GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Cupriavidus basilensis 4G11

Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate RR42_RS25005 RR42_RS25005 betaine-aldehyde dehydrogenase

Query= SwissProt::O34660
         (495 letters)



>FitnessBrowser__Cup4G11:RR42_RS25005
          Length = 495

 Score =  453 bits (1166), Expect = e-132
 Identities = 236/500 (47%), Positives = 327/500 (65%), Gaps = 11/500 (2%)

Query: 1   MSSLTMQVTKRLETFLQGTKKLYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVD 60
           MSS T  V  +   F+ GTK+L+I G +VP+ASG  FDT NPATGE +  L +A   D+D
Sbjct: 1   MSSTTYGV--QTPAFVGGTKRLFIGGAWVPAASGKAFDTVNPATGEVIARLAQADQTDID 58

Query: 61  KAVKAARKAFDQGEWRTMSPASRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGD 120
           +AV AAR+AF+ G W   + + R RL+ ++ D++E+H  ELA +ETLD G P+  T  G 
Sbjct: 59  RAVTAARQAFE-GPWNQWTHSDRQRLLIRIHDVVEKHFDELALIETLDMGAPLVRT-RGL 116

Query: 121 IPLAIEHMRYYAGWCTKITGQTIPVS---GAYFNYTRHEPVGVVGQIIPWNFPLLMAMWK 177
               ++ + +YA   T   G   P++   G +       PVGVV  IIPWN PLL   W 
Sbjct: 117 KSFLLQLILFYASQ-TAAGGVQTPLNALPGKFATLKIKAPVGVVAGIIPWNGPLLSQWWI 175

Query: 178 MGAALATGCTIVLKPAEQTPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAV 237
           +GA LATGCT VLKPAE   LSAL +AEL+ +AG PAGVIN++ G+G +AG AL  H  V
Sbjct: 176 LGATLATGCTAVLKPAEDASLSALRMAELLQEAGVPAGVINVVTGYGGEAGSALAEHPGV 235

Query: 238 DKIAFTGSTEIGKKIMSTAAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQG 297
           D+IAFTGS E G++I+  +A + KRV++ELGGKSP+I+  DANL KA+PG   GV  N G
Sbjct: 236 DRIAFTGSPETGRRIVRASAGNFKRVSVELGGKSPDIVFDDANLDKAVPGVAMGVFTNTG 295

Query: 298 QVCCAGSRVFIHKDQYDEVVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQK 357
           Q+C AG+RV + +  YDE ++ + +++ SL+ G GL    Q+GP+VS+ Q +RV+ Y+  
Sbjct: 296 QICAAGTRVLVQRRIYDEFIERLKAFSTSLKIGNGLDPQVQLGPIVSQRQLDRVMHYVDV 355

Query: 358 GKDEGAKAVTGG---SCPFEAGYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEV 414
           G  EGA+   GG        AGYFV PTVF  V ++MTIA+EEIFGPV + +P++T ++ 
Sbjct: 356 GGQEGAELACGGRRLGGELAAGYFVEPTVFTGVHNDMTIAREEIFGPVASVMPFDTPEQA 415

Query: 415 IERANHSEYGLAAGLWTENVKQAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGRE 474
           +  AN + +GLA G+WT+N+  AH  A  +QAGT+WVNCY V D    FGGYK SG G +
Sbjct: 416 LRIANDTSFGLAGGVWTQNLSTAHRFAQGIQAGTIWVNCYGVLDPQVGFGGYKLSGYGWK 475

Query: 475 MGSYALDNYTEVKSVWVNLE 494
             +  +D+Y   K+V++NL+
Sbjct: 476 GAAEQVDSYLYQKAVYMNLD 495


Lambda     K      H
   0.316    0.133    0.391 

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: 654
Number of extensions: 25
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: 495
Length of database: 495
Length adjustment: 34
Effective length of query: 461
Effective length of database: 461
Effective search space:   212521
Effective search space used:   212521
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