GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Granulicella mallensis MP5ACTX8

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_014266126.1 ACIX8_RS14625 SDR family oxidoreductase

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>NCBI__GCF_000178955.2:WP_014266126.1
          Length = 255

 Score =  132 bits (331), Expect = 1e-35
 Identities = 86/251 (34%), Positives = 133/251 (52%), Gaps = 8/251 (3%)

Query: 19  LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQ-GADVVAIKA 77
           LK K  ++TGAA GIG AI   FA+ QA +V+ D+  +K    A    E+  A    I  
Sbjct: 4   LKGKRAVVTGAASGIGLAIAELFAAHQADVVLLDLDAQKTAGAAKAIAEKTSASATGIAC 63

Query: 78  DVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYGC 137
           DVSR     ++A    +  G++D+LVNCAG+    + L  T ED  R +++++ G +   
Sbjct: 64  DVSRAD---SVAEAFSQAGGQLDILVNCAGIAHVGNLLSTTPEDMDRLYSVNVRGTYLCM 120

Query: 138 KAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNA 197
           +A +  M+E   G I+N+AS  +T  +   F Y + K  +L +T +   +Y  +GIR N 
Sbjct: 121 QAAIKPMLEAKHGVILNLASIAATAGLTDRFAYSMTKGAVLSMTLSAAKDYISQGIRCNC 180

Query: 198 IAPGYIETQLNVDYW--NGFADPHAERQRAF-DLHPPRRIGQPIEVAMTAVFLASDEAPF 254
           I+P  + T   VD +    +    AE+ +A     P  R+G P E+A+ A++L SDEA F
Sbjct: 181 ISPARVHTPF-VDGFLAKNYPGQEAEKMKALAQAQPIGRMGTPAEIAVLALYLCSDEASF 239

Query: 255 INASCITIDGG 265
           +      IDGG
Sbjct: 240 LTGVDYPIDGG 250


Lambda     K      H
   0.321    0.138    0.424 

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: 141
Number of extensions: 5
Number of successful extensions: 3
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: 272
Length of database: 255
Length adjustment: 25
Effective length of query: 247
Effective length of database: 230
Effective search space:    56810
Effective search space used:    56810
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: 47 (22.7 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