GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Pseudomonas stutzeri RCH2

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 GFF987 Psest_1019 acetyl-CoA carboxylase, biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__psRCH2:GFF987
          Length = 449

 Score =  441 bits (1133), Expect = e-128
 Identities = 221/449 (49%), Positives = 302/449 (67%), Gaps = 2/449 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           M  KVL+ANRGEIA+RV+RAC+ELG++TVAV+S AD+   HV  ADE+  IGPA +A SY
Sbjct: 1   MLEKVLIANRGEIALRVLRACKELGIKTVAVHSTADRDLMHVSLADESVCIGPAASAKSY 60

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L   ++I AA    AD IHPGYGFLAENA+FA +VE S FT++GP+AD +  +G+K  A+
Sbjct: 61  LSIPALIAAAEVTGADGIHPGYGFLAENADFAEQVEKSGFTFIGPTADVIRLMGDKVSAK 120

Query: 121 SLMQDADVPVVPGTTEPADSAE-DVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179
             M+ A VP VPG+  P    E +   +A + GYPV IKA GGGGGRG++VVH E+++  
Sbjct: 121 DAMKQAGVPTVPGSDGPLPEDEKEALRIAREVGYPVIIKAAGGGGGRGMRVVHKEEDLIA 180

Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239
             +  + E  A F N  VY+EK+L  PRH+E+Q+LAD  GN  HLG+RDCSLQRRHQKVI
Sbjct: 181 SAKLTRNEAGAAFGNPMVYLEKFLTNPRHVEIQVLADGQGNAIHLGDRDCSLQRRHQKVI 240

Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVT 299
           EEAP+P + E+ R ++     +      Y  AGT EFL EDG FYF+E+NTR+QVEH VT
Sbjct: 241 EEAPAPLIDEEARRKVQARCVKACIDIGYRGAGTFEFLYEDGNFYFIEMNTRVQVEHPVT 300

Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359
           E VTG+D+VK  L +  G++L   Q+DV I GH++E RINAE P + F P+ G +  +  
Sbjct: 301 EMVTGIDIVKEMLLIGGGQKLSIKQEDVVIRGHAVECRINAEDP-RTFMPSPGKVKHFHA 359

Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419
           PGG G+R+D  +  G  +   YDS+I KLI  G++R+E + R   AL+E  ++G++T  P
Sbjct: 360 PGGNGVRVDSHLYDGYSVPPHYDSLIGKLITFGANRDEAMGRMRNALDELIVDGIKTNAP 419

Query: 420 FHRLMLTDEAFREGSHTTKYLDEVLDPER 448
            HR ++ D  F +G     YL++ L  ++
Sbjct: 420 LHRDLVRDPGFCKGGVNIHYLEKKLGMDK 448


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: 641
Number of extensions: 22
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: 449
Length adjustment: 35
Effective length of query: 566
Effective length of database: 414
Effective search space:   234324
Effective search space used:   234324
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