GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimB in Marinobacter adhaerens HP15

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF4003 HP15_3943 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__Marino:GFF4003
          Length = 365

 Score =  470 bits (1209), Expect = e-137
 Identities = 236/364 (64%), Positives = 288/364 (79%)

Query: 30  LLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATGGNIARKALLRAGLPVTTAGTTIDRQ 89
           + GH I+HAV+RAGIDP  VEDV+MGAA Q+GA G NIAR A +RAGLPVTTAG +I+R 
Sbjct: 1   MAGHVIKHAVERAGIDPSIVEDVIMGAAYQEGAQGRNIARLAAIRAGLPVTTAGFSINRF 60

Query: 90  CASGLQAIALAARSVLFDGVEIAVGGGGESISLVQNDKMNTFHAVDPALEAIKGDVYMAM 149
           C+SGLQ+IALAA+ V+ + V   V GG ESISLVQN+K+N+FHA +  L   K ++Y++M
Sbjct: 61  CSSGLQSIALAAQRVVSEKVPAMVAGGVESISLVQNEKINSFHATNEWLMKNKPELYLSM 120

Query: 150 LDTAETVAKRYGISRERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVS 209
           ++TA+ VAKRY +SRE QDEYSL SQ+RTAAAQQ GKF+DEI P    M V DK TG VS
Sbjct: 121 IETADIVAKRYNVSREAQDEYSLISQQRTAAAQQAGKFDDEIVPFDATMLVKDKETGEVS 180

Query: 210 FKDITLSQDEGPRPETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAK 269
            K +TL  DE  RP TT EGLAGL+ VRG    ITAGNASQLSDGAS   +M+   A   
Sbjct: 181 EKQVTLKGDECNRPNTTLEGLAGLEPVRGPEQFITAGNASQLSDGASVCTVMNSTYAEKH 240

Query: 270 GLKPLGIFRGMVSYGCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCR 329
            ++P+GIFRG    GCEPDEMGIGPV+A+PRLL+R+GL++DDI LWELNEAFA QV+YCR
Sbjct: 241 NIEPMGIFRGFAVAGCEPDEMGIGPVYAIPRLLERNGLTMDDIDLWELNEAFASQVIYCR 300

Query: 330 DKLGIDPEKLNVNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAG 389
           D+LGI  EKLNVNGG+IS+GHP+G++GAR  GHALIEG+RR AKY V+TMC+GGG G+AG
Sbjct: 301 DRLGIPMEKLNVNGGSISIGHPFGVTGARQTGHALIEGKRRGAKYVVITMCIGGGQGAAG 360

Query: 390 LFEI 393
           LFE+
Sbjct: 361 LFEV 364


Lambda     K      H
   0.316    0.134    0.378 

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: 478
Number of extensions: 12
Number of successful extensions: 1
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: 395
Length of database: 365
Length adjustment: 30
Effective length of query: 365
Effective length of database: 335
Effective search space:   122275
Effective search space used:   122275
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 (21.6 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