GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_068174307.1 HTA01S_RS19000 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>NCBI__GCF_001592305.1:WP_068174307.1
          Length = 482

 Score =  203 bits (517), Expect = 9e-57
 Identities = 157/461 (34%), Positives = 231/461 (50%), Gaps = 12/461 (2%)

Query: 5   INGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAV 64
           + G W +G     V  NP +G V+       AA+  +A  AA  A+P W   +  ER AV
Sbjct: 16  VGGQWFSGTAHIEVS-NPATGAVIATVPRLGAAETREAIEAANRAWPAWRARTAKERSAV 74

Query: 65  VERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIA-ISIKAYHVRTGEQRSEM 123
           + ++ AL+ +N+ +L  I+  E GKP  EA  E+    + I   S +A  V      + +
Sbjct: 75  LAQWYALIMANQDDLALIMTSEQGKPLAEARGEIAYAASFIQWFSEEAKRVYGDTIPAPV 134

Query: 124 PDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVMRL 183
                 +   P GV A   P+NFP  +      PAL AG T++ KP+  TP +  A+  L
Sbjct: 135 ASQRIVVIKEPIGVCAAITPWNFPAAMITRKAGPALAAGCTMVVKPASQTPLTALALAVL 194

Query: 184 WQQAGLPPGVLNLVQG-GRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILAL 242
            ++AG+PPGV ++V G  R+ G  L+    +  L FTGS   G  L  + +   +K+ ++
Sbjct: 195 AERAGVPPGVFSVVTGSARDVGDELADNPLVRKLSFTGSTEVGRSLMARTAATVKKV-SM 253

Query: 243 EMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARL-VAV 301
           E+GGN P I+ E AD+DAAV   I S +  AGQ C CA RL + S    +AF A+L VAV
Sbjct: 254 ELGGNAPFIVFEDADLDAAVEGAIVSKYRNAGQTCVCANRLYVHSKVY-EAFAAKLAVAV 312

Query: 302 SQ-RLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGTSLLTP 360
           SQ ++  G   D     IG LI ++A  +V        A G R L   R    G S   P
Sbjct: 313 SQLKVGEGTGADVR---IGPLIDDKAVLKVEQHIADAVAKGARVLSGGRRHALGQSFFEP 369

Query: 361 GII-EMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLL 419
            I+ ++T    V  EE FGPL  ++R++T DE + MAN+T FGL+    + +  +  ++ 
Sbjct: 370 TILGDVTQDMLVAREETFGPLAPLFRFETEDEVVAMANDTEFGLASYFYARDLGRVWRVA 429

Query: 420 LEARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAAD 460
                G+V  N  L  +   APFGG+  SG  R  +    D
Sbjct: 430 ERLEYGMVGVNTGLI-SNEVAPFGGVKQSGIGREGSHLGMD 469


Lambda     K      H
   0.318    0.134    0.412 

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: 553
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: 492
Length of database: 482
Length adjustment: 34
Effective length of query: 458
Effective length of database: 448
Effective search space:   205184
Effective search space used:   205184
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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