GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Amantichitinum ursilacus IGB-41

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_053937789.1 WG78_RS10575 long-chain-fatty-acid--CoA ligase FadD

Query= BRENDA::A7KUK6
         (562 letters)



>NCBI__GCF_001294205.1:WP_053937789.1
          Length = 554

 Score =  196 bits (499), Expect = 2e-54
 Identities = 159/527 (30%), Positives = 241/527 (45%), Gaps = 49/527 (9%)

Query: 46  TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105
           TY+ L   S  F   L+      +G  + +  PN +  PV ++G L AG  +   NP YT
Sbjct: 50  TYQELDQLSTAFAAYLQQTLRLSRGARVGIMMPNLLQYPVALFGILKAGMVVVNINPLYT 109

Query: 106 VDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDAR-------- 157
             EL  QLK+S A+ +V  A+      +   K  +    +  IGD  D   R        
Sbjct: 110 PRELEHQLKDSGAEAIVIVANFAHTLDKCIGKTAVKHVIVSQIGDMLDFPKRQLVNAVIK 169

Query: 158 -VKHFTSVRNISGATRY-------RKQKITPAK----DVAFLVYSSGTTGVPKGVMISHR 205
            +K      N+ GA  +       R Q + P      D+AFL Y+ GTTGV KG M++HR
Sbjct: 170 YIKKMVPAYNLPGAVSFNHALADGRAQTLAPVNLTLDDLAFLQYTGGTTGVAKGAMLTHR 229

Query: 206 NIVANIRQQFIAEGEMLSWNGGPDGKG-DRVLAFLPFYHIYGLTC---LITQALYKGYHL 261
           NIVAN++Q         +W GG    G + ++  LP YHI+ LT    + T+      +L
Sbjct: 230 NIVANMQQAH-------AWIGGVVADGRELIVTALPLYHIFSLTANGMIFTKI--GATNL 280

Query: 262 IVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQE 321
           ++ +  DI  +   +  Y  +    V  +   L  HP   K D SS ++   G   + Q 
Sbjct: 281 LITNPRDIPGFIKELGKYPVTAITGVNTLFNALVNHPDFLKLDFSSWKLTLGGGMAVQQP 340

Query: 322 LVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGS 381
           + +       V + + YGL+ETSP          RE  G +G  +P+  A+     EDGS
Sbjct: 341 VADKWKKVTGVTLVEAYGLTETSPAAMINPMT-LREYNGMIGLPVPSTDAQIRG--EDGS 397

Query: 382 EPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDR 441
                  G  GEL++KGP V  GY +  + T   +  DG+  TGDV      G F I DR
Sbjct: 398 VQPP---GSAGELFIKGPQVMKGYWQRADETAKVIGADGYLATGDVAIMSPTGFFRIADR 454

Query: 442 VKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGT 501
            K+++   GF V P E+E  +  +  + +VA +G+  +  G  V +  VVR   + +   
Sbjct: 455 KKDMVLVSGFNVYPNEVEDVVARHPGVLEVACVGVPDDKSGEAVKI-FVVRKDPTLTE-- 511

Query: 502 SEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILK 548
                 A +I +   ++ ++K  R  V F D +PK+  GKILRR L+
Sbjct: 512 ------AALIAYCREQLTNYKVPR-KVEFRDALPKSNVGKILRRELR 551


Lambda     K      H
   0.317    0.136    0.410 

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: 674
Number of extensions: 34
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: 562
Length of database: 554
Length adjustment: 36
Effective length of query: 526
Effective length of database: 518
Effective search space:   272468
Effective search space used:   272468
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: 53 (25.0 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