GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Jannaschia aquimarina GSW-M26

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_043917234.1 jaqu_RS01820 acyl-CoA dehydrogenase

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>NCBI__GCF_000877395.1:WP_043917234.1
          Length = 405

 Score =  569 bits (1466), Expect = e-167
 Identities = 281/390 (72%), Positives = 323/390 (82%), Gaps = 2/390 (0%)

Query: 5   ASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGL 64
           +SF W DPLLL  QL++EERMV D A  +AQD L PRV+ A+R E TDP IFREMGE+GL
Sbjct: 15  SSFEWSDPLLLADQLSDEERMVVDGARSYAQDALQPRVIAAYRDETTDPGIFREMGEMGL 74

Query: 65  LGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKY 124
           LG TIPE+YGG G +YV YGL+ARE+ER+DSGYRSMMSVQSSLVM PI+ +G+EAQ+QKY
Sbjct: 75  LGVTIPEEYGGLGGSYVSYGLVAREIERVDSGYRSMMSVQSSLVMYPIHAYGSEAQRQKY 134

Query: 125 LPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWA 184
           LP LASGE IGCFGLTEP+ GSDPGSM TRA K   GYR++GSKMWI+N+PIAD+FVVWA
Sbjct: 135 LPGLASGELIGCFGLTEPDAGSDPGSMKTRAEKTATGYRISGSKMWISNAPIADIFVVWA 194

Query: 185 KDDA--GDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLK 242
           K +A  G IRGFVLEK   GLSAP + GK+ LRASITGEIVMD V V E+ + P V GLK
Sbjct: 195 KSEAHDGKIRGFVLEKSMAGLSAPKVGGKLSLRASITGEIVMDGVEVGEDALLPSVEGLK 254

Query: 243 GPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEIT 302
           GPF CLN ARYGISWG +GAAE CW  ARQY LDR+QFGRPLA  QL QKKLADMQTEI 
Sbjct: 255 GPFGCLNRARYGISWGVMGAAEFCWQAARQYGLDRKQFGRPLAQTQLFQKKLADMQTEIA 314

Query: 303 LALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHL 362
           L LQ  LR+GR+ DEG AA E+ S++KRN+CGKALD+AR++RDM GGNGIS+EF V RH+
Sbjct: 315 LGLQASLRVGRLMDEGKAAPEMISLIKRNNCGKALDVARLSRDMHGGNGISEEFQVIRHM 374

Query: 363 VNLEVVNTYEGTHDVHALILGRAQTGIQAF 392
           +NLE VNTYEGTHDVHALILGRAQTG+QAF
Sbjct: 375 MNLETVNTYEGTHDVHALILGRAQTGLQAF 404


Lambda     K      H
   0.320    0.137    0.413 

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: 557
Number of extensions: 20
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: 393
Length of database: 405
Length adjustment: 31
Effective length of query: 362
Effective length of database: 374
Effective search space:   135388
Effective search space used:   135388
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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