GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Cupriavidus basilensis 4G11

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate RR42_RS29420 RR42_RS29420 3-methylcrotonyl-CoA carboxylase

Query= reanno::PS:Dsui_0516
         (663 letters)



>FitnessBrowser__Cup4G11:RR42_RS29420
          Length = 666

 Score =  444 bits (1141), Expect = e-129
 Identities = 284/676 (42%), Positives = 380/676 (56%), Gaps = 43/676 (6%)

Query: 2   FKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61
           F+KILIANRGEIA RV+++A  +G +TVAVYS AD  A  VE A +AV IG A   +SYL
Sbjct: 7   FQKILIANRGEIALRVMRSATALGYRTVAVYSSADAGARHVEEAGQAVYIGQAQPAQSYL 66

Query: 62  VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121
             D II A +++GA+AVHPGYGFL+ENA F+R   E G+ FIGP   SI  MG+K  +K+
Sbjct: 67  RIDAIIEAARRSGADAVHPGYGFLAENAAFARACREAGLVFIGPSAESIVAMGNKAGAKR 126

Query: 122 LAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGF 181
           L + A V  IPGY             A++IG+PVMIKA+AGGGG+G+R+  +     E  
Sbjct: 127 LMMAADVPCIPGYQGEDQDEARLCAEAERIGFPVMIKATAGGGGRGMRLVPHARAFPELL 186

Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241
            S  +EA+ +FGD  V +E+ V+EPRHIEIQ+L D +GN ++L ERDCS+QRRHQK+IEE
Sbjct: 187 RSARSEAQGAFGDPEVILERAVVEPRHIEIQILADRYGNAIHLGERDCSVQRRHQKLIEE 246

Query: 242 APSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVT 301
           APSP V  E+R  MG  AVA  +A+ YE AGT+EF++      +YF+EMNTRLQVEHPVT
Sbjct: 247 APSPAVSAELRARMGATAVAAVKAIGYEGAGTLEFLLD-RDGNYYFMEMNTRLQVEHPVT 305

Query: 302 ELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQ- 360
           E ITGLDLV   +R+A GE LPL Q DV+ +G A+E R+ AED  +GF+P +G +  +Q 
Sbjct: 306 EAITGLDLVALQLRIAAGEPLPLRQEDVRFSGHAIEVRLCAEDADQGFMPQSGEIALWQA 365

Query: 361 PPAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISS 420
           PPA     +RV+  +  G  I  YYDSMIAKLI +G +R++A  ++   L   V  G+++
Sbjct: 366 PPA-----LRVEHALGSGAAIPPYYDSMIAKLISYGGTRDEARRKLSQGLEDLVALGVTT 420

Query: 421 NIPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFV-------- 472
           N  F    + H  F +G   T FI +      DA + P  D AL    AA          
Sbjct: 421 NQVFLGRCLAHPAFAAGEATTAFIGQHQ----DALLQP--DAALRQRAAALAALLLYETS 474

Query: 473 -HRRYIDRAAQVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLS 531
             R+    AA ++  LP     +G  + V  NG  H        G       GE      
Sbjct: 475 PERQPGAPAASLAPTLP-----IGLRYRV--NGAEHQASLAYGAGNRFAVAMGESRFAFE 527

Query: 532 DWRQGQSLFNGTCNGEEFTLQVERHRMTYQLFHWGT----RADMMVMSARAAELLALMPE 587
               G      +C+G   +    R   T  L + GT           +ARA E       
Sbjct: 528 TIALGAHSVRFSCDGLVESATFHRDASTLLLHYQGTPLRIEDHTRAAAARAGE------- 580

Query: 588 KAAPDLSKFLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISV 647
            AA D    L + M G +  V VA G +V+AG+ +  +EAMKME+I  A    +V  + V
Sbjct: 581 -AAGDGK--LRASMNGRVVNVMVAAGDQVEAGQPMVTLEAMKMEHIHVAPAAGRVGAVHV 637

Query: 648 TAGSSLSVDEIIIEFE 663
             G   +   +I E E
Sbjct: 638 QVGDQAAAMRVIAEIE 653


Lambda     K      H
   0.319    0.135    0.391 

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: 1044
Number of extensions: 54
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: 663
Length of database: 666
Length adjustment: 38
Effective length of query: 625
Effective length of database: 628
Effective search space:   392500
Effective search space used:   392500
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 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