GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimD in Cupriavidus basilensis 4G11

Align pimeloyl-CoA dehydrogenase large subunit (EC 1.3.1.62) (characterized)
to candidate RR42_RS28375 RR42_RS28375 acyl-CoA dehydrogenase

Query= metacyc::MONOMER-20676
         (396 letters)



>FitnessBrowser__Cup4G11:RR42_RS28375
          Length = 402

 Score =  355 bits (911), Expect = e-102
 Identities = 189/410 (46%), Positives = 262/410 (63%), Gaps = 26/410 (6%)

Query: 1   MDLNFSKEEIAFRDEVRQFFKDNVPAKTRQKLIEGRHNTKEEMVEWYRILNKKGWAVTHW 60
           M L FS  + AFR EVR F K  +P+  ++K+  G      + V W+RIL  +GW    W
Sbjct: 1   MQLEFSAADDAFRQEVRAFVKARLPSDIKRKVELGLRLEHADYVTWFRILEARGWITPGW 60

Query: 61  PKEYGGTGWSSVQHYIFNEELQAAPAPQPLAFGVSMVGPVIYTFGSEEQKKRFLPRIANV 120
           P E+GG GWS +Q YIF+EE     AP+ +A G+ M+GPV+  FG+ EQK R+LP I + 
Sbjct: 61  PVEHGGPGWSHLQRYIFDEETLLGGAPRIIASGIQMLGPVLIAFGTPEQKARYLPDIRHS 120

Query: 121 DDWWCQGFSEPGSGSDLASLKTKA--EKKGDKWIINGQKTWTTLAQHADWIFCLCRTDP- 177
           + WW QGFSEPG+GSDLA+++T A  E  G  +++NG K WT+ A     +F L RTDP 
Sbjct: 121 NTWWAQGFSEPGAGSDLAAVRTTAVLEPDGRHFVVNGHKVWTSYAHWCSMMFALVRTDPD 180

Query: 178 AAKKQEGISFILVDMKTKGITVRPIQTIDGGHEVNEVFFDDVEVPLENLVGQENKGWDYA 237
           AAK QEGISFIL+DM + G+ VRPI+ ++GG ++NE + D+V VP+ENLVG+ NKGW Y 
Sbjct: 181 AAKPQEGISFILIDMASPGVEVRPIRMLEGGTDLNECYLDNVRVPVENLVGEINKGWSYG 240

Query: 238 KFLLGNERTGIARVGMSKERIRRIKQLAAQVESGGKPVIEDPKFRDKLAAVEIELKALEL 297
           K+LLG+ERTGIA +G  K+++ R + LA +   G     +D   + +LA  EIEL ALE 
Sbjct: 241 KYLLGHERTGIAGIGSCKQQLARARTLADEQGLG-----DDAVLQCRLAQFEIELMALEY 295

Query: 298 TQLRVVADEGKHGKGKPNPASSVLKIKGSEIQQATTELLMEVIGPFAAPYD--------- 348
           T LR++ D  +     P+  +S+LK++G+E++QA  ELL+EV GP A P+D         
Sbjct: 296 TALRLLGDNQR--SRVPSVEASMLKVRGTELRQAIYELLVEVAGPHAVPFDEAAMLGAAG 353

Query: 349 ----VHGDDDSNETMDWTAQIAPGYFNNRKVSIYGGSNEIQRNIICKAVL 394
                  D  S  T+   A +A  Y ++RK+SIYGG NE+QRN+I KA L
Sbjct: 354 YEQSTAADAASPPTL---AALAANYLDSRKLSIYGGVNEVQRNLISKAFL 400


Lambda     K      H
   0.317    0.135    0.411 

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: 446
Number of extensions: 24
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: 396
Length of database: 402
Length adjustment: 31
Effective length of query: 365
Effective length of database: 371
Effective search space:   135415
Effective search space used:   135415
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