GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Sphingomonas histidinilytica UM2

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_079648301.1 B5X82_RS11530 long-chain-fatty-acid--CoA ligase

Query= BRENDA::A4YDR9
         (549 letters)



>NCBI__GCF_900167915.1:WP_079648301.1
          Length = 513

 Score =  224 bits (570), Expect = 8e-63
 Identities = 164/524 (31%), Positives = 252/524 (48%), Gaps = 36/524 (6%)

Query: 26  LFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEF 85
           L L R+    +DKTA+V+ D  ++Y+     V      L+R G    D+++ ++RN   F
Sbjct: 14  LMLRRSALRHRDKTALVFEDDAWSYAELDRLVDELGEGLLRLGVEAGDRVAILARNSHAF 73

Query: 86  LESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKAEII 145
           L   F V     VLVP+N  L P E+AY+++HS ++ +  D   L    E       EI+
Sbjct: 74  LALRFAVARIAAVLVPVNVMLGPAEVAYVLDHSGARLLFTDAALLPLAREATPATVEEIL 133

Query: 146 LLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGV 205
           +L   D+         E R     LV GG+    P    +   ++ + YTSGT   PKG 
Sbjct: 134 ILTGRDDSG-------ECRGWRALLVPGGA----PGDRADGADLLQIIYTSGTESRPKGA 182

Query: 206 MHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASW-GFSWATVAVGATNVCLDKVDY 264
           M  H        + + +     + + L  LP+FH A+    +   +  GAT++       
Sbjct: 183 MLSHAAVLWQYQSCLFDCDWSPDVIALHALPLFHCAALDAMAGPALLAGATSIIAASPAP 242

Query: 265 PLIYRLVEKERVTHMCAAPTVYVNL--ADYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQ 322
            LI  ++E+ R++   A PTV++ L  +   ++++L    R      GAA  PA +  + 
Sbjct: 243 ELIIPMIERHRISSFFAPPTVWIALLRSPLFEKHDLSSLTRGFY---GAAIMPAAV--ID 297

Query: 323 EIGGYM-----CHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDVF 377
           E+G  +      ++YG TE     ++         L  EE A      G P +  +  V 
Sbjct: 298 ELGARLPGLRLWNLYGQTEIAPVATV---------LRPEEHAARPTSAGRPTLHVQTRVV 348

Query: 378 DANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVVHPDGYIEI 437
           D   + V      IGE+V R   +  GY++ PE +  +F  GWFHSGD A +  +G+I +
Sbjct: 349 DDQMRDVA--PGEIGEIVHRSPQLLSGYWRQPEISEAAFAGGWFHSGDLATIDAEGFITV 406

Query: 438 VDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLT 497
           VDR KD+I +GGE VSS  VE+ +   P V  VAV G PD  W E VTA I  + G  ++
Sbjct: 407 VDRKKDMIKSGGENVSSREVEEAIYAHPHVSEVAVIGLPDPHWIEAVTAFIVPRNGADVS 466

Query: 498 EEEVIKFCKERLAHFECPKIVEFGP-IPMTATGKMQKYVLRNEA 540
            E++   C  RLA F+ PK + F P +P  A GK+ K  LR++A
Sbjct: 467 AEDIHAHCAGRLAGFKRPKRICFVPELPRNAAGKILKRELRDQA 510


Lambda     K      H
   0.319    0.136    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: 587
Number of extensions: 18
Number of successful extensions: 4
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: 549
Length of database: 513
Length adjustment: 35
Effective length of query: 514
Effective length of database: 478
Effective search space:   245692
Effective search space used:   245692
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 (21.7 bits)
S2: 52 (24.6 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