GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Methylocapsa aurea KYG

Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate WP_036259721.1 DL86_RS06940 fatty acid oxidation complex subunit alpha FadB

Query= metacyc::MONOMER-17591
         (715 letters)



>NCBI__GCF_000746085.1:WP_036259721.1
          Length = 720

 Score =  687 bits (1774), Expect = 0.0
 Identities = 358/719 (49%), Positives = 483/719 (67%), Gaps = 6/719 (0%)

Query: 1   MIYQGKAITVK----PLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGV 56
           M++ G+ + ++      E GI EL F+   E VNK + LT SELR A++ I A  ++KGV
Sbjct: 1   MLFDGQTVKLEWPGERQEEGIAELRFERGAEPVNKLDALTFSELRRALEIIAATPAIKGV 60

Query: 57  IVTSGKDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALG 116
           ++ S KD FIVGADI EF   F+ P E+++A   + ++I +   DL VPTVAAING+ALG
Sbjct: 61  LIASAKDAFIVGADIFEFTAIFKRPPEDIVAFVAQNSEIITALADLPVPTVAAINGLALG 120

Query: 117 GGLEMCLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKA 176
           GGLE+ LAADFRVMS+ A++G PEV LG++PG+GGTVRLPRLIG   + EWIASG + K 
Sbjct: 121 GGLELALAADFRVMSSAARIGFPEVHLGLFPGYGGTVRLPRLIGLVASAEWIASGAQQKP 180

Query: 177 EDALKVGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFET 236
           E AL+ GAVDAVVAPE L+AAAL   +RA+    +   RR+   + L++   E     ++
Sbjct: 181 EAALEEGAVDAVVAPEDLRAAALATLERAIEAPGEWSQRRRDLRKSLRIAPEEASRLLDS 240

Query: 237 AKGFVAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLN 296
           AK   A +  P+ PA   A++ ++ A++  RD AL +EA  F K AKT  A SL+ +F+N
Sbjct: 241 AKA-AAAKTLPHLPAAHIALELLEAASDLDRDSALTLEAQAFAKAAKTQAAASLVTIFIN 299

Query: 297 DQELKKKAKKYDEVAKDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNE 356
           +Q LKK ++ Y + A  V+ AAV+GAG+MGGGIAYQSA +G PI+MKDI E+ + +G++E
Sbjct: 300 EQALKKISRGYAKKAAPVRKAAVVGAGVMGGGIAYQSAARGVPIIMKDIAEQALDLGMSE 359

Query: 357 AAKLLGKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVE 416
           A KLL ++VE+GRL  AK    L  I P ++Y  F  VD+V+EAVVEN  VK+AVL+E+E
Sbjct: 360 ARKLLARQVEQGRLDQAKADAILGAIAPGLTYEGFDGVDVVIEAVVENIAVKKAVLSELE 419

Query: 417 GAVKEDAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIA 476
               E AI+ASNTS++ I  L + L+RP+ F GMHFFNPV  M LVEV+RG KT E  IA
Sbjct: 420 RVTGEAAILASNTSSLRIGDLTEGLRRPDKFIGMHFFNPVPRMALVEVVRGPKTSEETIA 479

Query: 477 TTVAYAKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMG 536
           T V YA  MGK+PIV+ DCPGF+VNR L PY   F +L+  G DF  +DKVME FGWPMG
Sbjct: 480 TIVGYADAMGKTPIVMQDCPGFVVNRALTPYLIAFLRLVHDGADFAHVDKVMETFGWPMG 539

Query: 537 PAYLSDVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDK 596
           PAYL DV+G+D  HH  ++++ GFP+RM     +A+D++    RLGQKNG GFY Y  D 
Sbjct: 540 PAYLIDVIGMDISHHVVEIVSAGFPERMQTSFASAIDILLREKRLGQKNGHGFYKYAKDA 599

Query: 597 RGKPKKVTDPQAYEVLKPIVVEQR-EVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEAD 655
           +G+P+K  DP+   +L       +  + +++IV  MM+PL  E  RC+EDG+V +  EAD
Sbjct: 600 KGRPRKELDPETDRLLAEARPNGKIAIGEDEIVERMMLPLIFEAARCVEDGVVGSRGEAD 659

Query: 656 MGLIYGIGFPPFRGGALRYIDSIGVAEFVALADKYAELGALYHPTAKLREMAKNGQKFF 714
           M LI G+G P + GGAL+Y D +GVA  VA A K+  LGA+Y P+     MA  G  F+
Sbjct: 660 MSLILGLGLPRYLGGALKYADHLGVANVVASAAKWESLGAIYRPSEGFSAMAAAGDVFY 718


Lambda     K      H
   0.318    0.137    0.388 

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: 1190
Number of extensions: 50
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: 715
Length of database: 720
Length adjustment: 40
Effective length of query: 675
Effective length of database: 680
Effective search space:   459000
Effective search space used:   459000
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: 55 (25.8 bits)

This GapMind analysis is from Apr 09 2024. 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