GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Trichormus variabilis ATCC 29413

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein

Query= BRENDA::Q88RC0
         (480 letters)



>NCBI__GCF_000204075.1:WP_011318370.1
          Length = 498

 Score =  328 bits (842), Expect = 2e-94
 Identities = 178/472 (37%), Positives = 276/472 (58%), Gaps = 9/472 (1%)

Query: 12  QAYINGEWLDADNGQTIKVTNPAT-GEVIGTVPKMGTAETRRAIEAADKALPAWRALTAK 70
           Q YING+WL+A    T+   NPA   E++ T P+    +T RA+ AA +A  +WR + A 
Sbjct: 8   QNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGSWRKVPAP 67

Query: 71  ERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDT 130
            R+  + R  EL+++++++LA+L++ E GKP+ EA+G++        + A E +R++G T
Sbjct: 68  ARAEYIFRVGELLLQHKEELAQLISREMGKPITEARGDVQEGVDCAFYSAGEGRRLFGQT 127

Query: 131 IPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSAL 190
            P   P+K  + ++ PIGV A ITPWNFP A+   KA PAL  G T++LKPA  TP  A 
Sbjct: 128 TPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACAT 187

Query: 191 ALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIK 250
            L+E+   AG+P GV+++V G   E G  L  +  +  +SFTGS+  G  + E C +  K
Sbjct: 188 KLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETCGRTHK 247

Query: 251 KVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLA 310
           +V LE+GG    +V +DADL+ A++GA+   +   GQ C   +R+ +   + + F   L 
Sbjct: 248 RVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKEKFTTMLR 307

Query: 311 AAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI------EGN 364
              ++L++G G E  T  GP+I+ + + +V E++  A  +GAK+L GG+++      +G 
Sbjct: 308 ERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTEGQLKQGY 367

Query: 365 FFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRV 424
           FF+PTIL +V     VA+EE FGP+  L       E IA+ NDT++GL+S  Y RD++R 
Sbjct: 368 FFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYTRDINRA 427

Query: 425 FRVAEALEYGMVGINTGLISNEV-APFGGIKASGLG-REGSKYGIEDYLEIK 474
           F     +E G+  IN   I  EV  PFGG+K +G G RE     ++ + E K
Sbjct: 428 FVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWK 479


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: 612
Number of extensions: 22
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: 480
Length of database: 498
Length adjustment: 34
Effective length of query: 446
Effective length of database: 464
Effective search space:   206944
Effective search space used:   206944
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: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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