GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Magnetospirillum magneticum AMB-1

Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_011384093.1 AMB_RS08515 aspartate aminotransferase family protein

Query= BRENDA::O30508
         (406 letters)



>NCBI__GCF_000009985.1:WP_011384093.1
          Length = 459

 Score =  166 bits (421), Expect = 1e-45
 Identities = 129/415 (31%), Positives = 205/415 (49%), Gaps = 47/415 (11%)

Query: 30  RGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRI--WHVSNVFTNEPAL 87
           RG+G RV+D++GR+ I+   G+  TSLG     LV+A   Q +++  +H+ +  T++  +
Sbjct: 38  RGQGVRVYDEAGRDYIEGLAGLWCTSLGWGEERLVEAAARQMRQLPFYHLFSHKTHDVGV 97

Query: 88  RLARKLVDATFA--ERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRT 145
            L  +L+        +VFLA SG+EAN+ A KL    AN +  P K +IIA   ++HG T
Sbjct: 98  ELCARLLAMAPVPMSKVFLAGSGSEANDTAIKLIHYRANALGTPDKKKIIAREKAYHGVT 157

Query: 146 LFTVNVGGQPKYSDGFGPKFEGITHV--PYN-------------------DLEALKAAIS 184
           + T ++ G       F     G+     P++                   +LEA+  A  
Sbjct: 158 VATASLTGLVNNQRSFDLPIPGVLRAACPHHYRFAKDGESEEDFSTRLAGELEAMILAEG 217

Query: 185 -DKTCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMH 243
            D   A   EP+ G GGV+     Y    + + D ++ LLV DEV  G GR G++F    
Sbjct: 218 PDTVAAFFAEPVMGAGGVIVPPAGYFPKIQAVLDRYDVLLVVDEVICGFGRTGKMFGTET 277

Query: 244 YGVVPDILSSAKSLGGGF-PIGAMLTT----GEIAK---HLSVGTHGTTYGGNPLASAVA 295
           +G+ PD+++ AK L  G+ PI A++      G +A+    + V  HG TYGG+P+++AVA
Sbjct: 278 FGIRPDMMTLAKGLSSGYAPISALMVNERVYGPVAEESGRIGVFGHGYTYGGHPVSAAVA 337

Query: 296 EAALDVINTPEVLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGK-- 353
              L++    ++L  V       +  L+ + + + +  E RG+GL+    L  +   +  
Sbjct: 338 LETLNIYAERDILAQVAEVGPVLQDGLRAL-RGHPLVGEARGVGLIGAVELVADKANRAP 396

Query: 354 --------ARDVLNAAEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAV 400
                   AR V  A  K   ++L+A  D V FAP LVI  A+I E L RF  A+
Sbjct: 397 FPPELAVGARVVAKAQAKG--VILRAMGDAVAFAPPLVISKADIAEMLRRFGLAL 449


Lambda     K      H
   0.318    0.135    0.394 

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: 479
Number of extensions: 29
Number of successful extensions: 5
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: 406
Length of database: 459
Length adjustment: 32
Effective length of query: 374
Effective length of database: 427
Effective search space:   159698
Effective search space used:   159698
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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