GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Magnetospirillum magneticum AMB-1

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= metacyc::MONOMER-16244
         (495 letters)



>NCBI__GCF_000009985.1:WP_011383248.1
          Length = 485

 Score =  323 bits (828), Expect = 8e-93
 Identities = 180/467 (38%), Positives = 260/467 (55%), Gaps = 13/467 (2%)

Query: 31  QSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKL 90
           Q +S  T   ++P+  E I Q+      ++  AV AA  AF   W+      R K+L K+
Sbjct: 10  QVESASTIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAF-PKWAGLPASQRAKLLRKV 68

Query: 91  ADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAA-YFRSCAGWTDKIKGSVIETGDTHF 149
            DLI++H D +A +E+LD G+S   +K  +   AA  F   A     + G    T D H 
Sbjct: 69  GDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGETYPTND-HL 127

Query: 150 NYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEA 209
           NYT  +P+GV G I PWN P + A+WK  P L  G T VLK +E +PLSA  L  LI EA
Sbjct: 128 NYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADRLGQLILEA 187

Query: 210 GAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGG 269
           G P GV N+V G+G   G  +  HP ++ V+FTGSTATG  I+++     LKK ++ELGG
Sbjct: 188 GIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQS---GGLKKYSMELGG 244

Query: 270 KSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKI 329
           KSPNI+FDD D +  +   +  ++ N GE C  G+RI VQ+G+YD+ V+        + +
Sbjct: 245 KSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALAERTRKVVV 304

Query: 330 GDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG-------ERFGNKGYFIKPT 382
           GDP  E T +G   ++    K+  YI++G  EGA V+ GG             G F++PT
Sbjct: 305 GDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHLKNGNFVRPT 364

Query: 383 IFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSN 442
           +  DV    ++ ++EIFGPV  + +FK   E + +AN + YGLA+ V T N + AI ++ 
Sbjct: 365 VLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTENGARAIRMAE 424

Query: 443 KINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489
            I +G ++VN+ N      PFGG   SG GRE G  + + + +VK V
Sbjct: 425 GIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNV 471


Lambda     K      H
   0.316    0.133    0.389 

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: 630
Number of extensions: 39
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: 495
Length of database: 485
Length adjustment: 34
Effective length of query: 461
Effective length of database: 451
Effective search space:   207911
Effective search space used:   207911
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 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