GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Dyadobacter tibetensis Y620-1

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>NCBI__GCF_000566685.1:WP_025763135.1
          Length = 384

 Score =  219 bits (559), Expect = 8e-62
 Identities = 146/397 (36%), Positives = 211/397 (53%), Gaps = 34/397 (8%)

Query: 14  MMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWH 73
           +  VY      PV+ +GS LWDQ G EY+D  GG AV ++GH HP  V  LTEQ  K   
Sbjct: 4   LFEVYPLYDIEPVKAQGSYLWDQNGIEYLDMYGGHAVISVGHCHPDYVARLTEQLSKISF 63

Query: 74  TGNGYTNEPVLRLAKQLIDAT-FAD-RVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131
             N         LA +L   + + D ++F CNSGAEANE ALKLA       F + +  +
Sbjct: 64  YSNSVQIPQQEELATKLGTLSGYPDYKLFLCNSGAEANENALKLAS------FHTGRKKV 117

Query: 132 VAFKNAFHGRTLFTVSAGGQPA------YSQDFAPLPPQIQHAIYNDLDSAKALIDDNTC 185
           VAF  AFHGRT   V+A   P+      Y++  + LP       +ND+++ +A I +   
Sbjct: 118 VAFTKAFHGRTAGAVAATDNPSIVAPVNYNEHVSFLP-------FNDIEALQAGITEEVA 170

Query: 186 AVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTP 245
           AVIVE +QG GG+     +FL+ LR+ CD   A LI D VQ G GRTG+ +++   G+ P
Sbjct: 171 AVIVEGIQGVGGIQVCSDEFLQALRKRCDETGAALILDSVQCGYGRTGKFFSHQFSGIHP 230

Query: 246 DLLSTAKALGGGFPI-GALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREV 304
           D+++ AK +G GFPI G L+A +  AS    G  GTT+GGN LACA    V   +   ++
Sbjct: 231 DMMTMAKGMGNGFPIAGVLIAPQFKAS---FGLLGTTFGGNHLACAAGIAVLDIMKDEQL 287

Query: 305 LNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAA-EEGL 363
           L+   +   +    +  +    G +K++RG GL+IG     E+    K + N+   E  +
Sbjct: 288 LDNATKIGAYLFHEIEEL----GGYKDLRGRGLMIGI----EFDFPVKELRNKLLFEHHI 339

Query: 364 MILIAGANVVRFAPALIISEDEVNSGLDRFELACKRF 400
              +AGA  +R  P+L IS+ E +  L+ +    K F
Sbjct: 340 FTGVAGAYTLRLLPSLAISQKEADQFLEAYRSCLKTF 376


Lambda     K      H
   0.321    0.137    0.412 

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: 393
Number of extensions: 20
Number of successful extensions: 7
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: 384
Length adjustment: 31
Effective length of query: 375
Effective length of database: 353
Effective search space:   132375
Effective search space used:   132375
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: 50 (23.9 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