GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Streptomyces kebangsaanensis SUK12

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_073948994.1 RH94_RS20650 aldehyde dehydrogenase family protein

Query= BRENDA::Q88RC0
         (480 letters)



>NCBI__GCF_001906585.1:WP_073948994.1
          Length = 462

 Score =  307 bits (787), Expect = 4e-88
 Identities = 181/472 (38%), Positives = 260/472 (55%), Gaps = 28/472 (5%)

Query: 14  YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73
           YI+G W  A     I+V NPA  +VI TVP     +   A+ AA  ALP W A    ER+
Sbjct: 8   YIDGAWRPAAGRDAIEVVNPADEQVIATVPAGTAEDVDAAVRAARAALPGWAATPPAERA 67

Query: 74  AKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG-----EIAYAASFIEWFAEEA-KRIY 127
           A+L    ++++  +D++A  +T E G PLA ++       IA A S+ +  A  A +   
Sbjct: 68  ARLTALRDVLVARKDEIAETVTAELGSPLAFSQAVHAGVPIAVAGSYADLAATYAFEEKV 127

Query: 128 GDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPY 187
           G++   H+P          +GV  AITPWN+P   I  KA PALAAGCT+VLKPA  TP 
Sbjct: 128 GNSTVHHEP----------VGVVGAITPWNYPLHQIVAKAAPALAAGCTIVLKPAEDTPL 177

Query: 188 SALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAK 247
           +A    E AH AGIPAGVL++VTG     G  L  +  V  +SFTGST +GR++      
Sbjct: 178 TAQLFAEAAHEAGIPAGVLNLVTGLGPVAGQALAEHPDVDLVSFTGSTAVGRRIGATAGA 237

Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAE 307
            +K+V+LELGG +  ++   ADL +AV   + +   N+GQTC    R+ V    YD   E
Sbjct: 238 AVKRVALELGGKSANVILPSADLARAVNVGVANVMSNSGQTCSAWTRMLVHRDQYDEAVE 297

Query: 308 KLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGG---KLIEGN 364
             A A AK         G   GP+++ K  A+V+ +IE  +++GA++++GG      +G 
Sbjct: 298 LAATAAAKY--------GDRIGPVVNAKQRARVRGYIEKGIAEGARLVAGGPEAPCEKGY 349

Query: 365 FFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRV 424
           F  PT+  DV     VA+EE FGP+  + R+ DE + + ++N T +GLA   +A D +  
Sbjct: 350 FVSPTVFADVTPDMTVAQEEIFGPVLSILRYDDEDDALRIANGTVYGLAGAVWAADETEA 409

Query: 425 FRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476
              A  ++ G V IN G   N +APFGG K SG+GRE   +G+ +YL+ K L
Sbjct: 410 VAFARRMDTGQVDINGGRF-NPLAPFGGYKQSGVGRELGAHGLTEYLQTKSL 460


Lambda     K      H
   0.317    0.134    0.384 

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: 548
Number of extensions: 14
Number of successful extensions: 5
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: 480
Length of database: 462
Length adjustment: 33
Effective length of query: 447
Effective length of database: 429
Effective search space:   191763
Effective search space used:   191763
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 (21.6 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