GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patA in Brucella inopinata BO1

Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate WP_008507916.1 BIBO1_RS13055 aspartate aminotransferase family protein

Query= BRENDA::P42588
         (459 letters)



>NCBI__GCF_000182725.1:WP_008507916.1
          Length = 403

 Score =  221 bits (564), Expect = 3e-62
 Identities = 136/395 (34%), Positives = 215/395 (54%), Gaps = 20/395 (5%)

Query: 65  AVEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD- 123
           A+ ++ G    L+   G+ +ID   G  + ++GH +P +V  ++ Q A++  H   + + 
Sbjct: 18  ALRFERGEGIWLITEDGERYIDFAAGIAVNSLGHSHPHLVETLKTQ-AEKLWHLSNIYEI 76

Query: 124 PLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAF 180
           P +  L + L   T       FF NSG E++E A+K A+ YQ   G   +F  I   GAF
Sbjct: 77  PAQEKLGRRLVENTFADKV--FFTNSGAEALECAIKTARRYQYVSGHPERFRIITFEGAF 134

Query: 181 HGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPI 240
           HG++L  ++A  ++ + + F P + GF  VPFG+  A+R A+        + A ++LEPI
Sbjct: 135 HGRTLATIAAGGQAKYLEGFGPKVEGFDQVPFGDEAALRAAITP------ETAGILLEPI 188

Query: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300
           QGEGG+   P  +L  VR++CDE G L++LDEVQTG+GRTGK FA E   ++PDI+ +AK
Sbjct: 189 QGEGGLRAFPEEFLRLVRQICDENGLLLLLDEVQTGVGRTGKFFAHEWAGIRPDIMAIAK 248

Query: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360
            +GGG  PIGA +AT E    +     +H TT+GGNPL  A   A ++V+L        +
Sbjct: 249 GIGGG-FPIGACLATAEAAKGM--TAGMHGTTYGGNPLGMAVGNAVLDVVLADGFMENVQ 305

Query: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLN 420
               ++  G   L   YP++V E RG+G+LM ++ V      +    +  + VL  G  +
Sbjct: 306 ATALVMKQGLASLVDRYPNVVSEIRGRGLLMGLKCVVPNT--SLIQALRDEHVLSVGAGD 363

Query: 421 NAKTIRIEPPLTLTIEQCELVIKAARKALAAMRVS 455
           N   +R+ PPL  T E+    +K    A+  + ++
Sbjct: 364 N--VVRLLPPLITTPEEAREALKHIETAVERLSIA 396


Lambda     K      H
   0.320    0.135    0.393 

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: 426
Number of extensions: 25
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: 459
Length of database: 403
Length adjustment: 32
Effective length of query: 427
Effective length of database: 371
Effective search space:   158417
Effective search space used:   158417
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