GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Methylocapsa aurea KYG

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-15108
         (486 letters)



>NCBI__GCF_000746085.1:WP_036262823.1
          Length = 506

 Score =  361 bits (927), Expect = e-104
 Identities = 193/480 (40%), Positives = 296/480 (61%), Gaps = 12/480 (2%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72
           +FI GK+VP++ G+TF+NI+P     + TVA   A +++LA+ AA  A  G W + +  E
Sbjct: 21  NFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAA-RGAWGRTSPAE 79

Query: 73  RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132
           R   L ++ D I ++ + L+++E++D GKP   + + D+P A  +F +F+  +R      
Sbjct: 80  RSLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEGGI 139

Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192
           +++D   + Y    P+GV+  I PWN PLL+  WKLAPALAAGN V++KPAE TPM+  V
Sbjct: 140 SEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMSVMV 199

Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252
           L ++  D  +P GV+N+++GFG   AG  L ++  +  ++FTGETTTG++IM  A++ + 
Sbjct: 200 LVDMIGDL-LPPGVLNVINGFGV-EAGKPLAQNKRIAKVAFTGETTTGRLIMQYASENII 257

Query: 253 RLSYELGGKNPNVIFAD--SNLDEVIETTMK--SSF-INQGEVCLCGSRIYVERPAYEAF 307
            ++ ELGGK+PN+ FAD     D+  +  ++  S F +NQGEVC C SR  V+   Y+ F
Sbjct: 258 PVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEVCTCPSRALVQEKIYDRF 317

Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPE--- 364
           +E+ VA+ K++  G+P D  T +GA  S++  E++  Y+ +  +EG  +L GG R +   
Sbjct: 318 MERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGGGRADVGP 377

Query: 365 GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWT 424
            L  G++++PTI+ G  +  R+ +EEIFGPV++V  F  +EE LE  NDT YGL A VWT
Sbjct: 378 ELAGGFYVQPTILEGHNK-MRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGLGAGVWT 436

Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484
            +  RA+R    IEAG VW N + L      FGG KQSGIGRE      + Y +  N+ +
Sbjct: 437 RNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQKTKNMLV 496


Lambda     K      H
   0.318    0.136    0.404 

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: 586
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: 486
Length of database: 506
Length adjustment: 34
Effective length of query: 452
Effective length of database: 472
Effective search space:   213344
Effective search space used:   213344
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