GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Marivita geojedonensis DPG-138

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_085640679.1 MGEO_RS17260 betaine-aldehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_002115805.1:WP_085640679.1
          Length = 485

 Score =  311 bits (798), Expect = 2e-89
 Identities = 170/461 (36%), Positives = 266/461 (57%), Gaps = 9/461 (1%)

Query: 16  GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIE 75
           G   PV  PATG+ +  +  A+   VD A+ AA  A   W   +   R   L + AD++ 
Sbjct: 23  GTPIPVIYPATGEQIATVYAATPAIVDKALAAAHRAQKAWAAMSGTERGRILRRAADMMR 82

Query: 76  ENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMI- 134
           E     + LE+ + GKP       +  +  D   +F G A    G   GE+++     + 
Sbjct: 83  ERNHDLSVLETYDTGKPYQETIAVDATSGADALEYFGGLA----GSLTGEHIQLGEDWVY 138

Query: 135 -RRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-F 192
            RR+PLGV   I  WNYP  +A WK APALA GN +V KPSE TPL ALK+AE+  +   
Sbjct: 139 TRREPLGVCVGIGAWNYPTQIACWKGAPALACGNAMVFKPSETTPLCALKVAEILHEAGL 198

Query: 193 PAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAP 252
           PAG+ N++ G G+ VG  L   P+V  VSLTGS+ TG+ + +  A  +K   MELGGK+P
Sbjct: 199 PAGIYNVVQGLGE-VGASLVTDPRVAKVSLTGSVPTGKKVYAAAAEQMKHVTMELGGKSP 257

Query: 253 VIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAP 312
           +++FDDAD+E  V G     +Y++GQ C+   R++ QKGI +  +++L   ++T   G P
Sbjct: 258 LLIFDDADLENAVGGAILGNFYSSGQVCSNGTRVFVQKGIKEAFLKRLTERLSTAVVGDP 317

Query: 313 DDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDD 372
            DE+T  GP+ S   ++ V   +E+ +  G  +++ GG +   +G+Y  PT+ A    D 
Sbjct: 318 LDEATNFGPMVSEKQMKIVLDYIEKGENEG-ARLVAGGRRLNRDGFYLQPTVFADVKDDM 376

Query: 373 AIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWV 432
            I ++E+FGPV++V  F+ EE+ +  AN +++GL++ V+T+D+ RAHRV A+L+ G  ++
Sbjct: 377 IIAREEIFGPVMAVLDFETEEEAITRANSTEFGLSAGVFTRDLSRAHRVIAQLEAGSCFI 436

Query: 433 NTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473
           N++     E P GG K+SG G++ S   +  Y+ ++ V V+
Sbjct: 437 NSYNDAPVEAPFGGTKMSGVGRENSKAAINHYSEMKSVYVR 477


Lambda     K      H
   0.317    0.134    0.397 

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: 569
Number of extensions: 30
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: 474
Length of database: 485
Length adjustment: 34
Effective length of query: 440
Effective length of database: 451
Effective search space:   198440
Effective search space used:   198440
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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