GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hcs in Desulfovibrio vulgaris Miyazaki F

Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate 8501897 DvMF_2612 pyruvate carboxyltransferase (RefSeq)

Query= curated2:Q01181
         (391 letters)



>FitnessBrowser__Miya:8501897
          Length = 455

 Score =  213 bits (542), Expect = 9e-60
 Identities = 146/375 (38%), Positives = 199/375 (53%), Gaps = 20/375 (5%)

Query: 21  LCDTTLRDGEQTAGVAFTRAEKRAIAEALQAAGVAEVEVGVPAMGEEERADIRAVAA-VL 79
           L DTTLR+GEQ+ G   + A++  +   L A GV E EVG    G E+  D+ A++A V 
Sbjct: 2   LLDTTLREGEQSFGTYLSMADRERVLRGLAAVGVPEAEVGWA--GREDLTDMLALSARVA 59

Query: 80  KTAAPVVWCRLRAEDLAAAQRTGVVRLHIGVPVSERQISAKLGKDAAWVRDKVEKLVRAA 139
              A   WCR R  DL AA   G  R+ +GVPVS+  ++ +LG   A + D +   +  A
Sbjct: 60  PGLAAAAWCRCRPGDLRAAVACGASRVCVGVPVSDAHLARRLGLGRAALLDLLAATLAEA 119

Query: 140 SWAG-HKVSVGAEDASRADPFFLAEIAHVAAEAGAIRFRISDTLGVLDPFAAHELV---- 194
              G   V+VG EDASRAD  F+  +A  AA  GA R R+SDT+G+  P    ++V    
Sbjct: 120 RMLGIEHVTVGMEDASRADRAFVFAVACHAAAHGAHRVRLSDTVGLYTPLEVADVVRALR 179

Query: 195 -----GRVVTRCP----LPVEFHGHNDLGMATANSLAAARAGASHLSVTVNGLGERAGNA 245
                 R     P    + +  H HND GMATAN+L A   GA    V+V GLGERAG A
Sbjct: 180 AELEGARQDDTAPRARRVSIGTHFHNDCGMATANALTALECGADCADVSVLGLGERAGVA 239

Query: 246 ALEEVAAALEAAGRATGVALGQLCALSELVARASGRPLSPQKPIVGEGVFTHECGIHVDG 305
            LEE+AAAL   GRA    L  L AL   VA+A+   +    P+ G  +F  E G+H  G
Sbjct: 240 RLEELAAALVVRGRAR-FELAPLRALCGQVAQAASLSVPRHWPVAGRDIFAVESGLHAHG 298

Query: 306 LMKDRATYESADLRPERFGRSHRIAIGKHSSAAGLARALAEAGLPADAATLAALMPALRD 365
           + +D + +E     PE  G S R+ +G+ S  A +A ALAE  +      L A++ A+RD
Sbjct: 299 VRRDPSLFE--PFPPELVGDSRRMGVGRKSGVAAVAAALAELSILPPPDELPAIVEAVRD 356

Query: 366 WAAITKRAAAPEDLA 380
            +A  +R   P +LA
Sbjct: 357 LSATLRRPLTPAELA 371


Lambda     K      H
   0.318    0.130    0.371 

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: 375
Number of extensions: 15
Number of successful extensions: 4
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: 391
Length of database: 455
Length adjustment: 32
Effective length of query: 359
Effective length of database: 423
Effective search space:   151857
Effective search space used:   151857
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 (21.7 bits)
S2: 50 (23.9 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