GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davD in Pedobacter sp. GW460-11-11-14-LB5

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

Query= BRENDA::Q88RC0
         (480 letters)



>FitnessBrowser__Pedo557:CA265_RS14635
          Length = 501

 Score =  252 bits (643), Expect = 2e-71
 Identities = 167/480 (34%), Positives = 246/480 (51%), Gaps = 18/480 (3%)

Query: 14  YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73
           YI G+++    G      +P  G+V          +   A++AA +A   W   ++ ERS
Sbjct: 17  YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKTWSKTSSTERS 76

Query: 74  AKLRRWFELMIENQDDLARLMTTEQGKPLAEA-KGEIAYAASFIEWFAEEAKRIYGDTIP 132
             L +  + M +N + LA + T + GK + E    ++        +FA   +   G    
Sbjct: 77  IILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSLSE 136

Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192
             Q    LIV  +PIGV A I PWNFP  M   K  PALAAG  +VLKPA  TP S + L
Sbjct: 137 LDQNTVSLIV-HEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIMVL 195

Query: 193 VELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKV 252
           +EL     +P GV++VV G   E+G  L  N  V K +FTGST  GR +M+   ++I  V
Sbjct: 196 MELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATENIIPV 254

Query: 253 SLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFA 306
           +LELGG +P I F      DDA LDKAVEGA++    N G+ C C +R+ +Q+ +Y+ F 
Sbjct: 255 TLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFAL-NQGEICTCPSRLLIQEDIYEKFI 313

Query: 307 EKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIE---- 362
            K+      +KIG+ L+     G         K+  +I+    +GA+VL+GG++ E    
Sbjct: 314 AKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINELPGE 373

Query: 363 ---GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419
              G + +PTI     K   + +EE FGP+  +  FK   E I ++NDT +GL +  + R
Sbjct: 374 LGGGYYIKPTIFKGHNK-MRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAGVWTR 432

Query: 420 DMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCIS 479
           D   +++V  A++ G V +N        APFGG K SG+GRE  K  +  Y + K + IS
Sbjct: 433 DAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKNMLIS 492


Lambda     K      H
   0.317    0.134    0.384 

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: 537
Number of extensions: 32
Number of successful extensions: 7
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: 480
Length of database: 501
Length adjustment: 34
Effective length of query: 446
Effective length of database: 467
Effective search space:   208282
Effective search space used:   208282
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 (21.6 bits)
S2: 52 (24.6 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