GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Methylocapsa aurea KYG

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_000746085.1:WP_036262823.1
          Length = 506

 Score =  213 bits (541), Expect = 2e-59
 Identities = 151/484 (31%), Positives = 240/484 (49%), Gaps = 17/484 (3%)

Query: 9   NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68
           N+I G+WV +   Q  + ++P    V+C V  S+ ED++ A   A  A   W + +   R
Sbjct: 21  NFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAARGAWGRTSPAER 80

Query: 69  ARILFNFQQLLSQHKEELAHLITIENGKNTKEA-LGEVGRGIENVEFAAGAPSLMMGDSL 127
           +  L      + Q  + LA + TI+NGK  +E    ++   +++  + AG      G  +
Sbjct: 81  SLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEG-GI 139

Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187
           + I  D  A ++  P+GVV  I P+NFP+++  W    A+A GN  ILKP+E+TP+    
Sbjct: 140 SEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMSVMV 199

Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKR 246
           LV++     LP GV NV+ G   +    + ++  I  ++F G    G  + +  SEN+  
Sbjct: 200 LVDMIGDL-LPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGRLIMQYASENIIP 258

Query: 247 VQSLTGAKNHTIVLND-ANLEDTVTNIVGAAFG----SAGERCMACAVVTVEEGIADEFM 301
           V    G K+  I   D A+ +D   +     F     + GE C   +   V+E I D FM
Sbjct: 259 VTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEVCTCPSRALVQEKIYDRFM 318

Query: 302 AKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVC-DGRENVSDD 360
            +   +V  IK GN LD    +G     D  ++ LSY++ G +EGA+++   GR +V  +
Sbjct: 319 ERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGGGRADVGPE 378

Query: 361 ---GYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTS 417
              G++V PTI +    +M I+++EIF PVLSV   K+ +EA+EIAN + +  GA ++T 
Sbjct: 379 LAGGFYVQPTILEG-HNKMRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGLGAGVWTR 437

Query: 418 NSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477
           N      F   I+AG +  N     P A   F G+K S  G    N K  +D Y + K +
Sbjct: 438 NGTRAYRFGRAIEAGRVWTNCYHLYP-AHAAFGGYKQSGIG--RENHKMMLDHYQKTKNM 494

Query: 478 TARY 481
              Y
Sbjct: 495 LVSY 498


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: 546
Number of extensions: 20
Number of successful extensions: 5
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: 506
Length adjustment: 34
Effective length of query: 453
Effective length of database: 472
Effective search space:   213816
Effective search space used:   213816
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