GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Magnetospirillum magneticum AMB-1

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_011385596.1 AMB_RS16315 acyl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>NCBI__GCF_000009985.1:WP_011385596.1
          Length = 392

 Score =  574 bits (1480), Expect = e-168
 Identities = 278/389 (71%), Positives = 327/389 (84%), Gaps = 1/389 (0%)

Query: 6   FHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLG 65
           F WDDP LL+ QL++DE+++RD+AHAY Q KL PRV +AFR ET D  I  EMGE+GLLG
Sbjct: 4   FKWDDPFLLEDQLSEDEKLIRDSAHAYCQEKLQPRVMKAFRDETFDREIMNEMGEMGLLG 63

Query: 66  PTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLP 125
           PTIPE+YGGPG+++V+YGLI+REVERVDSGYRS MSVQSSLVM PIF +G++ QK+KYLP
Sbjct: 64  PTIPEEYGGPGVNHVAYGLISREVERVDSGYRSAMSVQSSLVMHPIFSYGTEEQKKKYLP 123

Query: 126 KLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKL 185
           +LATGE IGCFGLTEP+ GSDPG M TRA+KV GGY L+GSKMWITNSPI+D+ +VWAK 
Sbjct: 124 RLATGEIIGCFGLTEPDAGSDPGGMRTRAKKVDGGYLLTGSKMWITNSPISDIAIVWAKS 183

Query: 186 DEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKGLRG 245
           D     +I+GFI+EKG KG + P I GK+ LRASITGEIVLDEAFVP+E ++P+  GL G
Sbjct: 184 DAH-EGKIKGFIVEKGIKGFTTPKIEGKLSLRASITGEIVLDEAFVPDEALMPNASGLGG 242

Query: 246 PFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITL 305
           PF CLN ARYGIAWG +GAAE CWH ARQY+LDRKQFGRPLAANQ+ Q KLA+M TEITL
Sbjct: 243 PFGCLNKARYGIAWGVIGAAEFCWHAARQYMLDRKQFGRPLAANQIPQLKLANMMTEITL 302

Query: 306 GLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLV 365
           GLQ  +R+GRM D+ T A E  S++KRN+CGKALDIAR+ARDM GGNGIS+EF V RH+V
Sbjct: 303 GLQACVRVGRMMDDHTWAPEAVSLIKRNNCGKALDIARMARDMHGGNGISEEFHVIRHMV 362

Query: 366 NLEVVNTYEGTHDIHALILGRAQTGIQAF 394
           NLE VNTYEG HD+HALILGRA TGIQAF
Sbjct: 363 NLETVNTYEGAHDVHALILGRAMTGIQAF 391


Lambda     K      H
   0.320    0.138    0.414 

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: 534
Number of extensions: 14
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: 395
Length of database: 392
Length adjustment: 31
Effective length of query: 364
Effective length of database: 361
Effective search space:   131404
Effective search space used:   131404
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 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