GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Burkholderia phytofirmans PsJN

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate BPHYT_RS29875 BPHYT_RS29875 betaine-aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__BFirm:BPHYT_RS29875
          Length = 483

 Score =  386 bits (992), Expect = e-112
 Identities = 204/475 (42%), Positives = 295/475 (62%), Gaps = 6/475 (1%)

Query: 22  LFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPA 81
           L I+G+       E    ++P T+ P+A +A+G + D+D A+ AAR   +   W+    A
Sbjct: 12  LLIDGKRLPPGTGEYSVDINPATEEPIALVAQGSAADVDTAVRAARAALKV--WNGIRTA 69

Query: 82  KRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE 141
           +R  +L +LA LM A+ EELA LE+LD GKPI   +R DIP A   + +YA   DK+ G+
Sbjct: 70  ERARILMRLAGLMRANLEELAALESLDAGKPIAAVMRQDIPAAIDTLEYYAGWCDKINGQ 129

Query: 142 VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAI 201
           V       L   +REPVGV+AAIVPWNFPL++  WK+ PALA G ++I+KP+E +PL+A+
Sbjct: 130 VVPVRPDALTYTLREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLTAL 189

Query: 202 RLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNM 261
           R+  LA EAG+P GVLN+VTG G   G AL  H  +D + FTGS   G+ +L+ A   N 
Sbjct: 190 RIGELALEAGVPPGVLNIVTGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAA-GNF 248

Query: 262 KRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLAL 321
           KRV LE GGKSAN++F D  +L  A  A A+GIF+N GQVC AG+R+L    + DE +  
Sbjct: 249 KRVTLELGGKSANLIFPDA-NLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVER 307

Query: 322 LKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG--RNAGLAAAI 379
           L  +A++ + G P    T+MG LI  A   +V  ++  G ++G  L+ G  R       +
Sbjct: 308 LAARAKSIKVGDPSSRETSMGPLISAAQMKTVLGYVETGRAEGASLVTGGARVGERGFFV 367

Query: 380 GPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHR 439
            PT+F +V+    +S+EEIFGPV  V RF  E  A+++AN + Y L A VW+ D+ R HR
Sbjct: 368 EPTVFANVEHEMRISQEEIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVHR 427

Query: 440 MSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISLE 494
           ++R L+AG+V++N Y   D+ +P+GG   SG GR+    A+E FTE K +W++++
Sbjct: 428 VARDLRAGTVWINTYGYTDVRLPWGGSGDSGFGREHGDVAIENFTEPKAVWLAID 482


Lambda     K      H
   0.317    0.133    0.389 

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: 612
Number of extensions: 31
Number of successful extensions: 5
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: 495
Length of database: 483
Length adjustment: 34
Effective length of query: 461
Effective length of database: 449
Effective search space:   206989
Effective search space used:   206989
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: 52 (24.6 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