GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF987 Psest_1019 acetyl-CoA
           carboxylase, biotin carboxylase subunit
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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