GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpF in Shewanella amazonensis SB2B

Align aconitate DELTA-isomerase (EC 5.3.3.7) (characterized)
to candidate 6939203 Sama_3297 hypothetical protein (RefSeq)

Query= BRENDA::Q8EJW4
         (397 letters)



>FitnessBrowser__SB2B:6939203
          Length = 396

 Score =  602 bits (1551), Expect = e-177
 Identities = 300/396 (75%), Positives = 340/396 (85%), Gaps = 5/396 (1%)

Query: 5   LFPPQIKVAATYMRGGTSKGVFFRLQDLPEAAQVPGPARDALLLRVIGSPDPYAKQIDGM 64
           +F PQI++ ATYMRGGTSKGVFFRL DLPEAA+VPG  RDALLLRVIGSPDPY K  DGM
Sbjct: 1   MFKPQIRIPATYMRGGTSKGVFFRLDDLPEAARVPGAERDALLLRVIGSPDPYGKHTDGM 60

Query: 65  GGATSSTSKTVILSHSSKANHDVDYLFGQVSIDKPFVDWSGNCGNLTAAVGAFAISNGLI 124
           GGATSSTSK VI++ SS   HDVDYL+GQVSID  FVDWSGNCGNL+ A GAFAI  GL+
Sbjct: 61  GGATSSTSKCVIMNKSSVPGHDVDYLYGQVSIDTAFVDWSGNCGNLSTAAGAFAIHAGLV 120

Query: 125 DAARIPRNGVCTVRIWQANIGKTIIAHVPITDGAVQETGDFELDGVTFPAAEVQIEFMNP 184
           DA+R+P NG+C VRIWQANIGKTIIAHVP+T+G VQETGDFELDGVTFPAAE+ +EF++P
Sbjct: 121 DASRVPENGICEVRIWQANIGKTIIAHVPVTNGEVQETGDFELDGVTFPAAEIVLEFVDP 180

Query: 185 AADDDGEGGCMFPTGNLVDVLEVPG----IGRFNATMINAGIPTIFINAEDLGYTGTELQ 240
            ADD  +GG MFPTGNLVD LEVP      G+  AT+INAGIPTIF+NAEDLGY G ELQ
Sbjct: 181 -ADDGEDGGAMFPTGNLVDELEVPSEVHPSGKIRATLINAGIPTIFVNAEDLGYRGDELQ 239

Query: 241 DDINSDNAALAKFETIRAHGALRMGLIKHIDEAASRQHTPKIAFVAPPKSYASSSGKTVA 300
           + IN +  ALA FE +RAHGA+RMGLIK +DEA +RQHTPK+AFV  P ++  SSGKTVA
Sbjct: 240 EAINGNPVALAMFEQLRAHGAIRMGLIKTLDEAKTRQHTPKVAFVTNPMTHVVSSGKTVA 299

Query: 301 AEDVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGEKEAVRFGHPSGTL 360
            ++VDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGE++AVRFGHPSGTL
Sbjct: 300 EDEVDLLVRALSMGKLHHAMMGTAAVAIGTAAAIPGTLVNLAAGGGERQAVRFGHPSGTL 359

Query: 361 RVGAQAVQENGEWTVIKAIMSRSARVLMEGFVRVPK 396
           RVGA+A Q +G+WTV KAIMSRSAR+LMEG VRVP+
Sbjct: 360 RVGAEAKQVDGQWTVTKAIMSRSARILMEGTVRVPQ 395


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: 612
Number of extensions: 20
Number of successful extensions: 3
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: 396
Length adjustment: 31
Effective length of query: 366
Effective length of database: 365
Effective search space:   133590
Effective search space used:   133590
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