GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Shewanella oneidensis MR-1

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 202599 SO3496 aldehyde dehydrogenase (NCBI ptt file)

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__MR1:202599
          Length = 498

 Score =  233 bits (595), Expect = 9e-66
 Identities = 159/478 (33%), Positives = 246/478 (51%), Gaps = 17/478 (3%)

Query: 8   KNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKT--WSKVAV 65
           K +INGE+ ++ +    D ++P    +L  V      D + A   A E F +  WSK A 
Sbjct: 22  KAFINGEYRDASSGNTFDCISPIDGRLLAPVASCDLMDANIAVANAREVFDSGVWSKAAP 81

Query: 66  PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGD 125
            +R +++  F +LL ++  ELA L T++ GK  + +      G       +G     + D
Sbjct: 82  VKRKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDVAGAARAIRWSGEAIDKLYD 141

Query: 126 SLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLT 185
            LA  A +      R P+GVV  I P+NFP+++ CW    A+  GN+ ILKPSE++PL  
Sbjct: 142 ELAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALVTGNSVILKPSEKSPLTA 201

Query: 186 EKLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVG-EYVYKKGSEN 243
            ++ EL  +AG+PKGV NV+ G  H V   +  H ++  + F GS  +  + +   G  N
Sbjct: 202 IRIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGESN 261

Query: 244 LKRVQSLTGAKNHTIVLNDA-NLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMA 302
           +KRV    G K+  IV NDA +L+        A   + GE C A + + VE G+ DE + 
Sbjct: 262 MKRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIGFNQGEVCTAGSRLLVESGVKDELVG 321

Query: 303 KLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSD-DG 361
            + E++A  + G+ L+     G V+ +      LSYI+ G  EGA LV  G++ +++  G
Sbjct: 322 LIAEELASWQPGHPLEPTTVSGAVVDKQQLDTILSYIKAGQNEGASLVYGGQQVLAETGG 381

Query: 362 YFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNA 421
            +V PT+F NV  +M I  +EIF PVLSVI    ++EAI IAN + +   A ++T++ + 
Sbjct: 382 VYVQPTVFSNVKNQMKIASEEIFGPVLSVIEFNGMEEAIAIANDTIYGLAAGVWTADISK 441

Query: 422 IRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKD----SVDFYTRKK 475
                + + +GM+ IN      M   PF G+K S       NG+D    S D YT  K
Sbjct: 442 AHKTAKALRSGMVWINHYDGGDMT-APFGGYKQS------GNGRDKSLHSFDKYTEIK 492


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: 582
Number of extensions: 31
Number of successful extensions: 6
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: 498
Length adjustment: 34
Effective length of query: 453
Effective length of database: 464
Effective search space:   210192
Effective search space used:   210192
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