GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Sphingomonas koreensis DSMZ 15582

Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate Ga0059261_0292 Ga0059261_0292 acetyl-CoA carboxylase, biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__Korea:Ga0059261_0292
          Length = 454

 Score =  447 bits (1149), Expect = e-130
 Identities = 230/446 (51%), Positives = 307/446 (68%), Gaps = 3/446 (0%)

Query: 4   KVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDH 63
           K+L+ANRGEIA+R+ RAC E+G++TVAV+S AD    HVR AD+A  IGP  AADSYL+ 
Sbjct: 6   KLLIANRGEIALRIHRACHEMGIKTVAVHSTADADAMHVRLADQAVCIGPPAAADSYLNI 65

Query: 64  ESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLM 123
            ++I AA  + ADAIHPGYGFL+ENA+FA  VE     +VGP  + +  +G+K +A+   
Sbjct: 66  PNIISAAEISGADAIHPGYGFLSENAKFAEIVELHNLIFVGPKPEHIRVMGDKVEAKRTA 125

Query: 124 QDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFET 183
               +P+VPG+       E+ K +A + GYPV IKA  GGGGRG+KV    D+ +   + 
Sbjct: 126 GALGLPLVPGSDGAISDVEEAKKLAAEIGYPVIIKAASGGGGRGMKVCTDPDQFETLMQQ 185

Query: 184 AKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEAP 243
           A  E +A F +A+VY+EKYL  PRHIE+Q+  D +GN  HLGERDCSLQRRHQKV+EEAP
Sbjct: 186 AGSEAKAAFGDATVYLEKYLGNPRHIEIQVFGDGNGNAIHLGERDCSLQRRHQKVLEEAP 245

Query: 244 SPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTEEVT 303
           SP LS + R RIGE   + +    Y  AGT+EFL E+GEFYF+E+NTR+QVEH VTE +T
Sbjct: 246 SPVLSTEERNRIGEICAKAMADMGYRGAGTIEFLWENGEFYFIEMNTRLQVEHPVTEAIT 305

Query: 304 GLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPPGGI 363
           GLD+V+ Q+RVA G  L   Q+DV+  GH++E RINAE P + FAP+ G +S Y  PGG+
Sbjct: 306 GLDLVREQIRVAEGHGLTLRQEDVQFRGHAIECRINAEDP-RTFAPSPGRVSQYHAPGGM 364

Query: 364 GIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIE--GLRTVIPFH 421
            +R+D  +  G ++   YDSMIAKLIV G+ R+  L R  RAL EF IE  G++T IP H
Sbjct: 365 NVRVDSGLYSGYKVPPYYDSMIAKLIVYGTTRQGALRRLRRALEEFVIEGDGMKTTIPLH 424

Query: 422 RLMLTDEAFREGSHTTKYLDEVLDPE 447
           + +L +  F++G +T K+L+E L  E
Sbjct: 425 QALLDNPQFQQGDYTIKWLEEWLARE 450


Lambda     K      H
   0.312    0.132    0.371 

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: 691
Number of extensions: 26
Number of successful extensions: 3
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: 601
Length of database: 454
Length adjustment: 35
Effective length of query: 566
Effective length of database: 419
Effective search space:   237154
Effective search space used:   237154
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 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