GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Dinoroseobacter shibae DFL-12

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__Dino:3609503
          Length = 492

 Score =  304 bits (778), Expect = 5e-87
 Identities = 173/457 (37%), Positives = 251/457 (54%), Gaps = 4/457 (0%)

Query: 16  GEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIE 75
           G   PV NPA GDV+  + +    +   A+ AADAA   W   T K RA+ L +  D+I 
Sbjct: 34  GATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQKPWAARTAKDRAQVLRRWFDLIV 93

Query: 76  ENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIR 135
            N    A + +   GKPL  A   E+        +FA  A+ L G     +L      + 
Sbjct: 94  GNADDLARILTAEMGKPLAEA-RGEVMYGASFVEWFAEEAKRLYGETIPGHLPDARIQVI 152

Query: 136 RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDI-FPA 194
           R P+GVV +I PWN+P+ M   K APALAAG   + KP+E TPL+AL LA LA+    PA
Sbjct: 153 RQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPAEDTPLSALALAVLAERAGIPA 212

Query: 195 GVINIL-FGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPV 253
           G+  +L       +G     +  VR ++ TGS   G  +++  A  +K+  MELGG AP 
Sbjct: 213 GLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRILLAQAADQVKKCSMELGGNAPF 272

Query: 254 IVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPD 313
           IVFDDAD++  VEG     + NAGQ C  A RIY Q G+YD   EKL AAV  LK G   
Sbjct: 273 IVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGVYDAFAEKLAAAVEELKVGDGA 332

Query: 314 DESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDA 373
            E   +GPL ++  +E+V   +++ +A G   V+TGGE     G ++ PT++ G  Q+  
Sbjct: 333 AEGVTIGPLINMPAVEKVQDHLDDLRAKGG-TVVTGGETHPLGGTFFTPTVVTGVTQEMK 391

Query: 374 IVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVN 433
           + ++E FGPV  +  F  E++V+  AND+ +GLA   + +D+GR  RVS  L+YG   +N
Sbjct: 392 VAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYARDIGRITRVSEALEYGIVGIN 451

Query: 434 THFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470
           T  +     P GG K SG G++ S +G+++Y  ++++
Sbjct: 452 TGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYI 488


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: 552
Number of extensions: 24
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: 492
Length adjustment: 34
Effective length of query: 440
Effective length of database: 458
Effective search space:   201520
Effective search space used:   201520
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