GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Dechlorosoma suillum PS

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Dsui_0437 Dsui_0437 succinate-semialdehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__PS:Dsui_0437
          Length = 483

 Score =  315 bits (807), Expect = 2e-90
 Identities = 185/474 (39%), Positives = 262/474 (55%), Gaps = 7/474 (1%)

Query: 1   MQHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTP 60
           ++ +  +NG+ V GE +  PV+NPA+G  L  +    A +  AA+ AADAA+  W   T 
Sbjct: 9   LRQQCYLNGQWVGGESDF-PVHNPASGAELARVPRFGAAETRAAIAAADAAWPAWRSRTA 67

Query: 61  KVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNG 120
           K R   L +  +++ ++    A L +   GKPL  A   E+        +FA  A+   G
Sbjct: 68  KERTGVLRRWFELMNQHADDLALLMTSEQGKPLAEA-RGEVAYAASFVEWFAEEAKRAYG 126

Query: 121 LAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLT 180
                       ++ + P+GV A+I PWN+P  M   K+APALAAG  VV+KP+E TPLT
Sbjct: 127 ETIPAVAADKRMLVIKQPIGVCAAITPWNFPAAMITRKVAPALAAGCTVVVKPAEQTPLT 186

Query: 181 ALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASS 239
           AL LAELA    FPAGV N++ G    +G  LT +P VR +S TGS   G  ++   A S
Sbjct: 187 ALALAELAHRAGFPAGVFNVITGDPVAIGGELTSNPTVRKLSFTGSTEVGRLLMGQCAPS 246

Query: 240 IKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEK 299
           IK+  +ELGG AP IVFDDAD++A VEG     Y N GQ C  A R+  Q GIY+    +
Sbjct: 247 IKKLSLELGGNAPFIVFDDADLDAAVEGAMISKYRNTGQTCVCANRLLVQDGIYEAFAAR 306

Query: 300 LGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGG---EKRKGN 356
           L A VATLK G   +     GPL     L +V   + +A A G  +V+ GG   E+ +  
Sbjct: 307 LAAKVATLKVGEGTEAGVTQGPLIDADALAKVEAHIADAVAHG-ARVLAGGRRHERYREG 365

Query: 357 GYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVG 416
           G ++ PT+LA       + ++E FGPV  +  F  EE+ +  AN +++GLAS  +++D+G
Sbjct: 366 GAFFQPTVLADVTPQMRVAREETFGPVAPLFRFQTEEEAIALANATEFGLASYFYSRDIG 425

Query: 417 RAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470
           R  RV   L+YG   VNT  +     P GG K SG G++ S YGLE+Y  V+++
Sbjct: 426 RIFRVGEALEYGMVGVNTGLISNEVAPFGGIKQSGLGREGSKYGLEEYLEVKYL 479


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: 536
Number of extensions: 23
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: 483
Length adjustment: 34
Effective length of query: 440
Effective length of database: 449
Effective search space:   197560
Effective search space used:   197560
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 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