GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Pseudomonas fluorescens FW300-N1B4

Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate Pf1N1B4_2417 Betaine aldehyde dehydrogenase (EC 1.2.1.8)

Query= BRENDA::P49189
         (494 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2417
          Length = 490

 Score =  482 bits (1240), Expect = e-140
 Identities = 245/475 (51%), Positives = 329/475 (69%), Gaps = 5/475 (1%)

Query: 23  ADASGTEKAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAAR 82
           A +  T +A  PA G V+AT   + +++V  AV +A+   KIW+  + MER RIL  A  
Sbjct: 18  ASSDATFEAINPANGEVLATVQRATKEDVERAVVSAEKGQKIWAAMTAMERSRILRRAVD 77

Query: 83  IIREREDEIATMECINNGKSIFEAR-LDIDISWQCLEYYAGLAASMAGEHIQLPGGSFGY 141
           I+RER DE+A +E ++ GK+  E R +DI      LEYYAGL  ++ GE I L   SF Y
Sbjct: 78  ILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEGEQIPLRTTSFVY 137

Query: 142 TRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAGV 201
           TRREPLG+  GIGAWNYP QIA WKSAPALA GNAM+FKPS  T ++ L LAEIY+EAG+
Sbjct: 138 TRREPLGIVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLKLAEIYTEAGL 197

Query: 202 PPGLFNVVQG-GAATGQFLCQHPDVAKVSFTGSVPTGMKIM-EMSAKGIKPVTLELGGKS 259
           P G+FNV+ G G   G +L +HP + K+SFTG   TG K+M   S   +K VT+ELGGKS
Sbjct: 198 PAGVFNVLTGSGREVGTWLTEHPRIEKISFTGGTDTGKKVMASASGSSLKDVTMELGGKS 257

Query: 260 PLIIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGD 319
           PLIIF D D++ A   A+MANF + GQVC NGTRVFV   +   F  ++V++  RI++G+
Sbjct: 258 PLIIFDDADLDRAADTAMMANFYSSGQVCTNGTRVFVPSHLKAAFEAKIVERVARIRVGN 317

Query: 320 PLLEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVLT 379
           P  E+T  GPL++  H+E VLG++   KE+GA++LCGGD     D +   G ++ P V T
Sbjct: 318 PEDENTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGGDRLT--DGEFAKGAFVAPTVFT 375

Query: 380 NCRDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQ 439
           +C D+MT V+EEIFGPVMSIL+++TE EV+ RANDT FGLAAGV T+D+ RAHRV+ +L+
Sbjct: 376 DCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTKDLNRAHRVIHQLE 435

Query: 440 AGTCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESAF 494
           AG C+IN +  S  ++P GGYK+SG GRENG  ++  ++++K+V VE+GD  S F
Sbjct: 436 AGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVELGDYASVF 490


Lambda     K      H
   0.320    0.137    0.411 

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: 682
Number of extensions: 28
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: 494
Length of database: 490
Length adjustment: 34
Effective length of query: 460
Effective length of database: 456
Effective search space:   209760
Effective search space used:   209760
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: 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