GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pseudomonas fluorescens GW456-L13

Align NAD+-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate PfGW456L13_3932 Aldehyde dehydrogenase A (EC 1.2.1.22)

Query= metacyc::MONOMER-16246
         (477 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3932
          Length = 477

 Score =  798 bits (2062), Expect = 0.0
 Identities = 393/475 (82%), Positives = 441/475 (92%), Gaps = 1/475 (0%)

Query: 3   SSVPVHRNYIDGAFVESAAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARK 62
           SSVPV+ N+IDG FV SAAHL+V NPA GA+LS+VPA++AE+VERALAAA AAQK WARK
Sbjct: 2   SSVPVYENFIDGQFVASAAHLDVINPATGAVLSKVPASTAEDVERALAAACAAQKGWARK 61

Query: 63  PAIERAGHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLE 122
           PA +RAG+LRRIAAK+R +   +ARTITLEQGKI+ LAEVEVNFTADYLDYMAEWARR+E
Sbjct: 62  PANDRAGYLRRIAAKLRENVAHLARTITLEQGKISGLAEVEVNFTADYLDYMAEWARRIE 121

Query: 123 GEIIASDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPN 182
           GEII SDR  ENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIV+KPSEETPN
Sbjct: 122 GEIITSDRQNENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVIKPSEETPN 181

Query: 183 NCFEFARLVAETDLPRGVFNVVCGAGQVGGALSSHPGVDLISFTGSVETGARIMAAAAPN 242
           NCFEFARLVAETDLP GVFNVVCG G+VG ALSSH GVD+ISFTGSV+TG+RIMAAAAPN
Sbjct: 182 NCFEFARLVAETDLPPGVFNVVCGDGKVGAALSSHKGVDMISFTGSVDTGSRIMAAAAPN 241

Query: 243 LTKLNLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIER 302
           +TKLNLELGGKAPAIVLADADL+LAV+AIRDSRIINSGQVCNCAERVYV+R+VA+ FIER
Sbjct: 242 ITKLNLELGGKAPAIVLADADLDLAVRAIRDSRIINSGQVCNCAERVYVERKVADQFIER 301

Query: 303 IAAAMAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERP-GH 361
           IAAAM+ATRYGDP+A+P+VEMGPLINR GL+ ++ KVRTAL+QGA+L++GG +A+ P G 
Sbjct: 302 IAAAMSATRYGDPIAQPDVEMGPLINRQGLDSVNRKVRTALSQGASLISGGQMADLPNGF 361

Query: 362 HYQPTVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKA 421
           H+QPTVL GCRAD  IMREEIFGPVLPIQI+DDLDEAIALANDC+YGLTSS++TRDL+K 
Sbjct: 362 HFQPTVLAGCRADMEIMREEIFGPVLPIQIIDDLDEAIALANDCDYGLTSSIYTRDLSKT 421

Query: 422 MHALRELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYLQ 476
           M A+RELDFGETY+NRE+FEAMQGFHAGVRKSGIGGADGKHGLYEYTHTH VYLQ
Sbjct: 422 MQAMRELDFGETYVNRENFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHAVYLQ 476


Lambda     K      H
   0.320    0.136    0.395 

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: 749
Number of extensions: 17
Number of successful extensions: 2
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: 477
Length of database: 477
Length adjustment: 33
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
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.

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