GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Cupriavidus basilensis 4G11

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate RR42_RS28980 RR42_RS28980 fatty acid--CoA ligase

Query= BRENDA::D3GE78
         (556 letters)



>FitnessBrowser__Cup4G11:RR42_RS28980
          Length = 580

 Score =  211 bits (536), Expect = 8e-59
 Identities = 159/506 (31%), Positives = 240/506 (47%), Gaps = 35/506 (6%)

Query: 58  LAAGLRKSGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTFVARELAYQLQDSG 117
           +A  L + G+ +GDRV L   N   +P VF G ++ G I T  N  +   EL Y L DSG
Sbjct: 87  IAHALIRDGVTKGDRVALAMRNLPEWPAVFYGALLTGAIVTPLNAWWTGAELEYGLADSG 146

Query: 118 ATYLLCASNSLETGLEAAKQAKLPQSHIFAYDTSIYDGVTNPQKGCAYWSDLLASEEEGA 177
           +   +     L   +E      LP          IY    N     A  SD   S+ E  
Sbjct: 147 SKIAIVDDERLGRIIE-----HLPGCPALE---KIYVSRAN-----APASDARISQLESL 193

Query: 178 AFTWDE-LSTPALSSTTLALN--------YSSGTTGRPKGVEISHRNYV--------ANM 220
             T D+  S PAL    +A++        Y+SGTTG+PKG   +HRN          + M
Sbjct: 194 IGTPDQWASLPALPVPVVAIDADDDATIFYTSGTTGKPKGALGTHRNATNVAVAAAFSPM 253

Query: 221 LQYCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIFIAAALYRATPVYIMSKFDFVKML 280
                     P       +   L  +P +H       +  AL   T + +M ++D V+ +
Sbjct: 254 RNCLRRGETIPAPDPGAPQKGMLLSVPFFHVTGCMAVLNGALASGTKIVLMRRWDAVRAM 313

Query: 281 EYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGREVCEEVEKLWPPG 340
              +R R T    VP +   + +HP   ++DLSS+E V  G AP   E+   +++++P  
Sbjct: 314 GLIERERCTAAGGVPTIAWQIIEHPERERFDLSSLENVNYGGAPASAELVRRIKEVFPHS 373

Query: 341 KINIKQGWGMTEATCSVTGWNPAE-ISTSASVGELNANCEAKIMFDGVEVKERNSRGELW 399
              I  GWGMTE + + T  +  E +    S G      E K++            GEL 
Sbjct: 374 APGI--GWGMTETSATFTSHSAEEYVERPESGGPALPIGEMKVVDGRGHSLPTGETGELM 431

Query: 400 VRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMKELIKVKGNQVAP 459
           VR  NV++GYW   +AT +T   DGWL TGDIA +D++G  ++VDRMK+++   G  +  
Sbjct: 432 VRGANVVRGYWNKPEATAQTFI-DGWLKTGDIARLDEEGFVYIVDRMKDMLIRGGENIYS 490

Query: 460 AELEALLLEHPAISDVAVIGVVINN-DERPRAYVVLRPGQSATANEIAHYLDNKVSAFKR 518
            E+E+ L +HPAI D A++G+      E P A V L+PG  AT  E+  ++  +++AFK 
Sbjct: 491 IEVESALYDHPAIMDAALVGIPHRTLGEEPAAVVSLKPGAQATEAELQAFVGERLAAFKV 550

Query: 519 ITGGVVFLEAIPKNPSGKILRMKLRE 544
               V   + +P+N +GKIL+  LR+
Sbjct: 551 PVRIVFCPDMLPRNANGKILKSTLRK 576


Lambda     K      H
   0.319    0.134    0.403 

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: 693
Number of extensions: 33
Number of successful extensions: 7
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: 556
Length of database: 580
Length adjustment: 36
Effective length of query: 520
Effective length of database: 544
Effective search space:   282880
Effective search space used:   282880
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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