GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Synechococcus elongatus PCC 7942

Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase

Query= curated2:P39616
         (456 letters)



>FitnessBrowser__SynE:Synpcc7942_0489
          Length = 459

 Score =  425 bits (1093), Expect = e-123
 Identities = 215/443 (48%), Positives = 289/443 (65%)

Query: 12  KAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYSTEIGIVLEEI 71
           +A F  G TR L  RL  L+ L + V  +EA+L+ AL  DL K   EAY++EI  V ++I
Sbjct: 17  QATFDRGDTRTLAFRLARLQDLAKLVADNEAELLQALASDLRKPALEAYASEIYFVRDQI 76

Query: 72  SFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLALSPLIGAIAA 131
               K LR+W +P++    L     ++    EP G VL+I PWNYP QL ++PLIGAIAA
Sbjct: 77  KLTCKHLRRWMQPEKQSISLMQQPGQAYRQAEPLGVVLIIGPWNYPFQLLITPLIGAIAA 136

Query: 132 GNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPFDYIFFTGSVA 191
           GN  VLKPSE  PA S+++ +LIS  F  DY+ + EG   VS AL+ QPFD+IFFTG  A
Sbjct: 137 GNCAVLKPSELAPATSSLIQRLISDRFDPDYIRVLEGDASVSQALITQPFDHIFFTGGTA 196

Query: 192 VGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAGQTCIAPDYLF 251
           +G+ VM AAA+ L PVTLELGGKSPCIV  D D+ +AA+RI +GKF NAGQTCIAPDYL 
Sbjct: 197 IGRKVMAAAAENLTPVTLELGGKSPCIVDTDIDLDVAARRIAWGKFFNAGQTCIAPDYLL 256

Query: 252 VHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDGIPLTGGQSDP 311
           V   +     E +   I++FYG  P+++  Y +IVS+RH+QRL S L DG    GGQ D 
Sbjct: 257 VQRTVAEPFIEALIDNIQQFYGEDPQQSADYARIVSDRHWQRLNSLLVDGTIRHGGQVDR 316

Query: 312 NHHKIAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRPKPLALYLFTTNK 371
           +   IAPT++  V    P++QEEIFGP+LP+  Y  + E I +++++PKPLALYLF+ ++
Sbjct: 317 SDRYIAPTLITDVNWRDPILQEEIFGPLLPILIYDQLDEAIAQIRAQPKPLALYLFSRDR 376

Query: 372 EIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSFNTFTHKKSVVKQ 431
           +++  VL   S G  C+NDT++ V  P   FGGVG SG+G YHG  SF TF+H K V+K+
Sbjct: 377 QVQERVLAETSAGSVCLNDTILQVGVPDAAFGGVGPSGMGGYHGKASFETFSHYKLVLKR 436

Query: 432 TNRFDFAFRYPSSKNGLRMIRKI 454
               D A RYP   + + + RK+
Sbjct: 437 PFWLDLALRYPPYGDKINLFRKL 459


Lambda     K      H
   0.320    0.137    0.401 

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: 565
Number of extensions: 13
Number of successful extensions: 1
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: 456
Length of database: 459
Length adjustment: 33
Effective length of query: 423
Effective length of database: 426
Effective search space:   180198
Effective search space used:   180198
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 (21.8 bits)
S2: 51 (24.3 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