Alignments for a candidate for pccA in Sphingomonas koreensis DSMZ 15582

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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources