GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Cupriavidus basilensis 4G11

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate RR42_RS25010 RR42_RS25010 betaine-aldehyde dehydrogenase

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__Cup4G11:RR42_RS25010
          Length = 485

 Score =  451 bits (1160), Expect = e-131
 Identities = 237/475 (49%), Positives = 308/475 (64%), Gaps = 3/475 (0%)

Query: 38  QIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMD 97
           ++ I   W +A S KTF  +NPST E++C VAE +  D+D AV AAR AF   S W  M 
Sbjct: 14  RLLIGGRWVEAASGKTFEVINPSTEELLCHVAEANSADIDAAVAAARHAFD-NSSWVGMS 72

Query: 98  ASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYH 157
              R R L R+AD I+R    LAA+ETLDNG P   S  V         RYY GW  K  
Sbjct: 73  PHARTRALLRIADQIDRHADELAAIETLDNGMPLWFSTAV-ATTAADIFRYYGGWCTKIL 131

Query: 158 GKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLT 217
           G TIP D   F YT  EP+GVCGQIIPWN P+LM + KL  AL  GN +++K AE   LT
Sbjct: 132 GSTIPSDASGFVYTLREPLGVCGQIIPWNVPILMASIKLANALCCGNTLILKPAELACLT 191

Query: 218 ALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSS 277
           +L +A LI+E   PPGV+N++PGFG TAGAA+A H DVDK+AFTGST IG+ I V A +S
Sbjct: 192 SLRLAELIQETDLPPGVINMLPGFGATAGAALALHPDVDKIAFTGSTAIGKQI-VQASTS 250

Query: 278 NLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVE 337
           NLK+VTLELGGKSPN+I +DAD+D AV+ A      N GQ C AG+R FV E ++DE  E
Sbjct: 251 NLKKVTLELGGKSPNVIFADADLDKAVQAAVKTFCGNSGQVCSAGTRLFVHESVHDEVSE 310

Query: 338 RSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYF 397
           R    A +  VG+P    T+ GP +   Q  ++L YI  G+  GA L  GG   + RGYF
Sbjct: 311 RVTRLAATYTVGDPLAPDTKLGPLISAKQRDRVLSYIEAGQAGGASLQLGGSQWSGRGYF 370

Query: 398 IQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKAN 457
           + P VF  V +GM IA+EEIFGPV+ I+ F+  ++ V + N++TYGL+AAV+T+D+ +A+
Sbjct: 371 VAPAVFDGVTNGMRIAQEEIFGPVLSIIPFRDEDDAVFKGNDTTYGLSAAVWTRDVARAH 430

Query: 458 YLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512
            +++AL+AG VW+N Y       PFGGYK SG GRE G+  + AYT+VK V +++
Sbjct: 431 KVARALKAGRVWINTYGEADPAMPFGGYKQSGWGREFGQESIDAYTQVKAVMLRM 485


Lambda     K      H
   0.319    0.136    0.409 

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: 705
Number of extensions: 35
Number of successful extensions: 4
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: 517
Length of database: 485
Length adjustment: 34
Effective length of query: 483
Effective length of database: 451
Effective search space:   217833
Effective search space used:   217833
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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