GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Dinoroseobacter shibae DFL-12

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 3607155 Dshi_0577 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Dino:3607155
          Length = 483

 Score =  260 bits (665), Expect = 6e-74
 Identities = 156/477 (32%), Positives = 240/477 (50%), Gaps = 4/477 (0%)

Query: 10  YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRA 69
           YI+G W E  T Q E+     T +++     +    +D A   A  A   W    + +R 
Sbjct: 8   YIDGAWTEG-TAQIENRNPSDTTDLIGMYAQADAGQLDTALAAARRAQPAWWAAGIQKRH 66

Query: 70  RILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS 129
            +L      L    +E+  L++ E GK   E  GEV R  +   + A       GD   S
Sbjct: 67  DVLMAIGTELMARSDEIGRLLSREEGKPLAEGKGEVYRAGQFFTYFAAEALRQHGDLAES 126

Query: 130 IATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLV 189
           +   +E    R  +GVV  I+P+NFP+  P W    A+A GN  + KP+  TP     L 
Sbjct: 127 VRPGIEIDVRREAVGVVAIISPWNFPVATPAWKIAPALAFGNAVVWKPANVTPASAIALT 186

Query: 190 ELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQ 248
           E+  +  +PKG+FN+V G   DV   ++E  E+ AISF GS PVG  +     +N+ +VQ
Sbjct: 187 EIIARQDIPKGLFNLVAGPGRDVGQRLVESAEVDAISFTGSVPVGRGIAAAAVQNMTKVQ 246

Query: 249 SLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKV 308
              G+KN  IV++D +L+  V +   +AFG  G++C A + + V   + D F+ KL    
Sbjct: 247 MEMGSKNPLIVMDDCDLDLAVAHAASSAFGGTGQKCTAASRLIVHSAVHDAFVEKLVAAA 306

Query: 309 ADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDG-RENVSDDGYFVGPT 367
             +K+G+ L+DG  LGPV+ E    + + YI  G +EGA L+C G R  ++ DGYF+ P 
Sbjct: 307 RAMKVGHALEDGTQLGPVVSESQLNQNMEYIGVGKDEGAELLCGGDRLEMATDGYFMAPA 366

Query: 368 IFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRE 427
           +F     +M I ++E+FAP+ +V RV +  EA+  AN ++F   A + T++     +FR 
Sbjct: 367 VFAGTANDMRINREEMFAPITAVQRVDSYDEALARANDTQFGLTAGIMTTSLARASHFRA 426

Query: 428 NIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTARYPAP 484
           ++ AG + +NL         PF G  +S FG     G  + +FYT  K       AP
Sbjct: 427 HMRAGCVMVNLPTAGTDYHVPFGGRGASSFGP-REQGSYAAEFYTTVKTAYVAAGAP 482


Lambda     K      H
   0.318    0.136    0.396 

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: 523
Number of extensions: 27
Number of successful extensions: 3
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: 487
Length of database: 483
Length adjustment: 34
Effective length of query: 453
Effective length of database: 449
Effective search space:   203397
Effective search space used:   203397
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.

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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