GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Pseudomonas fluorescens FW300-N2C3

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 AO356_08195 AO356_08195 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_08195
          Length = 451

 Score =  442 bits (1138), Expect = e-128
 Identities = 223/442 (50%), Positives = 300/442 (67%), Gaps = 2/442 (0%)

Query: 4   KVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDH 63
           KVL+ANRGEIA+R++RAC+E+G++TVAVYS+ADK   H+  ADE+  IGPA AA SYL  
Sbjct: 7   KVLIANRGEIALRILRACKEMGIKTVAVYSKADKELMHLGLADESVCIGPASAAHSYLHI 66

Query: 64  ESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLM 123
            ++I AA    A AIHPGYGFLAENA+FA +VE+S F ++GP AD +  +G+K  A+  M
Sbjct: 67  PAIIAAAEVTGATAIHPGYGFLAENADFAEQVENSGFAFIGPKADTIRLMGDKVSAKHAM 126

Query: 124 QDADVPVVPGTTEP-ADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFE 182
             A VP VPG+  P  +  E    +  + GYPV IKA GGGGGRG++VVH E+++    +
Sbjct: 127 IAAGVPTVPGSDGPLPEDEETALRIGREVGYPVIIKAAGGGGGRGMRVVHKEEDLISSAK 186

Query: 183 TAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEA 242
             + E  A F N  VY+EK+L  PRH+EVQ+L+D  G   HLG+RDCSLQRRHQKV+EEA
Sbjct: 187 LTRSEAGAAFGNPMVYLEKFLTNPRHVEVQVLSDGQGQAIHLGDRDCSLQRRHQKVLEEA 246

Query: 243 PSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTEEV 302
           P+P + E  R+ +     +      Y  AGT EFL E+G FYF+E+NTR+QVEH V+E V
Sbjct: 247 PAPGIDEQARQEVLARCVKACIDIGYRGAGTFEFLYENGRFYFIEMNTRVQVEHPVSEMV 306

Query: 303 TGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPPGG 362
           TG+D+VK  L +AAG +L F+QDDV I GH++E RINAE P K F P+ GT+  +  PGG
Sbjct: 307 TGIDIVKEMLSIAAGNKLSFTQDDVVIRGHALECRINAEDP-KTFMPSPGTVKHFHAPGG 365

Query: 363 IGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPFHR 422
            G+R+D  +  G  +  +YDS+I KLI  G+ REE + R   AL+E  ++G++T IP HR
Sbjct: 366 NGVRVDSHLYSGYAVPPNYDSLIGKLITYGATREEAMARMRNALDEIVVDGIKTNIPLHR 425

Query: 423 LMLTDEAFREGSHTTKYLDEVL 444
            ++ DE F +G     YL+  L
Sbjct: 426 DLVRDEGFCKGGVNIHYLEHKL 447


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: 645
Number of extensions: 22
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: 601
Length of database: 451
Length adjustment: 35
Effective length of query: 566
Effective length of database: 416
Effective search space:   235456
Effective search space used:   235456
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