GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Marinobacter algicola DG893

Align 2-methyl-aconitate isomerase; Cis-trans isomerase; EC 5.3.3.- (characterized)
to candidate WP_007153590.1 MDG893_RS09680 2-methylaconitate cis-trans isomerase PrpF

Query= SwissProt::Q937N7
         (396 letters)



>NCBI__GCF_000170835.1:WP_007153590.1
          Length = 390

 Score =  583 bits (1504), Expect = e-171
 Identities = 288/393 (73%), Positives = 333/393 (84%), Gaps = 4/393 (1%)

Query: 1   MTHVPQIKIPATYIRGGTSKGVFFRLQDLPETAQVPGPARDALLMRVIGSPDPYGKQIDG 60
           M++VPQI+IPATY+RGGTSKGVFFRL+DLPE AQ PGP RD+LLMRVIGSPDPY KQIDG
Sbjct: 1   MSNVPQIRIPATYMRGGTSKGVFFRLEDLPEGAQTPGPIRDSLLMRVIGSPDPYQKQIDG 60

Query: 61  MGAATSSTSKTVILSKSTRPDHDVDYLFGQVSIDQPFVDWSGNCGNLSAAVGPFAISAGL 120
           +G  TSSTSKTVI+S+S RPDHDVDYLFGQV ID+ FVDWSGNCGNL+ AVG FAISAGL
Sbjct: 61  LGNGTSSTSKTVIVSRSERPDHDVDYLFGQVGIDRAFVDWSGNCGNLTTAVGAFAISAGL 120

Query: 121 VDASRIPHNGVAVVRIWQANIGKTIIGHVPVTNGEVQETGDFELDGVTFPAAEVQLEFMD 180
           V A  +  N VA VRIWQANIGKTII  VP+T+G+VQETGDFELDGV FPAA++ LEF+D
Sbjct: 121 VAADTLEQNSVAAVRIWQANIGKTIIARVPMTDGQVQETGDFELDGVAFPAAKIALEFLD 180

Query: 181 PAAEEEGAGGAMFPTGNVVDDLEVPAVGTLKATMINAGIPTIFVNAESIGYTGTELQDAI 240
           PA +E    GA+FPTGN VD+L+VP +G  + TMI AGIPTIFV A+++GYTGTELQDAI
Sbjct: 181 PAGDE----GAIFPTGNPVDELDVPGLGKFRVTMITAGIPTIFVEADAVGYTGTELQDAI 236

Query: 241 NSDTRALAMFEDHPCYGALRMGLIKNVDEAAKRQHTPKVAFVRQAGDYVASSGKKVAAAD 300
           N+D +ALAMFE    +GAL+MGL++ + EA  RQHTPK+AFV    DYVA+SGK++   D
Sbjct: 237 NNDPQALAMFESIRGHGALQMGLVETLAEAENRQHTPKIAFVAGPSDYVAASGKRITIDD 296

Query: 301 VDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERNAVRFGHPSGTLRVG 360
           VDLLVR LSMGKLHHAM GT AVAIG A AIPGT+VN AAGGG + +VRFGHPSGTLRVG
Sbjct: 297 VDLLVRGLSMGKLHHAMPGTVAVAIGAAHAIPGTIVNTAAGGGNQTSVRFGHPSGTLRVG 356

Query: 361 AEAQQVDGEWAVKKAIMSRSARVLMEGWVRVPG 393
           AEA++ +GEW V+KAIMSRSARVLMEGWVRVPG
Sbjct: 357 AEARESNGEWVVEKAIMSRSARVLMEGWVRVPG 389


Lambda     K      H
   0.317    0.134    0.394 

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: 551
Number of extensions: 15
Number of successful extensions: 2
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: 396
Length of database: 390
Length adjustment: 31
Effective length of query: 365
Effective length of database: 359
Effective search space:   131035
Effective search space used:   131035
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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