GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Trichormus variabilis ATCC 29413

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_000204075.1:WP_011318370.1
          Length = 498

 Score =  305 bits (781), Expect = 2e-87
 Identities = 173/475 (36%), Positives = 258/475 (54%), Gaps = 6/475 (1%)

Query: 8   KNYINGEWVESKTDQYEDVVNPATK-EVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVP 66
           +NYING+W+ + T+   +  NPA K E++   P S  +D D A   A +A+ +W KV  P
Sbjct: 8   QNYINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAYGSWRKVPAP 67

Query: 67  RRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDS 126
            RA  +F   +LL QHKEELA LI+ E GK   EA G+V  G++   ++AG    + G +
Sbjct: 68  ARAEYIFRVGELLLQHKEELAQLISREMGKPITEARGDVQEGVDCAFYSAGEGRRLFGQT 127

Query: 127 LASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTE 186
             S   +  A   R PIGV   I P+NFP+ +PCW    A+  GNT ILKP+E TP    
Sbjct: 128 TPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACAT 187

Query: 187 KLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLK 245
           KL+E+F  AGLP GV N+V+G   +    ++EHP I  +SF GS   G YV +      K
Sbjct: 188 KLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETCGRTHK 247

Query: 246 RVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQ 305
           RV    G KN  +V+ DA+LE  +   +  AFG+ G+RC A + + +   I ++F   L+
Sbjct: 248 RVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKEKFTTMLR 307

Query: 306 EKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGR---ENVSDDGY 362
           E+ + +++G G +    +GP+I     +R   Y+    EEGA+++  G    E     GY
Sbjct: 308 ERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTEGQLKQGY 367

Query: 363 FVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAI 422
           F  PTI DNVT +M + ++EIF PV+++I V   +EAI I N +++   + ++T + N  
Sbjct: 368 FFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYTRDINRA 427

Query: 423 RYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477
                +I+ G+  IN          PF G K +  G   A G  ++D +T  K V
Sbjct: 428 FVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREA-GTTALDVFTEWKSV 481


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: 558
Number of extensions: 27
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: 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 Apr 09 2024. 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