GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Marinobacter adhaerens HP15

Align aconitate DELTA-isomerase (EC 5.3.3.7) (characterized)
to candidate GFF1972 HP15_1929 AcnD-accessory protein PrpF

Query= BRENDA::Q8EJW4
         (397 letters)



>FitnessBrowser__Marino:GFF1972
          Length = 379

 Score =  605 bits (1560), Expect = e-178
 Identities = 303/379 (79%), Positives = 337/379 (88%), Gaps = 4/379 (1%)

Query: 17  MRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGMGGATSSTSKTVI 76
           MRGGTSKGVFFRL+DLPEA Q PG ARD LLLRVIGSPDPY KQIDGMGGATSSTSKTVI
Sbjct: 1   MRGGTSKGVFFRLKDLPEACQSPGEARDKLLLRVIGSPDPYQKQIDGMGGATSSTSKTVI 60

Query: 77  LSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLIDAARIPRNGVCT 136
           L+  ++ +HDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAI++G +   RIP NG CT
Sbjct: 61  LAEPTQPDHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAINSGFVAKDRIPENGTCT 120

Query: 137 VRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNPAADDDGEGGCMF 196
           VRIWQANI KTI+AHVPIT+G VQETGDFELDGVTFPAAEVQ+EFM+PA   DGEG  MF
Sbjct: 121 VRIWQANIKKTIVAHVPITNGEVQETGDFELDGVTFPAAEVQVEFMDPA---DGEGS-MF 176

Query: 197 PTGNLVDVLEVPGIGRFNATMINAGIPTIFINAEDLGYTGTELQDDINSDNAALAKFETI 256
           PTGNLVD LEVPG G   ATMINAGIPTIF+NA D+GY GTELQDDINSD AALA+FETI
Sbjct: 177 PTGNLVDDLEVPGEGTLKATMINAGIPTIFVNAGDIGYKGTELQDDINSDPAALARFETI 236

Query: 257 RAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVAAEDVDLLVRALSMGKL 316
           RAHGA++MGLI++I+EAA+RQHTPK+AFVA P  Y SSSGK++ AEDVD+LVRALSMGKL
Sbjct: 237 RAHGAVKMGLIQNIEEAANRQHTPKVAFVAKPSDYVSSSGKSIGAEDVDVLVRALSMGKL 296

Query: 317 HHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTLRVGAQAVQENGEWTVI 376
           HHAMMGTAAVAI TA+A+PGTLVNLAAGGG++  V FGHPSGTLRVGA+A + +G+WT  
Sbjct: 297 HHAMMGTAAVAIATASAVPGTLVNLAAGGGDRTHVTFGHPSGTLRVGAEAKEVDGQWTAT 356

Query: 377 KAIMSRSARVLMEGFVRVP 395
           KAIMSRSARVLMEG+VRVP
Sbjct: 357 KAIMSRSARVLMEGWVRVP 375


Lambda     K      H
   0.318    0.134    0.393 

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: 577
Number of extensions: 16
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: 397
Length of database: 379
Length adjustment: 30
Effective length of query: 367
Effective length of database: 349
Effective search space:   128083
Effective search space used:   128083
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 17 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