GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Escherichia coli BW25113

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate 15537 b1415 aldehyde dehydrogenase A, NAD-linked (NCBI)

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__Keio:15537
          Length = 479

 Score =  347 bits (889), Expect = e-100
 Identities = 185/468 (39%), Positives = 282/468 (60%), Gaps = 1/468 (0%)

Query: 14  YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73
           Y+DG +V       I V NPAT  +I  +P   A + R+AI+AA++A P W AL A ERA
Sbjct: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69

Query: 74  NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRIYGDTIPG 133
           + LR+    + E   +++ L+  E GK    A+ E+A+ A ++++  E A+R  G+ I  
Sbjct: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129

Query: 134 HQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALALA 193
            +P + I++ K+ +GVT  I PWNFP  +I RK  PAL  G T+V+KP+  TP +A+A A
Sbjct: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189

Query: 194 ELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKVS 253
           ++ +  G+P+GVF++V G    VG EL  NP V  ++ TGS   G ++MA  A++I KV 
Sbjct: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249

Query: 254 LELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKAAV 313
           LELGG AP IV DDADL+ AV+  + S+  N+GQ C CA R+YVQ G+YD FV++L  A+
Sbjct: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309

Query: 314 AKLNIGNGLEAG-VTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGGTFFEPTI 372
             +  GN  E   +  GPLI+A A+ +VE+ +A AV +GA+V  GGK     G ++ PT+
Sbjct: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369

Query: 373 LVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAEQ 432
           L+DV +   +  +ETFGP+ PV  F    + I+M+ND+++GL S  Y ++L    +  + 
Sbjct: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429

Query: 433 LEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480
           L++G   IN            G + SG+G    K+G+ +YL+ + + L
Sbjct: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477


Lambda     K      H
   0.317    0.135    0.391 

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: 564
Number of extensions: 16
Number of successful extensions: 3
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: 483
Length of database: 479
Length adjustment: 34
Effective length of query: 449
Effective length of database: 445
Effective search space:   199805
Effective search space used:   199805
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