GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocD in Brucella inopinata BO1

Align ornithine aminotransferase (EC 2.6.1.13) (characterized)
to candidate WP_002968535.1 BIBO1_RS18510 aspartate aminotransferase family protein

Query= BRENDA::B1A0U3
         (469 letters)



>NCBI__GCF_000182725.1:WP_002968535.1
          Length = 484

 Score =  180 bits (457), Expect = 8e-50
 Identities = 126/412 (30%), Positives = 205/412 (49%), Gaps = 45/412 (10%)

Query: 58  AKGSSVWDPEGNKYIDFLSGYSAVNQGHCHPKILKALHDQADRLTVSSRAFYNDRFPVFA 117
           A+G   +D  G + +DF  G+ ++  GH HP+I+ A     + L       +  ++    
Sbjct: 68  AEGMYYYDQNGRRILDFFGGFGSLAFGHNHPRIIAARRKFQEELRHEIAIAFMSQYAAAL 127

Query: 118 EYLTALFG---YDMVLPMNTGAEGVETALKLARKWGYEKKKIPNDEALIVSCCGCFNGRT 174
            Y  A       DMV   ++G+E +E A+K+A +    KK        IV     F+G+T
Sbjct: 128 AYDLAACSPGDLDMVFLGSSGSEAMEAAIKVAERAAGPKKP------KIVYAENSFHGKT 181

Query: 175 LGVISMSCDNEATRGFGPLMPGHLKVDFGDAEAIERIFKEKGDRVAAFILEPIQGEAGVV 234
            GV+S++ D    RG   L+   ++V FGD  AIE  F+   + +   +LE +QG  G++
Sbjct: 182 KGVLSIT-DGGLYRGEFKLVDNTVRVPFGDITAIENAFRSDPE-IGTIVLETVQGGGGII 239

Query: 235 IPPDGYLKAVRDLCSKYNVLMIADEIQTGLARTGKMLACDWEDVRPDVVILGKALGGGIL 294
                + + +R LC +Y V+ +ADE+Q G  RTGK  A +   V PDV  L K+LGGG  
Sbjct: 240 QADAEFWQKLRQLCDRYGVIWVADEVQCGFGRTGKFYAFEHYGVIPDVTALAKSLGGGKA 299

Query: 295 PVSAVLADKDVMLCIKPGQHG----------STFGGNPLASAVAIAALEVIKEERLTERS 344
            ++A++A +D+ +      +G          +TFGG   A   AI A+ ++ +E+L + S
Sbjct: 300 AMAAMIARRDIYM----KAYGTPKTAMIHAMATFGGIGEACITAIEAVNILYDEQLIDNS 355

Query: 345 TKLGGELLGLLHKIQKKHPEHVKEVRGKGLFIGVE------------------LNSESLS 386
            ++G  LL  L ++Q ++P  +K+VRGKG+ +G+E                  L+ +   
Sbjct: 356 AEVGDYLLERLKELQVRYPGLLKDVRGKGMMVGLEFHDFSQAMPMVLRPMLAMLDDKLKG 415

Query: 387 PVSGFELSEKLKERGVLAKST--HDTIIRFTPPLCISADEIQQGSKALAEVL 436
            + GF  S  L++ GVL   T  +  +IR  PPL      + +  KAL EVL
Sbjct: 416 SLPGFIGSHLLRDHGVLVAFTEYNRNVIRLEPPLICQRAHVDEFIKALDEVL 467


Lambda     K      H
   0.319    0.137    0.409 

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: 501
Number of extensions: 34
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: 469
Length of database: 484
Length adjustment: 33
Effective length of query: 436
Effective length of database: 451
Effective search space:   196636
Effective search space used:   196636
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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