GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Pedobacter sp. GW460-11-11-14-LB5

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate CA265_RS13660 CA265_RS13660 oxidoreductase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5967
         (272 letters)



>FitnessBrowser__Pedo557:CA265_RS13660
          Length = 262

 Score =  154 bits (389), Expect = 2e-42
 Identities = 93/257 (36%), Positives = 135/257 (52%), Gaps = 5/257 (1%)

Query: 19  LKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGA-DVHA--L 75
           LK K+ L+TG   GIG  I    A     ++    Q+E  +       E  + D H    
Sbjct: 7   LKGKIALVTGVTSGIGLGIAKMMAKAGCTVIGCAEQSETSDVAQRFLAEMESFDAHTDYF 66

Query: 76  KADVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAIDLDGAWY 135
           KAD+   +D+  +       +GR+D+LV+ AG NVF      TE++W+    ++L   W 
Sbjct: 67  KADMVVTEDIDGLVSDITNDYGRLDILVSNAGQNVFTGLENSTEKNWQFNLDLNLSAHWR 126

Query: 136 GCKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRV 195
             K     ++    G II +AS H+   IPGC PY +AK  L GL R+L IE+ P G+R 
Sbjct: 127 LAKRC-KSLLNTNNGVIIVMASNHAFASIPGCAPYNIAKTALTGLVRSLAIEWGP-GIRT 184

Query: 196 NAIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFI 255
             IAPG+I+T  N  ++N F  P  ERQR ++LHP +++G   E+    VFL+S+ A F 
Sbjct: 185 IGIAPGFIDTPGNQQWFNSFIQPEEERQRTINLHPVKKLGTVEEIGGWCVFLSSEYAGFA 244

Query: 256 NASCITIDGGRSVMYHD 272
           + +   IDGGRS M  D
Sbjct: 245 SGTTYLIDGGRSAMMQD 261


Lambda     K      H
   0.321    0.137    0.419 

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: 182
Number of extensions: 8
Number of successful extensions: 4
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: 262
Length adjustment: 25
Effective length of query: 247
Effective length of database: 237
Effective search space:    58539
Effective search space used:    58539
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: 47 (22.7 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