GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA in Pseudomonas fluorescens FW300-N2E3

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 AO353_13675 AO353_13675 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_13675 AO353_13675 acetyl-CoA
           carboxylase biotin carboxylase subunit
          Length = 453

 Score =  440 bits (1131), Expect = e-128
 Identities = 222/442 (50%), Positives = 299/442 (67%), Gaps = 2/442 (0%)

Query: 4   KVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDH 63
           KVL+ANRGEIA+R++RAC+E+G++TVAVYS+ADK   H+  ADE+  IGPA AA SYL  
Sbjct: 9   KVLIANRGEIALRILRACKEMGIKTVAVYSKADKELMHLGLADESVCIGPASAAHSYLHI 68

Query: 64  ESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLM 123
            ++I AA    A AIHPGYGFLAENA+FA +VE+S F ++GP A+ +  +G+K  A+  M
Sbjct: 69  PAIIAAAEVTGATAIHPGYGFLAENADFAEQVENSGFAFIGPKAETIRLMGDKVSAKHAM 128

Query: 124 QDADVPVVPGTTEPADSAEDVKA-VADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFE 182
             A VP VPG+  P    E+    +  + GYPV IKA GGGGGRG++VVH E+++    +
Sbjct: 129 IAAGVPTVPGSDGPLPEDEETALRIGREVGYPVIIKAAGGGGGRGMRVVHKEEDLISSAK 188

Query: 183 TAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEA 242
             + E  A F N  VY+EK+L  PRH+EVQ+L+D  G+  HLG+RDCSLQRRHQKV+EEA
Sbjct: 189 LTRSEAGAAFGNPMVYLEKFLTNPRHVEVQVLSDGQGHAIHLGDRDCSLQRRHQKVLEEA 248

Query: 243 PSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTEEV 302
           P+P + E  R+ +     +      Y  AGT EFL E+G FYF+E+NTR+QVEH V+E V
Sbjct: 249 PAPGIDEKARQEVFARCVKACIDIGYRGAGTFEFLYENGSFYFIEMNTRVQVEHPVSEMV 308

Query: 303 TGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPPGG 362
           TG+D+VK  L +AAG  L F+QDDV I GH++E RINAE P K F P+ GT+  +  PGG
Sbjct: 309 TGIDIVKEMLSIAAGNPLSFTQDDVVIRGHALECRINAEDP-KTFMPSPGTVKHFHAPGG 367

Query: 363 IGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPFHR 422
            G+R+D  +  G  +  +YDS+I KLI  G+ REE + R   AL+E  ++G++T IP HR
Sbjct: 368 NGVRVDSHLYSGYAVPPNYDSLIGKLITYGATREEAMARMRNALDEIVVDGIKTNIPLHR 427

Query: 423 LMLTDEAFREGSHTTKYLDEVL 444
            +  DE F +G     YL+  L
Sbjct: 428 DLTRDEGFCKGGVNIHYLEHKL 449


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: 636
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: 453
Length adjustment: 35
Effective length of query: 566
Effective length of database: 418
Effective search space:   236588
Effective search space used:   236588
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.

Links

Downloads

Related tools

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 paper from 2022 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