GapMind for catabolism of small carbon sources

 

Alignments for a candidate for drdehyd-beta in Burkholderia phytofirmans PsJN

Align 2-deoxy-D-ribose dehydrogenase β subunit (characterized)
to candidate BPHYT_RS32805 BPHYT_RS32805 acylaldehyde oxidase

Query= metacyc::MONOMER-20833
         (739 letters)



>FitnessBrowser__BFirm:BPHYT_RS32805
          Length = 756

 Score =  389 bits (999), Expect = e-112
 Identities = 277/772 (35%), Positives = 394/772 (51%), Gaps = 72/772 (9%)

Query: 14  LSRRRFL--ASTAVGALVIGFG-LPLGAGRVQAATSAERGTQVP--AFLEIRPDGTVRLL 68
           L RR FL   + AVGALV+G+  LP G     +     +G+QV    +++I  D +V ++
Sbjct: 2   LKRRTFLLGGAGAVGALVVGWSVLPPGQRLTTSMPLPAQGSQVALNGWVKIAADNSVTIM 61

Query: 69  SPFMEGGQGTHTAMAQIVGEELDADPATFIVEAAPPGEAY-------------------- 108
               E GQG HT +A ++ EELDAD +   VE +P  + Y                    
Sbjct: 62  MCKAEMGQGIHTGLAMLLAEELDADWSQVRVEDSPIDKIYNSVQSIIDDLPFRPDDDSTV 121

Query: 109 ----------VVMENGLRITGGSMSVRMSYPTMRRLGALARAMLLQAGAKQWGVPVGELT 158
                     +V E G  +TGGS S+   +  MR  GA ARAML+ A A QW VP GE  
Sbjct: 122 KRTTVWMTRKLVREAGTMMTGGSSSINDLWTPMREAGASARAMLIGAAAAQWKVPPGECR 181

Query: 159 TQPGRVVHAASGRSLGYGELASSALDMPVPDPASITLRDPSQFRWIGKPVKRLDAYDKST 218
            + G+V+H  SG    +GEL+S A    +P    +TL+DP+ F+ IGKP++R++A  K  
Sbjct: 182 AEGGQVLHP-SGHKASFGELSSMAAQQALP--RKVTLKDPANFKLIGKPLRRIEAASKIN 238

Query: 219 GKALYSIDLKVDNMLHAAVQHAPRLGMTVGSLRNQSQVEGMKGVHSVHVLP-----GAVA 273
           G A + ID+  D +L+A+V+  P LG +V      +  +    + +  V P     G VA
Sbjct: 239 GTARFGIDVLPDGLLYASVEMCPTLGGSVAKFDATAAGKMPGFIKAFAVAPYNGGTGGVA 298

Query: 274 VVAERWWHAKRAVEAIQVDWQEAAA------DSALRVMPADFSSDKHREFLAAQQGPTRD 327
           V+A+  + A  AV A+ V W +  A      D+  R+  A   +D H  +          
Sbjct: 299 VIADNPFRAMNAVAAVDVTWHDGPAAKLSNADADRRLAQALDDNDGHAYY---------- 348

Query: 328 DENEGDVAGALKGAKTQVEATYHNQYLNHAQLEPPSALARFNPDGTLEIWLPNQAPDMFR 387
             + GDV  AL  A   V A Y   YL H  +EP +   +   DG   +W+  Q P + R
Sbjct: 349 --HLGDVDAALTRAARTVSAEYRAPYLAHGAVEPLNCTVQV-ADGAATVWVSTQMPGLAR 405

Query: 388 ADIAKRTGLDPAQITLHSPLLGGFFGRHFLYDSANPYPQAIALAK-AVSRPIKLIWSREE 446
             +AK   LD  ++ + + LLGG FGR    D      QA A+A+    RP++ +WSR +
Sbjct: 406 HHVAKVLDLDADKVDVQTFLLGGAFGRRLELDFI---AQAAAIAREGGGRPVQTLWSRAQ 462

Query: 447 EFLRDVLRPLAVVKFRAALDDKGLPVAIEAVSATEGPT-EALAGKQGDK---IDPTAVEG 502
           +F  D  RP  + + +A  D+ G  VA +A SA++    EALA   G     ID T  EG
Sbjct: 463 DFTHDFYRPACLSRLKAGFDNDGKLVAWQAASASQAIVPEALARYYGAPRLPIDKTTCEG 522

Query: 503 LSGKSYAIPNKRIAQIYVKGAPMLGYWRSVGNSLNDFFYESFLDELADKGGHDPYELRLH 562
              + Y  P  R+A   V+    +G+WRSVG+S   FF E F DELA   G DP   R  
Sbjct: 523 AFDQPYEWPAARVAHKIVELPVPVGFWRSVGHSHQAFFTEGFTDELAVATGKDPIAFRAA 582

Query: 563 LLRDNPRLTTLLQAAGELSGGWKRGPFTAEDGTRRARGVAMASPFGSHTAAIAEVSIENG 622
           LL  +PR   +L+ A  LS  W+     A DG  RARGVA+   FGS  A +AEVSI  G
Sbjct: 583 LLEQHPRHLAVLKRAAALSD-WEHPLTHAADGAPRARGVALHEAFGSVVAQVAEVSIGPG 641

Query: 623 K-VKVHDIWQAIDPGSIVNPAIVEAQVNGAVALGLSQTLLEEAVYVDGKPRARNYDLYPI 681
           K ++VH +   ID G  VNP ++  Q+  AV  GLS  L +E   V+G+ + +N+  +P+
Sbjct: 642 KKIRVHRVVCVIDCGIPVNPNLIRQQMESAVVFGLSAALQDEITLVNGQVQQKNFLDFPV 701

Query: 682 LAPAQMARVHVRVVESGEKMGGIGEPPLPAVAPAVANAVAQLTGQRVRSLPL 733
           +       +   ++ S     G+GE  +P VAPAVANAV +LTGQR+RSLPL
Sbjct: 702 VRIDDCPVIDTDIMPSQLHPQGVGEAGVPPVAPAVANAVFKLTGQRLRSLPL 753


Lambda     K      H
   0.317    0.134    0.394 

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: 1379
Number of extensions: 72
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 739
Length of database: 756
Length adjustment: 40
Effective length of query: 699
Effective length of database: 716
Effective search space:   500484
Effective search space used:   500484
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 (21.7 bits)
S2: 55 (25.8 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