GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucD in Saccharomonospora marina XMU15

Align L-fuconate dehydratase; FucD; EC 4.2.1.68 (characterized)
to candidate WP_009153233.1 SACMADRAFT_RS07685 fuconate dehydratase

Query= SwissProt::Q8P3K2
         (441 letters)



>NCBI__GCF_000244955.1:WP_009153233.1
          Length = 425

 Score =  596 bits (1536), Expect = e-175
 Identities = 283/424 (66%), Positives = 341/424 (80%)

Query: 1   MRTIIALETHDVRFPTSRELDGSDAMNPDPDYSAAYVVLRTDGAEDLAGYGLVFTIGRGN 60
           M  IIAL+THD+RFPTS+ LDGSDAMNPDPDYSA+YV LRTD A+ L G+G VFTIGRGN
Sbjct: 1   MARIIALQTHDIRFPTSKTLDGSDAMNPDPDYSASYVRLRTDAADGLEGHGFVFTIGRGN 60

Query: 61  DVQTAAVAALAEHVVGLSVDKVIADLGAFARRLTNDSQLRWLGPEKGVMHMAIGAVINAA 120
           DVQ AA+ AL  H+VG  V + + DLG   R L +DSQLRWLGPEKG+MHMAIGA +NA 
Sbjct: 61  DVQVAALRALEGHLVGRDVAETLDDLGGVWRELVHDSQLRWLGPEKGIMHMAIGAAVNAL 120

Query: 121 WDLAARAANKPLWRFIAELTPEQLVDTIDFRYLSDALTRDEALAILRDAQPQRAARTATL 180
           WDL A+ A  PLWR ++ L+PE++VD IDFRYL+DALTR++ALA+LR A+P RA R   L
Sbjct: 121 WDLKAKRAGVPLWRLLSSLSPEEIVDLIDFRYLTDALTREDALALLRSAEPGRAERETRL 180

Query: 181 IEQGYPAYTTSPGWLGYSDEKLVRLAKEAVADGFRTIKLKVGANVQDDIRRCRLARAAIG 240
           + QGYPAYTT+PGWLGY D+KL +L +EA+  GF  IKLKVGA++ DD+RR R+AR   G
Sbjct: 181 LAQGYPAYTTTPGWLGYDDDKLAKLCREAIEQGFTHIKLKVGADLDDDLRRLRIARDICG 240

Query: 241 PDIAMAVDANQRWDVGPAIDWMRQLAEFDIAWIEEPTSPDDVLGHAAIRQGITPVPVSTG 300
           PDI +AVDANQRWDV  AI W + LA FDIAW+EEPTSPDDVL HAAI + + PVPV+TG
Sbjct: 241 PDIKIAVDANQRWDVAEAIRWTKALARFDIAWVEEPTSPDDVLAHAAIAKAVAPVPVATG 300

Query: 301 EHTQNRVVFKQLLQAGAVDLIQIDAARVGGVNENLAILLLAAKFGVRVFPHAGGVGLCEL 360
           EH  NRVVFKQLLQ+G + ++Q+DA RV GVNEN+AILLLAAKFGV V PHAGGVGLCE 
Sbjct: 301 EHIANRVVFKQLLQSGGLSVLQLDATRVAGVNENIAILLLAAKFGVPVCPHAGGVGLCEA 360

Query: 361 VQHLAMADFVAITGKMEDRAIEFVDHLHQHFLDPVRIQHGRYLAPEVPGFSAEMHPASIA 420
           VQHLAM DFVA++G ++ R IEFVDHLH+HF+ PV ++ GRYLAP  PG   EM+P SIA
Sbjct: 361 VQHLAMFDFVAVSGSLDGRVIEFVDHLHEHFVTPVDVRGGRYLAPAAPGAGTEMYPTSIA 420

Query: 421 EFSY 424
           E+++
Sbjct: 421 EYTH 424


Lambda     K      H
   0.321    0.136    0.409 

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: 674
Number of extensions: 22
Number of successful extensions: 1
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: 441
Length of database: 425
Length adjustment: 32
Effective length of query: 409
Effective length of database: 393
Effective search space:   160737
Effective search space used:   160737
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 (21.9 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