GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Klebsiella michiganensis M5al

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate BWI76_RS13210 BWI76_RS13210 aldehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__Koxy:BWI76_RS13210
          Length = 479

 Score =  850 bits (2197), Expect = 0.0
 Identities = 421/479 (87%), Positives = 457/479 (95%)

Query: 1   MSVPVQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEW 60
           M+ PVQHPMYIDGQF   RGDAWIDV+NPATEA++SRIPDG AEDAR+AI AAERAQP W
Sbjct: 1   MTAPVQHPMYIDGQFEPGRGDAWIDVINPATEALLSRIPDGSAEDARRAILAAERAQPGW 60

Query: 61  EALPAIERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWAR 120
           EALPAIERA WLRKI+AGIRERA EI+ALIV EGGKIQQLA VEV+FTADY+DYMAEWAR
Sbjct: 61  EALPAIERARWLRKIAAGIRERAEEIAALIVAEGGKIQQLAAVEVSFTADYLDYMAEWAR 120

Query: 121 RYEGEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEF 180
           RYEGEI+QSDR GENIL+FKRALGVTTGILPWNFPFFLIARK+APAL+TGNTIVIKPSEF
Sbjct: 121 RYEGEIVQSDRTGENILVFKRALGVTTGILPWNFPFFLIARKLAPALITGNTIVIKPSEF 180

Query: 181 TPNNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMAT 240
           TPNNAIAFA+IV +IGLP+GVFNLVLGRGETVGQELA NPKVAMVSMTGSV+AGEKIMA 
Sbjct: 181 TPNNAIAFAQIVHDIGLPKGVFNLVLGRGETVGQELASNPKVAMVSMTGSVAAGEKIMAA 240

Query: 241 AAKNITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQ 300
           AAKNITKVCLELGGKAPAIVMDDADLELAVKA+VDSRVINSGQVCNC ERVYVQKGIYD+
Sbjct: 241 AAKNITKVCLELGGKAPAIVMDDADLELAVKAVVDSRVINSGQVCNCVERVYVQKGIYDR 300

Query: 301 FVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEG 360
           FVNRLGEA++AVQFG+PA R+DIAMGPLINAAAL RVEQKVA+AV +GARVA GGKAV G
Sbjct: 301 FVNRLGEALKAVQFGDPASRDDIAMGPLINAAALARVEQKVAKAVAQGARVALGGKAVTG 360

Query: 361 KGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNL 420
           +GY+YPPTLLLDVRQEM I+HEETFGPVLPVVAFDTLE+A++MANDSDYGLTSSIYT++L
Sbjct: 361 RGYFYPPTLLLDVRQEMDIVHEETFGPVLPVVAFDTLEEALAMANDSDYGLTSSIYTRDL 420

Query: 421 NVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQS 479
           NVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADG+HGL+EYLQTQVVYLQ+
Sbjct: 421 NVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGRHGLNEYLQTQVVYLQA 479


Lambda     K      H
   0.318    0.135    0.392 

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: 820
Number of extensions: 15
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: 479
Length of database: 479
Length adjustment: 34
Effective length of query: 445
Effective length of database: 445
Effective search space:   198025
Effective search space used:   198025
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: 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