GapMind for catabolism of small carbon sources

 

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

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate CA265_RS19780 CA265_RS19780 aldehyde dehydrogenase family protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_805
         (497 letters)



>FitnessBrowser__Pedo557:CA265_RS19780
          Length = 513

 Score =  190 bits (482), Expect = 1e-52
 Identities = 143/466 (30%), Positives = 227/466 (48%), Gaps = 25/466 (5%)

Query: 36  TFECISPVDGRLLGKIASCDAADAQRAVENARATFNSGVWSRLAPTKRKSTMIRFAGLLK 95
           T E  SPVDG+L+       A D    V  A+  F +  W  +   KR   + +F   L+
Sbjct: 35  TLESFSPVDGKLIASAKIATADDYDAVVLKAQEAFTA--WRSVPAPKRGEIVRQFGDALR 92

Query: 96  QHAEELALLETLDMGKPISDSL-----YIDVPGAAQALSWSGEAIDKIYDEVAATPHDQL 150
           ++ + L  L + +MGK + +        ID+   A  LS     +    +  +   ++Q 
Sbjct: 93  ENKDALGTLVSYEMGKSLQEGFGEVQEMIDICDFAVGLSRQLYGLTMHSERPSHRMYEQW 152

Query: 151 GLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAIR----IAEL 206
                 P+G+VG I  +NFP+ +  W    AL  GN  I KPSEK+PLTAI     IA++
Sbjct: 153 -----HPLGIVGIISAFNFPVAVWSWNTALALVCGNVCIWKPSEKTPLTAIACQHIIAKV 207

Query: 207 AVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYSGESNMKRVWL 266
             +  I +GV N++ G    VG+ +     +  +  TGST++ K +    G + + +  L
Sbjct: 208 FKDNDIAEGVCNLILG-DREVGERMTNDGRIPLISATGSTRMGKAVGAAVG-ARLGKSLL 265

Query: 267 EAGGKSPNIVFADAPNLQDAAEAAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPLVIEAL 326
           E GG +  I+   A        A  GA+    G+ CT+  RL++  S+ D F   +++A 
Sbjct: 266 ELGGNNAIIISEHADLDMSLIGAVFGAVG-TAGQRCTSTRRLIIHESVYDAFTAKLVKAY 324

Query: 327 KAWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHADGARLVAGGKRTLQE--TGGTYVE 384
              + G+PLD   +VG L+DT  +   L  I    A+G   V  G     +  T G YV+
Sbjct: 325 GQLRIGDPLDQNNHVGPLIDTDAVAAYLDSIAKCKAEGGNFVVEGGVLSGDAYTSGCYVK 384

Query: 385 PTIFDGVSNAMKIAQEEIFGPVLSVIEFDSAEEAIAIANDTPYGLAAAVWTADISKAH-- 442
           P I + V N  KI Q E F P+L +I++ + +EAIA+ N  P GL++A+ T ++ +A   
Sbjct: 385 PCIAE-VQNDFKIVQHETFAPILYLIKYKTLDEAIALQNGVPQGLSSAIMTLNLREAEQF 443

Query: 443 LTARALRAGSVWVN-QYDGGDMTAPFGGFKQSGNGRDKSLHAFDKY 487
           L+A+    G   VN    G ++   FGG K++G GR+    A+  Y
Sbjct: 444 LSAKGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWRAY 489


Lambda     K      H
   0.316    0.132    0.390 

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: 644
Number of extensions: 35
Number of successful extensions: 5
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: 497
Length of database: 513
Length adjustment: 34
Effective length of query: 463
Effective length of database: 479
Effective search space:   221777
Effective search space used:   221777
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