GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galdh in Jannaschia aquimarina GSW-M26

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate WP_043917268.1 jaqu_RS02010 SDR family oxidoreductase

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



>NCBI__GCF_000877395.1:WP_043917268.1
          Length = 246

 Score =  147 bits (372), Expect = 2e-40
 Identities = 90/252 (35%), Positives = 135/252 (53%), Gaps = 8/252 (3%)

Query: 18  RLKNKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAEKVETVAAHWRERGADVHALKA 77
           RLK+K  ++TG A G G  IV  FA++ AR++I+D+  +  E +A    +     HA +A
Sbjct: 2   RLKDKTAIVTGGASGFGAGIVRKFAAEGARVLIADLNGDDAEALAEELEQ-----HATEA 56

Query: 78  DVSNQQDLHAMARHAVERHGRIDVLVNCAGVNVFRDPLE-MTEEDWRRCFAIDLDGAWYG 136
           DVS+   + AM R A    G +D+LVN AG+     P+E ++E D+ R FA++    +  
Sbjct: 57  DVSDGASVGAMVREAQRLFGEVDILVNNAGITHLPAPMEEVSESDFDRVFAVNCKSVYLT 116

Query: 137 CKAVLPQMIEQGVGSIINIASTHSSHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGVRVN 196
            +  +P M  +G G+I+N+AST      P    Y  +K  ++  TRA+ +E AP+GVRVN
Sbjct: 117 ARHAVPLMKARGAGAILNVASTAGVSPRPRLNWYNASKGWMITATRAMAVELAPEGVRVN 176

Query: 197 AIAPGYIETQLNVDYWNGFADPYAERQRALDLHPPRRIGQPIEVAMTAVFLASDEAPFIN 256
           A+ P   ET L   +     D    R + L   P  R   P ++   A FL SDEA  I 
Sbjct: 177 ALNPVAGETPLLKSFMG--EDTPEIRAKFLSTIPLGRFSTPEDMGNAACFLCSDEASMIT 234

Query: 257 ASCITIDGGRSV 268
             C+ +DGGR +
Sbjct: 235 GVCMQVDGGRCI 246


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: 155
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: 246
Length adjustment: 24
Effective length of query: 248
Effective length of database: 222
Effective search space:    55056
Effective search space used:    55056
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 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