GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Caulobacter crescentus NA1000

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 CCNA_03320 CCNA_03320 biotin carboxylase

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__Caulo:CCNA_03320
          Length = 1078

 Score =  359 bits (922), Expect = e-103
 Identities = 238/611 (38%), Positives = 331/611 (54%), Gaps = 82/611 (13%)

Query: 3   SKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLD 62
           S+VL+ANRGEIAVR+ R   E G+ +VA+Y+  D    HV  AD A  + P   A +YLD
Sbjct: 4   SRVLIANRGEIAVRIARTAAEAGLESVAIYAADDAQSPHVSAADHAVAL-PGAGARAYLD 62

Query: 63  HESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSL 122
             +V+ AA+    DA+HPGYGFL+EN   AR   ++   ++GPS + +   G+K  AR+L
Sbjct: 63  IAAVVAAAKAQGCDALHPGYGFLSENPHLARACAEAGIVFIGPSPEHLTTFGDKAAARAL 122

Query: 123 MQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFE 182
             +  +P++PGT   A + E  +A   ++G  + +KA  GGGGRG+++V    E+D  F 
Sbjct: 123 AAERGLPLIPGTG--AITLEAARAFQAEHG-AIMLKARAGGGGRGMRMVLDPGELDAAFA 179

Query: 183 TAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEA 242
             +RE  A F +  +Y EK +E  RHIEVQI+ D    V  LG+RDCSLQRR+QK++E A
Sbjct: 180 ACEREALAAFGDGGLYAEKLIERARHIEVQIVGDGD-QVLALGDRDCSLQRRNQKLVEIA 238

Query: 243 PSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-------DGEFYFMEVNTRIQVE 295
           P+ AL ++LR  +   + R    A Y    TVEFLV+        GE +F+EVN R+QVE
Sbjct: 239 PA-ALPDNLRAALAGWSER--LCAGYRGLATVEFLVDADPHSPSGGEAFFIEVNPRLQVE 295

Query: 296 HTVTEEVTGLDVVKWQLRVAAGE---ELDFSQDDVEIEGHSMEFRINAEA--PEKEFAPA 350
           HTVTEEVTGLD+V+ Q  +AAG+   EL+ +       G +++ RINAE   PE +  P+
Sbjct: 296 HTVTEEVTGLDLVRLQFDLAAGKRLGELELTNTPPPF-GVAIQARINAETLTPEGQVRPS 354

Query: 351 TGTLSTYDPPGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFD 410
           TGTLS + PPGG G+R+D  V  G  IG  YDS++AK+IV G    E   R +RAL E  
Sbjct: 355 TGTLSAWTPPGGPGVRVDAGVAAGLTIGAAYDSLLAKVIVRGRTPSEAASRLDRALTELK 414

Query: 411 IEGLRTVIPFHRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVAGDEEEGEV 470
           + G+ T  P  R +L       G  TT ++ +    E + A  +R +PE  A       V
Sbjct: 415 VAGVATTAPLVRAILAHPTAVTGEATTTFIAQ--HAETLAAEAQRLTPETTA------SV 466

Query: 471 TERTFTVEVNGKRFEVSLEERGAPAIPLGGASAAASASKPSGPRKRREESDEGGQQVIEG 530
           T           RFEV           L GA                             
Sbjct: 467 T-----------RFEV-----------LAGA----------------------------- 475

Query: 531 DGESVAAEMQGTILAVEVDEGDDVEPGDTVCILEAMKMENDVVAERGGTVSQVLVGEGDS 590
             E V A +  T+ A+ + EGD V PG  + +LEAMKME+ V A  GG V +++V  G +
Sbjct: 476 --EPVVAPLAATVGAITIREGDLVRPGQALAVLEAMKMEHLVSASAGGRVVKIVVQGGAT 533

Query: 591 VDMGDVLLVLE 601
           V  G  L+ LE
Sbjct: 534 VAEGQPLVFLE 544


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: 1330
Number of extensions: 56
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 601
Length of database: 1078
Length adjustment: 41
Effective length of query: 560
Effective length of database: 1037
Effective search space:   580720
Effective search space used:   580720
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: 55 (25.8 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:

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