GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Escherichia coli BW25113

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 16751 b2661 succinate-semialdehyde dehydrogenase I, NADP-dependent (NCBI)

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__Keio:16751
          Length = 482

 Score =  344 bits (883), Expect = 3e-99
 Identities = 183/461 (39%), Positives = 275/461 (59%), Gaps = 1/461 (0%)

Query: 11  IDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERAS 70
           I+G+++       IDV NPA    +  +P   A++ R AIDAA RA P W AL A ERA+
Sbjct: 15  INGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWRALTAKERAT 74

Query: 71  WLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSD 130
            LR     + E   +++ L+  E GK    A+ E+++ A +I++ AE  +R  G+ I   
Sbjct: 75  ILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTIPGH 134

Query: 131 RPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAK 190
           +  + +++ K+ +GVT  I PWNFP  +I RK  PAL  G T+V+KP+  TP +A+A A+
Sbjct: 135 QADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSALALAE 194

Query: 191 IVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCL 250
           +    G+P GVFN+V G    VG EL  NP V  +S TGS   G ++M   AK+I KV L
Sbjct: 195 LAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQLMEQCAKDIKKVSL 254

Query: 251 ELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQ 310
           ELGG AP IV DDADL+ AV+  + S+  N+GQ C CA R+YVQ G+YD+F  +L +A+ 
Sbjct: 255 ELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDRFAEKLQQAVS 314

Query: 311 AVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLL 370
            +  G+  + N + +GPLI+  A+ +VE+ +A A+E+GARV  GGKA E  G ++ PT+L
Sbjct: 315 KLHIGDGLD-NGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAHERGGNFFQPTIL 373

Query: 371 LDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGL 430
           +DV     +  EETFGP+ P+  F    D I+ AND+++GL +  Y ++L+   +  + L
Sbjct: 374 VDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLSRVFRVGEAL 433

Query: 431 KFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQ 471
           ++G   IN            G + SG+G    K+G+ +YL+
Sbjct: 434 EYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLE 474


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: 567
Number of extensions: 19
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: 479
Length of database: 482
Length adjustment: 34
Effective length of query: 445
Effective length of database: 448
Effective search space:   199360
Effective search space used:   199360
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.

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