GapMind for catabolism of small carbon sources

 

Alignments for a candidate for QDPR in Pseudarthrobacter sulfonivorans Ar51

Align flavohemoprotein; EC 1.14.12.17 (characterized)
to candidate WP_058930069.1 AU252_RS06790 globin domain-containing protein

Query= CharProtDB::CH_003330
         (396 letters)



>NCBI__GCF_001484605.1:WP_058930069.1
          Length = 386

 Score =  202 bits (514), Expect = 1e-56
 Identities = 135/400 (33%), Positives = 212/400 (53%), Gaps = 28/400 (7%)

Query: 1   MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKE-IFNMSNQRNGDQREALFN 59
           ML  ++   ++AT+PL+      +T  FY R+F  +PEL + +F+ SNQR+G+Q++AL  
Sbjct: 1   MLSDKSRPVIEATLPLVGSRIGAITPKFYARLFAAHPELLDGLFSRSNQRSGNQQQALAG 60

Query: 60  AIAAYASNIENLPALLP--AVEKIAQKHTSFQIKPEQYNIVGEHLLAT----LDEMFSPG 113
           +IAA+A+++ N P  LP   + +IA +H S  I   QY +V EHL A     L E+ +P 
Sbjct: 61  SIAAFATHLVNNPGTLPETVLSRIAHRHASLGITEPQYQVVYEHLFAAIAEDLAEVITP- 119

Query: 114 QEVLDAWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELE 173
            E+ +AW + Y ++A+  I  E  +Y   A++A G   T  +++ AK P      +F LE
Sbjct: 120 -EIAEAWTEVYWLMADALIKLEKGLY---AAQANGKMWT-PWKVAAKIPAGIGSMTFTLE 174

Query: 174 PVDGGAVAEYRPGQYLGVWLK-PEGFPHQEIRQYSLTRKPDGKGYRIAVKREEGGQVSNW 232
           P D   V    PGQY+ V ++ P+G   +++RQYSL+    G       K ++GG+VS  
Sbjct: 175 PADDTPVTAALPGQYVSVKVQLPDGL--RQVRQYSLSGDA-GTSRSFTTKLDDGGEVSPV 231

Query: 233 LHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDTLAKAGHTAQVNW 292
           LHN   VGD++++  P G+  +   D  PV L SAG+G TP  ++L +LA++G   QV  
Sbjct: 232 LHNTVEVGDILEISNPYGEITLKDGDG-PVVLASAGIGCTPTASILRSLAESGSDRQVLV 290

Query: 293 FHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEGAF 352
            HA    D  A   ++ +  + L       W  +P           +EG M L +++   
Sbjct: 291 LHAESTLDSWALRGQMTDDVERLADADLQLWLEEPRAG-------ANEGFMSLREVD--- 340

Query: 353 SDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP 392
                  YLCGP+ FM+    + +  G+    IHYE FGP
Sbjct: 341 LPANASLYLCGPLPFMKHIRNEAISAGIPATRIHYEVFGP 380


Lambda     K      H
   0.318    0.135    0.404 

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: 380
Number of extensions: 22
Number of successful extensions: 8
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: 396
Length of database: 386
Length adjustment: 31
Effective length of query: 365
Effective length of database: 355
Effective search space:   129575
Effective search space used:   129575
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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