Alignments for a candidate for pccA in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Paraburkholderia phymatum STM815

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 WP_012403275.1 BPHY_RS20055 urea carboxylase

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_000020045.1:WP_012403275.1
          Length = 1203

 Score =  338 bits (868), Expect = 6e-97
 Identities = 187/447 (41%), Positives = 268/447 (59%), Gaps = 7/447 (1%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           MF KVL+ANRG IA R++R   EL V  +AVYSEAD+   HV  AD A+++G   A+ +Y
Sbjct: 1   MFDKVLIANRGAIACRILRTLRELNVEGIAVYSEADRASRHVSLADTAWSLGDGAASVTY 60

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           LD   ++E AR   A AIHPGYGFL+ENA FA   E +   ++GP+   +   G K  AR
Sbjct: 61  LDIAKILEIARARGAQAIHPGYGFLSENAAFAEACEAAGIAFIGPTPAQLRAFGLKHTAR 120

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
           ++  +  VP++ GT    D  E     A   GYPV +K+  GGGG G++V  S++E+ GQ
Sbjct: 121 AIAAEQGVPMLEGTGL-LDGLEAALEAAKRVGYPVMLKSTAGGGGIGMRVCRSDEELAGQ 179

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
           F+  KR G+  F +A V++EKY+E  RH+EVQ+  D  G    LG RDCS+QRR+QKV+E
Sbjct: 180 FDIVKRLGQNNFSDAGVFLEKYIEKARHLEVQVFGDGKGAAIALGVRDCSVQRRNQKVLE 239

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVED--GEFYFMEVNTRIQVEHTV 298
           E P+P L + +   + +AA R  +A  Y +AGTVEF+ +     FYF+EVNTR+QVEH V
Sbjct: 240 ETPAPNLPDGVEAALCDAAIRLAQAVSYRSAGTVEFVYDSDAARFYFLEVNTRLQVEHGV 299

Query: 299 TEEVTGLDVVKWQLRVAAG--EELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLST 356
           TE+V G+D+V+W + +AAG    LD    D++  GH+++ R+ AE P ++F P  G L+ 
Sbjct: 300 TEQVWGVDLVRWMIELAAGTLAPLDVLSRDLQPRGHAIQARLYAEDPGRDFKPCPGLLTD 359

Query: 357 YDPPGGIG--IRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGL 414
              P   G  +R+D  +  G E+   +D M+AKLI     R++     + AL    I G+
Sbjct: 360 VSFPSADGRTLRIDTWIEAGCEVPPWFDPMLAKLIAWQPTRDDARRALDAALEASRIYGV 419

Query: 415 RTVIPFHRLMLTDEAFREGSHTTKYLD 441
            T   + R +L D  F  G   T+ L+
Sbjct: 420 ETNRDYLRQILADVPFASGHPWTRCLE 446



 Score = 53.1 bits (126), Expect = 7e-11
 Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 1/72 (1%)

Query: 531  DGE-SVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGD 589
            DG+ +V +E+ G +  V V+ G  VE GD + ++E+MKME  VVA   GTV ++ V  G 
Sbjct: 1129 DGQIAVDSEIAGNLWQVRVEPGATVEAGDVLLVIESMKMEISVVAPCAGTVGEIHVAPGS 1188

Query: 590  SVDMGDVLLVLE 601
             V  G  ++V+E
Sbjct: 1189 PVRAGQRVVVIE 1200


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: 1545
Number of extensions: 74
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 601
Length of database: 1203
Length adjustment: 42
Effective length of query: 559
Effective length of database: 1161
Effective search space:   648999
Effective search space used:   648999
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: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources