GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Sphingomonas koreensis DSMZ 15582

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate Ga0059261_3993 Ga0059261_3993 Acetyl/propionyl-CoA carboxylase, alpha subunit

Query= SwissProt::Q5LUF3
         (681 letters)



>FitnessBrowser__Korea:Ga0059261_3993
          Length = 669

 Score =  778 bits (2010), Expect = 0.0
 Identities = 408/687 (59%), Positives = 499/687 (72%), Gaps = 24/687 (3%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF KIL+ANRGEIACRV +TA++MGI+TVA+YSDAD +A HV MADEAV +GP PA +SY
Sbjct: 1   MFKKILVANRGEIACRVFRTAKRMGIATVAVYSDADARAPHVLMADEAVRLGPAPAAESY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           +  + ++AA +ATGA A+HPGYGFLSE   FA A    G+ FVGPP GAI AMGDKI SK
Sbjct: 61  LKAELILAAAKATGADAIHPGYGFLSERESFARACAEAGIAFVGPPPGAIAAMGDKIESK 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
           K+A+EA V+ VPG++G+I+D + AVKI+ +IGYPVM+KASAGGGGKGMR+A+++Q+ REG
Sbjct: 121 KLAKEAGVNVVPGFVGVIDDTEHAVKIAAEIGYPVMMKASAGGGGKGMRLAYSEQDVREG 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
           F+++K E   SFGDDR+FIEKF+  PRHIEIQVL D HGN +YLGERECSIQRR+QKVVE
Sbjct: 181 FEATKREGLASFGDDRVFIEKFIESPRHIEIQVLGDQHGNIVYLGERECSIQRRHQKVVE 240

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQ----KNFYFLEMNTRLQVE 296
           EAPSPF+    RR MGEQAVAL++AVGY SAGTVE IV G     + FYFLEMNTRLQVE
Sbjct: 241 EAPSPFVTPEMRRKMGEQAVALSRAVGYYSAGTVELIVSGADTSGEGFYFLEMNTRLQVE 300

Query: 297 HPVTELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLT 356
           HPVTE +TG+DLVEQMIRVAAGE L+  Q DVKLTGWAIENR+YAEDPYR FLPS GRL 
Sbjct: 301 HPVTEAVTGLDLVEQMIRVAAGETLAFGQDDVKLTGWAIENRIYAEDPYRSFLPSTGRLV 360

Query: 357 RYRPPA--ETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAP 414
           RYRPPA  +T  G +            GE  VR D GV EGGE+SM+YDPMIAKL TW  
Sbjct: 361 RYRPPAAQDTPYGEV-----------GGEGYVRVDDGVAEGGEVSMFYDPMIAKLITWGQ 409

Query: 415 TRAAAIEAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNL 474
           TR AA +    ALD FE+EG+G+N+ FLSA+M HP+F SG++TT FIAEEYPEGF G   
Sbjct: 410 TRDAAADLQVAALDRFELEGLGNNIDFLSALMQHPRFRSGELTTGFIAEEYPEGFAGAPA 469

Query: 475 PETDLRRVAAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAADHDG 534
                RR+A  AA +      R + +SG++         +WVV L      V++    DG
Sbjct: 470 DAMLTRRLATIAAVLSWRQSERASMISGQL-GAMPVAKRDWVVHLAAIAHEVSLG---DG 525

Query: 535 STVSFDDGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVRTP 594
           + V   DG  +  + +W PGD++A    D   L ++V K   G+ + TRGA  +V V  P
Sbjct: 526 AIV---DGELVEGSVEWAPGDRIAVARGDDGELAVRVAKTRTGWVLTTRGAAHRVEVYRP 582

Query: 595 RQAELARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRA 654
           R AELA+ M EK+PPD S+ LL PMPGL+ +V+V VG +V+ GQ L  +EAMKMENILRA
Sbjct: 583 RVAELAKHMIEKIPPDMSRFLLAPMPGLLTRVEVAVGDKVEAGQPLAVVEAMKMENILRA 642

Query: 655 EKKGVVAKINASAGNSLAVDDVIMEFE 681
           EK GVV  +N  AG SLAVD  I+EFE
Sbjct: 643 EKTGVVKAVNFGAGESLAVDAAILEFE 669


Lambda     K      H
   0.317    0.134    0.387 

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: 1224
Number of extensions: 71
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: 681
Length of database: 669
Length adjustment: 39
Effective length of query: 642
Effective length of database: 630
Effective search space:   404460
Effective search space used:   404460
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: 54 (25.4 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