GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Sphingomonas koreensis DSMZ 15582

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate Ga0059261_0292 Ga0059261_0292 acetyl-CoA carboxylase, biotin carboxylase subunit

Query= metacyc::MONOMER-13597
         (509 letters)



>FitnessBrowser__Korea:Ga0059261_0292
          Length = 454

 Score =  406 bits (1043), Expect = e-118
 Identities = 219/450 (48%), Positives = 300/450 (66%), Gaps = 7/450 (1%)

Query: 1   MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALD 60
           +P   ++L+ANRGEIA R+ +A  EMG+  +AV+S AD  A+H + AD+A  IG   A D
Sbjct: 1   LPEIKKLLIANRGEIALRIHRACHEMGIKTVAVHSTADADAMHVRLADQAVCIGPPAAAD 60

Query: 61  SYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLD 120
           SYLNI +II AAE +  DAIHPGYGFLSENA+FAE VE   + F+GP  E +R + DK++
Sbjct: 61  SYLNIPNIISAAEISGADAIHPGYGFLSENAKFAEIVELHNLIFVGPKPEHIRVMGDKVE 120

Query: 121 GKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLM 180
            KR A   G+P  PGSDG ++ ++EA KLA +IGYP+++KAASGGGG G+    + DQ  
Sbjct: 121 AKRTAGALGLPLVPGSDGAISDVEEAKKLAAEIGYPVIIKAASGGGGRGMKVCTDPDQFE 180

Query: 181 DVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKL 240
            + ++    A  AFG A +++EKY  NPRHIE Q+ GD  GN +   ER+C++QRR+QK+
Sbjct: 181 TLMQQAGSEAKAAFGDATVYLEKYLGNPRHIEIQVFGDGNGNAIHLGERDCSLQRRHQKV 240

Query: 241 IEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEH 300
           +EEAPSP L  EER  + E   K    + Y   GT E  F   + +FYF+E+N RLQVEH
Sbjct: 241 LEEAPSPVLSTEERNRIGEICAKAMADMGYRGAGTIE--FLWENGEFYFIEMNTRLQVEH 298

Query: 301 PTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFV 360
           P TE I  +DLV+ QI++A G  L   QED+  + RG AIE RINAED    F  S G V
Sbjct: 299 PVTEAITGLDLVREQIRVAEGHGLTLRQEDV--QFRGHAIECRINAEDP-RTFAPSPGRV 355

Query: 361 TYYREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKI--G 418
           + Y  P G  VRVDSG+ SG  VPPYYDS+++KLIVYG +R+ A++   RAL ++ I   
Sbjct: 356 SQYHAPGGMNVRVDSGLYSGYKVPPYYDSMIAKLIVYGTTRQGALRRLRRALEEFVIEGD 415

Query: 419 GIKTTIELYKWIMQDPDFQEGKFSTSYISQ 448
           G+KTTI L++ ++ +P FQ+G ++  ++ +
Sbjct: 416 GMKTTIPLHQALLDNPQFQQGDYTIKWLEE 445


Lambda     K      H
   0.317    0.135    0.385 

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: 569
Number of extensions: 25
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: 509
Length of database: 454
Length adjustment: 34
Effective length of query: 475
Effective length of database: 420
Effective search space:   199500
Effective search space used:   199500
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 (21.6 bits)
S2: 51 (24.3 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