R        P + +L
Sbjct: 187 IVTYPVNRTELGTFIDELINAIDHSQKPVIICGNGMTSPALVDAIRTLRNYWPAPVSHSL 246

Query: 232 KGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNT-FAPHASV 290
            G+G ++ D    LG  G  G++ A  A+ ECDLL+ +G+R D R TG L T FA +A +
Sbjct: 247 LGVGVLDTDDSGSLGFHGHTGSQLAGKAIAECDLLLVLGSRLDVRQTGTLKTAFASNAKI 306

Query: 291 IHMDIDPAEMNKLRQAH-VALQGDLNALLPALQ------QPLNQYDWQQHCAQLRDEHSW 343
             +D+D  E+   R AH  A+Q +L     AL        P N   W    +Q + + +W
Sbjct: 307 FRVDLDIGELTDSRIAHHKAVQAELEQFFDALHPKFAQLSPPNLSSWHNTISQWKAQLAW 366

Query: 344 RY-DHPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPEN-FITSSGLG 401
            Y D+PG  I   LLL++LS+  P + +VTT VG HQ W A+H     P     TS+G G
Sbjct: 367 PYPDYPG--IAPKLLLEKLSNSLPENTIVTTGVGAHQHWVARHFRFALPHRQLFTSAGHG 424

Query: 402 TMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMV 461
           TMG+ LP A+GA +  P  T++CI+GDGSF MN+QELG +K   L +KI++LDN RLG+V
Sbjct: 425 TMGYDLPTAIGAAIHSPESTILCIAGDGSFQMNIQELGVIKELGLKIKILVLDNHRLGLV 484

Query: 462 RQWQQLFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLH 521
            Q+ QL   E  +      +P+F ++A  +GI   H +   ++E  L   + +D   LLH
Sbjct: 485 SQF-QLMNWETDTACGNKQSPNFALIAQGYGIKALHCSDSAKLEQTLAEFIETDESILLH 543

Query: 522 VSIDELENVWPLVPPGASNSEM 543
           + I    +V P++  G +  +M
Sbjct: 544 IEIATQHDVLPMLLGGQTTDKM 565


Lambda     K      H
   0.320    0.135    0.410 

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: 773
Number of extensions: 28
Number of successful extensions: 6
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: 548
Length of database: 581
Length adjustment: 36
Effective length of query: 512
Effective length of database: 545
Effective search space:   279040
Effective search space used:   279040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 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