GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Halioglobus japonicus S1-36

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_066048767.1 C0029_RS01835 aldehyde dehydrogenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>NCBI__GCF_002869505.1:WP_066048767.1
          Length = 497

 Score =  335 bits (858), Expect = 3e-96
 Identities = 182/471 (38%), Positives = 272/471 (57%), Gaps = 9/471 (1%)

Query: 12  QAFIDGAWVDADNGQTIKVNNPATGEILGTVPKMGAAETRRAIEAADKALP--AWRALTA 69
           +AFI+G  VDA +GQT    NPATG+ L  V     A+   A+  A +      W  + A
Sbjct: 21  RAFINGRRVDAASGQTRTTYNPATGQALAEVANCAPADADEAVRIARETFEQGTWAGMPA 80

Query: 70  KERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKG-EIVYAASFIEWFAEEAKRIYG 128
            ER   L RW ELI ++ D+LA L TL+ GKP+A+    ++  +   I W  E   ++Y 
Sbjct: 81  AERKMVLVRWAELIEQHADELALLETLDVGKPIADTVNVDVPSSVRTIRWTGEAIDKVYD 140

Query: 129 DVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFS 188
            + P       LI  + P+GV AAI PWNFP +    K  PALA G +++LKPAS TP +
Sbjct: 141 QISPTRDNCMGLIT-RLPLGVVAAIVPWNFPLSTTAWKLAPALATGNSVILKPASNTPLT 199

Query: 189 AFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAK- 247
           A  +A+LA +AG+P GV  V+ G  G +G  + ++  +  L+FTGST +G+QLM    + 
Sbjct: 200 ALRIADLATQAGLPDGVLHVLPGPGGSLGEHIATHMGIDGLTFTGSTPVGKQLMVYSGQS 259

Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAE 307
           ++K+V LELGG +P IVF DAD+DKA   A ++ Y N GQTC    RL + + ++D F E
Sbjct: 260 NLKRVFLELGGKSPNIVFPDADIDKAASAAALAVYYNGGQTCTAGTRLIVHESIHDTFIE 319

Query: 308 KLKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGG----KPMEG 363
           K+  A +    GN L+  T  GP++D+     V E++A    +GA ++AGG    +   G
Sbjct: 320 KVIEAASGWAPGNPLDPATAMGPMVDKGQCDTVAEYVAIGRDEGAKLVAGGGTVMEDTGG 379

Query: 364 NFFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGR 423
           ++ EPTI   V N   +A+EE FGP+  +  F  E++ +A++ND+ +GLA   +++++  
Sbjct: 380 HYHEPTIFAGVNNQMRIAQEEIFGPVLAVIPFSTESEAVAIANDSIYGLAGAVWSQNINT 439

Query: 424 VFRVAEALEYGMVGVNTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474
             RVAE +  G +G+N     +   PFGG K SG GR+ S +  +DY E+K
Sbjct: 440 AHRVAEQVRVGTMGINNYFGGDITVPFGGFKESGNGRDKSMHAFDDYTELK 490


Lambda     K      H
   0.317    0.135    0.390 

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: 623
Number of extensions: 28
Number of successful extensions: 6
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: 497
Length adjustment: 34
Effective length of query: 446
Effective length of database: 463
Effective search space:   206498
Effective search space used:   206498
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