GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Coprobacter fastidiosus NSB1

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_022603146.1 NSB1T_RS28555 AMP-binding protein

Query= BRENDA::A7KUK6
         (562 letters)



>NCBI__GCF_000473955.1:WP_022603146.1
          Length = 550

 Score =  167 bits (423), Expect = 1e-45
 Identities = 149/563 (26%), Positives = 256/563 (45%), Gaps = 60/563 (10%)

Query: 14  EVDLWTFLFERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKGDVL 73
           E  L  FL    ++    + I+Y D D +  +TY        +  KG+ A+    K   +
Sbjct: 5   EKTLGDFLEYWAEKTPDKEFIVYSDRDLR--FTYSEFNKRVNNLAKGMMAIGV-EKDSKV 61

Query: 74  ALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQA-------- 125
            ++  N  D    ++ +   G  +   N  Y   EL + ++N+    L            
Sbjct: 62  GIWATNVPDWLTFLFASAKIGAILVTVNTNYKQHELEYLVENADIHTLCISNGTFDSDYV 121

Query: 126 ----SVLPVAREAA----KKVGMPEDR-IILIGDQRDPDARVKHFTSVRNISGAT----- 171
               ++LP  + +     K    P  R ++ IG ++    R  + T+   + G T     
Sbjct: 122 DMTYTMLPELKTSQRGHLKSNKFPYMRNVVYIGQEKH---RGMYNTAELLLLGNTITDEK 178

Query: 172 -RYRKQKITPAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDG 230
              +KQK     DV  + Y+SGTTG PKGVM++H NI  N        G+ + ++     
Sbjct: 179 LETQKQKFN-CYDVVNMQYTSGTTGFPKGVMLTHHNITNN----GYCIGQCMKFS----- 228

Query: 231 KGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPV 290
           + DRV   +P +H +G+   I   +  G   +++ +FD     A V   RC+  Y VP +
Sbjct: 229 ENDRVCLPVPLFHCFGIVLGIMAIITNGGCAVMLERFDPLVVLASVHKERCTALYGVPTM 288

Query: 291 VLLLGKHPVVDKYDLSSLR--MMNSGAAP--LTQELVEAVYSRIKVGIKQGYGLSETSPT 346
            +    HP+   +DLSSLR  +M     P  L +E+++ +Y +    I   YGL+ETSP 
Sbjct: 289 FIAELNHPMFSMFDLSSLRTGIMAGSLCPEWLMREVMDKMYMK---EITSVYGLTETSPG 345

Query: 347 THSQRWEDWREAMGS-VGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGY 405
               + +D  E   S VG  +P ++ + +    D    +E   G  GE+  +G N+  GY
Sbjct: 346 MTQSKVDDPVEVRASTVGSDLPGVEVRVI----DPETLEECPVGVQGEMCCRGYNIMKGY 401

Query: 406 HENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDN 465
           ++ PEAT   + ++G+  +GD+G +  +GN+ IT R+K++I   G  + P E+E +L   
Sbjct: 402 YKMPEATAAIIDKNGFLHSGDLGIKTPEGNYKITGRIKDMIIRGGENIYPREIEEFLYQI 461

Query: 466 DAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLR 525
             I DV V  + S+ +G EV    +++  +S             +  +   K++ HK + 
Sbjct: 462 PQIKDVQVAAVPSKKYGEEVGAFIILKEGESLHD--------CDVKDFCKGKISRHK-IP 512

Query: 526 GGVHFVDEIPKNPSGKILRRILK 548
             + F+D+ P   SGKI +  LK
Sbjct: 513 KYIFFIDQFPLTGSGKIQKYKLK 535


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: 700
Number of extensions: 37
Number of successful extensions: 5
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: 550
Length adjustment: 36
Effective length of query: 526
Effective length of database: 514
Effective search space:   270364
Effective search space used:   270364
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