GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Phaeobacter inhibens BS107

Align 4-trimethylammoniobutyraldehyde dehydrogenase (EC 1.2.1.47) (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB

Query= BRENDA::P49189
         (494 letters)



>FitnessBrowser__Phaeo:GFF2135
          Length = 485

 Score =  486 bits (1250), Expect = e-141
 Identities = 255/473 (53%), Positives = 323/473 (68%), Gaps = 9/473 (1%)

Query: 24  DASGTE-KAFEPATGRVIATFTCSGEKEVNLAVQNAKAAFKIWSQKSGMERCRILLEAAR 82
           D +GT       ATG  IAT   +    V  A+  AKAA K W++ +G ER RIL  AA 
Sbjct: 20  DTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAAQKAWARMTGTERGRILRRAAD 79

Query: 83  IIREREDEIATMECINNGKSIFEARL-DIDISWQCLEYYAGLAASMAGEHIQLPGGSFGY 141
           I+RER  +++ +E  + GK + E  + D       LEY+ GLAAS+ GEHI L G  + Y
Sbjct: 80  IMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASLTGEHIPL-GEDWVY 138

Query: 142 TRREPLGVCVGIGAWNYPFQIASWKSAPALACGNAMVFKPSPFTPVSALLLAEIYSEAGV 201
           T+RE LG+CVGIGAWNYP QIA WK APALACGN+MVFKPS  TP+ AL +AEI  EAG 
Sbjct: 139 TKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCALKVAEILIEAGA 198

Query: 202 PPGLFNVVQGGAATGQFLCQHPDVAKVSFTGSVPTGMKIMEMSAKGIKPVTLELGGKSPL 261
           P G+FNVVQG    G  L   P V KVS TGSVPTG K+   +A+G+K VT+ELGGKSPL
Sbjct: 199 PAGVFNVVQGMGEVGGALVTDPRVDKVSLTGSVPTGKKVYAAAAEGMKHVTMELGGKSPL 258

Query: 262 IIFSDCDMNNAVKGALMANFLTQGQVCCNGTRVFVQKEILDKFTEEVVKQTQRIKIGDPL 321
           IIF D D++NAV GA+  NF + GQVC NGTRVFVQK I +KF   + ++T    +GDP+
Sbjct: 259 IIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARLAERTGNAILGDPM 318

Query: 322 LEDTRMGPLINRPHLERVLGFVKVAKEQGAKVLCGGDIYVPEDPKLKDGYYMRPCVLTNC 381
            E T  GP++    +  VLG+++  KE+GA+++CGG           DGY++ P V  + 
Sbjct: 319 DEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGG------RRADMDGYFIEPTVFADV 372

Query: 382 RDDMTCVKEEIFGPVMSILSFDTEAEVLERANDTTFGLAAGVFTRDIQRAHRVVAELQAG 441
            DDMT  +EEIFGPVMS+L FDTE EV+ RANDT FGL+AGVFT+D  RAHRV+  L+AG
Sbjct: 373 TDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTRAHRVIGNLEAG 432

Query: 442 TCFINNYNVSPVELPFGGYKKSGFGRENGRVTIEYYSQLKTVCVEMGDVESAF 494
           +CFIN+YN +PVE PFGG K SG GREN +  I+++SQ+K+V V MGDVE+AF
Sbjct: 433 SCFINSYNDAPVEAPFGGVKASGVGRENSKEAIKHFSQVKSVYVRMGDVEAAF 485


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: 704
Number of extensions: 37
Number of successful extensions: 4
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: 485
Length adjustment: 34
Effective length of query: 460
Effective length of database: 451
Effective search space:   207460
Effective search space used:   207460
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