GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcD in Cupriavidus basilensis 4G11

Align D-lactate oxidase, FAD-linked subunit (EC 1.1.3.15) (characterized)
to candidate RR42_RS17300 RR42_RS17300 glycolate oxidase

Query= reanno::Cup4G11:RR42_RS17300
         (497 letters)



>FitnessBrowser__Cup4G11:RR42_RS17300
          Length = 497

 Score =  988 bits (2555), Expect = 0.0
 Identities = 497/497 (100%), Positives = 497/497 (100%)

Query: 1   MNAPHEVSLVADDARRSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALP 60
           MNAPHEVSLVADDARRSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALP
Sbjct: 1   MNAPHEVSLVADDARRSALLAGLAKILPDAALLWKPEDTVPYECDGLAAYRQVPMAVALP 60

Query: 61  DNEDQVCAILRLCHSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTA 120
           DNEDQVCAILRLCHSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTA
Sbjct: 61  DNEDQVCAILRLCHSLQVPVVPRGAGTSLSGGAMPIATGLVLSLAKFKRIVSVDVRSRTA 120

Query: 121 VVQPGVRNLAISEAAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRV 180
           VVQPGVRNLAISEAAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRV
Sbjct: 121 VVQPGVRNLAISEAAAQYNLYYAPDPSSQIACTIGGNVSENSGGVHCLKYGLTVHNVLRV 180

Query: 181 RAVTMEGDVVEFGSEAPDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFD 240
           RAVTMEGDVVEFGSEAPDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFD
Sbjct: 181 RAVTMEGDVVEFGSEAPDAPGLDLLAAVIGSEGMLAVVTEVSVKLIPKPQLAQVIMASFD 240

Query: 241 DVAKGGNAVADVIGAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEV 300
           DVAKGGNAVADVIGAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEV
Sbjct: 241 DVAKGGNAVADVIGAGIIPAGLEMMDKPATAAVEEFVRAGYDLDAAAILLCESDGTPEEV 300

Query: 301 AEEVERMSEVLRASGASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKH 360
           AEEVERMSEVLRASGASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKH
Sbjct: 301 AEEVERMSEVLRASGASRIQVSQSEPERLRFWSGRKNAFPAAGRISPDYYCMDGTIPRKH 360

Query: 361 IGTLLKRIEEMERKYGLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESCVE 420
           IGTLLKRIEEMERKYGLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESCVE
Sbjct: 361 IGTLLKRIEEMERKYGLRCMNVFHAGDGNMHPLILFDGADQDEWHRAELFGSDILESCVE 420

Query: 421 LGGTVTGEHGVGVEKLNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKAIPTLARCAEYG 480
           LGGTVTGEHGVGVEKLNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKAIPTLARCAEYG
Sbjct: 421 LGGTVTGEHGVGVEKLNSMCVQFSAQERDLFFGVKAAFDPARLLNPDKAIPTLARCAEYG 480

Query: 481 RMHVKRGLLPHPDLPRF 497
           RMHVKRGLLPHPDLPRF
Sbjct: 481 RMHVKRGLLPHPDLPRF 497


Lambda     K      H
   0.319    0.136    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: 929
Number of extensions: 18
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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: 52 (24.6 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