GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galactonolactonase in Pantoea rwandensis LMG 26275

Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate WP_084931726.1 HA51_RS02640 lactonase family protein

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



>NCBI__GCF_002095475.1:WP_084931726.1
          Length = 369

 Score =  202 bits (514), Expect = 1e-56
 Identities = 134/379 (35%), Positives = 209/379 (55%), Gaps = 30/379 (7%)

Query: 22  SAEDYQL-LVGSYTA-----------GQSQGIYRLAFDSRTGQIDASPLQVIKSANPSWL 69
           +AE +Q  LVG++T+             S+G+YRL  +S  G +  +PL VIK  +PSW+
Sbjct: 4   AAEHHQTALVGTWTSIPDAPSEQKPDHPSEGLYRLKVNS-DGTL--TPLDVIKMKSPSWI 60

Query: 70  TLSKDQRHLFVVNENGPGQTDPVGRVSSFAIDPKTHALSLISQVQSLGNEPTHSSLSIDG 129
             S+D R  +  NE         G V++ +ID ++  + +++ V S G +PTH+++S DG
Sbjct: 61  VKSRDGRFAYTTNEEN------AGAVTALSID-RSGKVQVLNVVDSHGQQPTHATISPDG 113

Query: 130 SHLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSS--HPASRVNPERQASAHVHSTIP 187
             LFV+NYSVA+   G ++V P+  DGKL   VQ  +  H    V   RQ   H HST  
Sbjct: 114 KFLFVANYSVAKGGAG-VSVFPIHHDGKLGEQVQHFAFEHGTGAVKG-RQDGGHAHSTTF 171

Query: 188 SPDGRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGKHA 247
           + DG+Y++A DLG DK+ AYR+   A+   PL   +   V    GSGPRH++F+ +G+HA
Sbjct: 172 THDGKYLYAADLGGDKLHAYRYH--ADKAQPLEADSARDVNFTAGSGPRHMVFAPNGQHA 229

Query: 248 WLTMEMSAQVAVFDYHDGQLEQTQMVDL-AAGQPVSDKAAAALHASADGKFLYVSNRGTA 306
           ++T EM+ ++ VF     +LE    + L +     + ++   +  S +GKF+  +NRG+ 
Sbjct: 230 YVTTEMAGEIVVFAVKQDRLEPAAHIKLNSENNSEAYRSGGGIILSPNGKFVIAANRGSD 289

Query: 307 NQLLVFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDARTG 366
           N+LLVF I+ A G L +       G  PR F+ D SGK+L + N  +N I +   DA +G
Sbjct: 290 NKLLVFKIE-ADGMLGKPMSYKANGIEPRAFAFDSSGKYLYVTNVFTNNISLFHFDANSG 348

Query: 367 LLGKTVQKLPMDAPSDLRF 385
            L        +  P+D++F
Sbjct: 349 ELKAAGDAAKISTPTDIKF 367


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: 476
Number of extensions: 45
Number of successful extensions: 15
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