GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoB in Caldicellulosiruptor hydrothermalis 108

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_013402170.1 CALHY_RS01030 phosphoglucosamine mutase

Query= BRENDA::Q6I7B6
         (450 letters)



>NCBI__GCF_000166355.1:WP_013402170.1
          Length = 449

 Score =  165 bits (417), Expect = 3e-45
 Identities = 148/467 (31%), Positives = 231/467 (49%), Gaps = 46/467 (9%)

Query: 2   RLFGTAGIRGTLWEKVTPELAMKVGMA-----VGTYKSGKALVGRDGRTSSVMLKNAMIS 56
           +LFGT G+RG   +++T ELA  +G A       T +  K L+G+D R S  ML+ A+ +
Sbjct: 3   KLFGTDGVRGVANKELTCELAFDLGRAGAYVLTETKQKPKILIGKDTRISCDMLEAALCA 62

Query: 57  GLLSTGMEVLDADLIPTPALAWGTRKLA-DAGVMITASHNPPTDNGVKVFNGDGTEFYVE 115
           GL S G +V  A +I TPA+A   +    DAG+MI+ASHNP   NG+K FN  G +   +
Sbjct: 63  GLTSVGADVYLAGVITTPAIAHLVKSHGFDAGIMISASHNPYEFNGIKFFNSQGFKLSDQ 122

Query: 116 QERGLEEIIFSGNFRK---ARWDEIKPVRNVEV---IPDYINAVLDFVGHETNLKVLYDG 169
            E  +E+II +  + +   A++D I  V  V++     +Y+ + L+    +  LK++ D 
Sbjct: 123 IEEKIEDIILNRKWNEVPHAQFDAIGRVNRVDLKKNYQEYLKSTLNGASFK-GLKIVIDC 181

Query: 170 ANGAGSLVAPYLLREMGAKVLSVNAHVDGHFPGRKPEPRYENIAYLGKLVRELGVDLAIA 229
           ANGA   +AP +  E+GA+V+ +N   DG       E    ++  L + V +   D  IA
Sbjct: 182 ANGAAYKIAPEVFEELGAEVVVINNQPDG--TNINKECGSTHLKMLQQEVVKNKADFGIA 239

Query: 230 QDGDADRIAVFDEKGNYVDEDTVIALFAKLYVEEHG---GGTVVVSIDTGSRIDAVVERA 286
            DGDADR    DE+G+ VD D ++ L A+  +++ G     T+VV++ +   +    +  
Sbjct: 240 YDGDADRTLFVDEEGSIVDGDKIMLLLAQ-NLKQQGKLQRNTLVVTVMSNMGLFVAAKEL 298

Query: 287 GGRVVRIPLGQPHDGIKRYK---AIFAAEPWKLVHPKFGPWIDPFVTMGLLIKLIDENG- 342
           G  +    +G  +   K  +   +I   +   ++   F    D  +T   L KLI E+G 
Sbjct: 299 GINLEVTKVGDRYVLEKMLEGGYSIGGEQSGHIILLDFATTGDGILTSLQLTKLIKESGK 358

Query: 343 PLSELVKEIPTYYLKKANVLC----PDEY-KAEVVRRAAEEVERKLSSEIKEVLTISGFR 397
            LS+L K +  Y     N        D Y K  V+  A ++VE K               
Sbjct: 359 KLSDLAKIMKVYPQVLVNAKVENGKKDLYSKDPVILEAIKKVEEK--------------- 403

Query: 398 IALNDGSWILIRPSGTEPKIRVVAEAPT-EKRRDELFEMAYSTVSRI 443
             LN    +LIRPSGTEP IRV+ E    E+ + +  E+A    SR+
Sbjct: 404 --LNGKGRVLIRPSGTEPLIRVMIEGEDYEEIKKDAHELASLIESRL 448


Lambda     K      H
   0.318    0.138    0.402 

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: 475
Number of extensions: 29
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: 450
Length of database: 449
Length adjustment: 33
Effective length of query: 417
Effective length of database: 416
Effective search space:   173472
Effective search space used:   173472
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 (21.6 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