GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcF in Burkholderia phytofirmans PsJN

Align D-lactate oxidase and glycolate oxidase, iron-sulfur subunit (EC 1.1.3.15) (characterized)
to candidate BPHYT_RS31655 BPHYT_RS31655 glycolate oxidase

Query= reanno::psRCH2:GFF3770
         (405 letters)



>FitnessBrowser__BFirm:BPHYT_RS31655
          Length = 409

 Score =  598 bits (1542), Expect = e-176
 Identities = 291/408 (71%), Positives = 341/408 (83%), Gaps = 4/408 (0%)

Query: 1   MQTNLSEAAKKLPRAEEAESILRSCVHCGFCNATCPTYQLLGDELDGPRGRIYLMKQMFE 60
           MQTNLS+AAK L RA+EAE ILRSCVHCGFCNATCPTYQLLG+ELDGPRGRIYL+KQM E
Sbjct: 1   MQTNLSDAAKTLSRADEAEQILRSCVHCGFCNATCPTYQLLGNELDGPRGRIYLIKQMLE 60

Query: 61  GGEVTESTQLHLDRCLTCRNCETTCPSGVKYHNLLDIGRDFIEQQVQRPLGERVVRGGLR 120
           G  VT+ TQ+HLDRCL+CRNCETTCPSGV YH LLDIGR  +E+++ RP  ER+ R  LR
Sbjct: 61  GEPVTQKTQMHLDRCLSCRNCETTCPSGVTYHALLDIGRAELERRIVRPALERLQRESLR 120

Query: 121 TVIPRPGLFKALLGAGNALKPLMPASLKDHLPREIRPAKPRPQVMHSRRVLILEGCVQPS 180
            VIP   +F ALL  G A++P +P +L   +P     AK RP+  HSR++L+LEGCVQ +
Sbjct: 121 HVIPHRAVFGALLKTGQAMRPFLPTALGRKIPGRSARAKTRPEPRHSRKMLMLEGCVQRA 180

Query: 181 LSPSTNAAAARVLDRLGISVSPAREAGCCGAVDYHLNAQDAGLDRARRNIDAWWPAIEAG 240
           LSP+TNAAAARVLDRLGIS+  A  A CCGA DYHLNAQ+AGL RARRNIDAWWPAI+AG
Sbjct: 181 LSPNTNAAAARVLDRLGISIVNAERADCCGATDYHLNAQEAGLARARRNIDAWWPAIQAG 240

Query: 241 AEAIVQTASGCGAFVKEYGHLLKDDPAYAAKAARVSELAKDLVEVLRSAELE----KLNV 296
           AEAIVQTASGCGAFVKEYGHLL+DD  YA+KA RVSELA+D+VEVL +  ++     L+ 
Sbjct: 241 AEAIVQTASGCGAFVKEYGHLLRDDLRYASKAQRVSELARDIVEVLANEPIQPIQTNLSG 300

Query: 297 RADKRMAFHCPCTLQHAQKLGGAVEDVLTRLGYQLTAVPDAHLCCGSAGSYSITQPEISH 356
              +++AFHCPCTLQHAQKLGGAVE VL RLG+ L+AVPDAHLCCGSAG+YSITQPE++ 
Sbjct: 301 TPQQKIAFHCPCTLQHAQKLGGAVEAVLQRLGFDLSAVPDAHLCCGSAGTYSITQPELAK 360

Query: 357 QLRDNKLNALESGKPEVIVTANIGCQTHLDGAGRTPVKHWIEVVEESM 404
           +LR NKL+ALESGKP++IVTANIGCQTHLDGAGRTPV+HWIE+VE S+
Sbjct: 361 KLRSNKLDALESGKPDLIVTANIGCQTHLDGAGRTPVRHWIELVEASL 408


Lambda     K      H
   0.319    0.135    0.410 

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: 609
Number of extensions: 12
Number of successful extensions: 2
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: 405
Length of database: 409
Length adjustment: 31
Effective length of query: 374
Effective length of database: 378
Effective search space:   141372
Effective search space used:   141372
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: 50 (23.9 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