GapMind for catabolism of small carbon sources

 

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

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__Pedo557:CA265_RS14635
          Length = 501

 Score =  300 bits (769), Expect = 6e-86
 Identities = 170/463 (36%), Positives = 257/463 (55%), Gaps = 15/463 (3%)

Query: 23  NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82
           +P  G V  + A ++ E ++ AV AA  AF  W +T+   R+  L K+A  +E+N +  A
Sbjct: 35  SPIDGKVFTKAAHSTKEDLELAVDAAHEAFKTWSKTSSTERSIILNKIAQRMEDNLEYLA 94

Query: 83  ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGVV 142
            +E+ + GK +      ++P  VD FR+FAG  R   G +  E  +   S+I  +P+GVV
Sbjct: 95  AVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEG-SLSELDQNTVSLIVHEPIGVV 153

Query: 143 ASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILFG 202
           A I PWN+PL+M  WKLAPALAAGNCVVLKP+E TP++ + L EL  D+ P GV+N++ G
Sbjct: 154 AQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIMVLMELIGDLLPPGVVNVVNG 213

Query: 203 RGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVF------ 256
            G  +G  L  +PKV   + TGS  TG  ++ +   +I    +ELGGK+P I F      
Sbjct: 214 FGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATENIIPVTLELGGKSPNIFFSSVMAE 273

Query: 257 DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDES 316
           DDA ++  VEG   F   N G+ CT   R+  Q+ IY+  + K+      +K G+P D +
Sbjct: 274 DDAFLDKAVEGAVMFA-LNQGEICTCPSRLLIQEDIYEKFIAKVIERTKAIKIGSPLDRT 332

Query: 317 TELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK-----GNGYYYAPTLLAGALQD 371
             +G  +S    E++   ++  K  G  +V+TGGE  +     G GYY  PT+  G    
Sbjct: 333 VMMGAQASKIQFEKIAAYIKLGKEEG-AEVLTGGEINELPGELGGGYYIKPTIFKGH-NK 390

Query: 372 DAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTW 431
             I Q+E+FGPV++VT F   E+ +  AND+ YGL + VWT+D    ++V   +Q G  W
Sbjct: 391 MRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAGVWTRDAHELYQVPRAIQAGRVW 450

Query: 432 VNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           VN +    +  P GG K SG G++     L  Y   +++++ +
Sbjct: 451 VNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKNMLISY 493


Lambda     K      H
   0.317    0.134    0.397 

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: 559
Number of extensions: 28
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: 474
Length of database: 501
Length adjustment: 34
Effective length of query: 440
Effective length of database: 467
Effective search space:   205480
Effective search space used:   205480
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: 52 (24.6 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