GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galactonolactonase in Flavobacterium glycines Gm-149

Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate WP_066330220.1 BLR17_RS12195 lactonase family protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314
         (389 letters)



>NCBI__GCF_900100165.1:WP_066330220.1
          Length = 369

 Score =  202 bits (515), Expect = 1e-56
 Identities = 127/368 (34%), Positives = 203/368 (55%), Gaps = 23/368 (6%)

Query: 21  ASAEDYQLLVGSYTAG-QSQGIYRLAFDSRTG--QIDASPLQVIKSANPSWLTLSKDQRH 77
           A  + + L++G+YT   +S+GIY   F++ TG  Q  +S   VI   NPS++++SK+   
Sbjct: 19  AQEKKFNLIIGTYTKSCESKGIYVYDFNAETGDFQFKSSTENVI---NPSFVSVSKNNDF 75

Query: 78  LFVVNENGPGQTDPVGRVSSFAIDPKTHALSLISQVQSLGNEPTHSSLSIDGSHLFVSNY 137
           ++ VNE+GP  T     VS+F  D     +  +++ Q + N P    +  D  ++  +NY
Sbjct: 76  IYSVNEDGPKST-----VSAFKYDTSNAKIEFVNK-QEIHN-PGPCYIINDDKNVITANY 128

Query: 138 SVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASAHVHSTIPSPDGRYVFAN 197
           +     GG++AV     +G L  + Q+  H    +NP RQ  +HVHS   SPD ++V A 
Sbjct: 129 T-----GGSVAVFGKNKNGSLTELKQLIKHSGKGINPARQEKSHVHSVQFSPDHQFVLAT 183

Query: 198 DLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGKHAWLTMEMSAQV 257
           DLG DK++ Y+++PK    L L  +    +++  GSGPRH  FS +G+  +L  E+   +
Sbjct: 184 DLGTDKMYLYQYNPKVAKPLELKDS----IKVKAGSGPRHFAFSKNGQQLYLLQELDGTL 239

Query: 258 AVFDYHDGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYVSNRGTANQLLVFAIDPA 317
           +VF+Y+ G+L   Q   + A        AA +H S D +FLY +NR  AN +  F I   
Sbjct: 240 SVFNYNKGKLVLVQETTVLAPDFKGTSTAADIHISPDQRFLYATNRKEANTISCFKI-LK 298

Query: 318 TGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDARTGLLGKTVQKLPM 377
            G L+   R +  GD PR F++DP+G FLL+ +Q +N +VV +R+  TG L  T +++ +
Sbjct: 299 DGKLALASRTSSLGDGPRNFAIDPTGNFLLVGHQYTNNVVVFKRNKETGALTDTGKRIEL 358

Query: 378 DAPSDLRF 385
            AP  L F
Sbjct: 359 CAPVCLVF 366


Lambda     K      H
   0.316    0.132    0.382 

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: 375
Number of extensions: 19
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: 389
Length of database: 369
Length adjustment: 30
Effective length of query: 359
Effective length of database: 339
Effective search space:   121701
Effective search space used:   121701
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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