GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Williamsia sterculiae CPCC 203464

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate WP_076477023.1 BW971_RS04825 gamma-aminobutyraldehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>NCBI__GCF_900156495.1:WP_076477023.1
          Length = 500

 Score =  402 bits (1033), Expect = e-116
 Identities = 210/466 (45%), Positives = 278/466 (59%), Gaps = 2/466 (0%)

Query: 7   INGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAEC 66
           + G    G G    V  PAT +V+  ++ A+A  VD AV AA  A   W   TP  R+  
Sbjct: 16  VEGAEFRGSGPLHRVIAPATDEVVATMSLATAADVDTAVAAARRALPAWSGATPAQRSTV 75

Query: 67  LLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEY 126
           LL  A V++      A  E  + GK +  A   ++P  +D   FFAG AR L G A  EY
Sbjct: 76  LLDFARVLDREAHALAVQEVSHTGKTIRLASEFDVPGSIDNVTFFAGVARDLVGKATAEY 135

Query: 127 LEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAE 186
              HTS IRR+ +GVV SI PWNYP+ MA WK  PA+AAG  +VLKP+EITPLT + LA 
Sbjct: 136 SPDHTSSIRREAVGVVGSITPWNYPIQMAVWKALPAIAAGCTLVLKPAEITPLTTITLAR 195

Query: 187 LAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHM 245
           LA +   P GV N+L G G  VG  L GHP V +V+ TGS   G  +++  A    R  +
Sbjct: 196 LASEAGLPDGVFNVLTGTGAEVGAALAGHPGVDLVTFTGSTGVGRQVMAQAAVHGTRVQL 255

Query: 246 ELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVA 305
           ELGGKAP +VFDDAD+EA V G       NAGQDCTAA R      +YD  V  +   +A
Sbjct: 256 ELGGKAPFVVFDDADLEAAVHGAVAGSLINAGQDCTAATRAIVAPALYDDFVSGVAELMA 315

Query: 306 TLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLL 365
            ++ G P D +T++G LSS  H E+V   V+ A+ TG I+V+TGG    G G +Y PTLL
Sbjct: 316 GVRVGDPTDPATDMGSLSSRHHREKVAAMVDRARDTG-IRVVTGGHVPDGPGAFYPPTLL 374

Query: 366 AGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARL 425
           A   +   + + E+FGPV++V+ F +++  +  A D+ YGLA+S WT+DV RA R S  +
Sbjct: 375 ADVGEGAEVYRDEIFGPVLTVSSFTDDDDALRRAGDTVYGLAASAWTRDVYRAQRASREI 434

Query: 426 QYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVM 471
           + GC W+N H  +VSEMPHGG + SG+GKDMS Y +++Y  V HVM
Sbjct: 435 RAGCVWINDHIPIVSEMPHGGLRASGFGKDMSTYSMDEYLTVEHVM 480


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: 590
Number of extensions: 17
Number of successful extensions: 3
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: 500
Length adjustment: 34
Effective length of query: 440
Effective length of database: 466
Effective search space:   205040
Effective search space used:   205040
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 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