GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_0191 Echvi_0191 acetyl-CoA carboxylase, biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__Cola:Echvi_0191
          Length = 449

 Score =  447 bits (1150), Expect = e-130
 Identities = 223/442 (50%), Positives = 315/442 (71%), Gaps = 3/442 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           MF+K+L+ANRGEIA+R++R C+E+G++TVAVYS ADK   HVR+ADEA  IG A + +SY
Sbjct: 1   MFNKILIANRGEIALRIIRTCKEMGIKTVAVYSTADKDSLHVRFADEAVCIGAAPSRESY 60

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L+   VI AA   +ADAIHPGYGFL+ENAEF++  E+    ++G S++ ++++G+K  A+
Sbjct: 61  LNIPRVIAAAEITNADAIHPGYGFLSENAEFSKICEEYNIKFIGASSEMIDKMGDKATAK 120

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
           + M+ A VP +PG+    DS E    +A++ GYPV +KA  GGGGRG+++V  E E    
Sbjct: 121 ATMKAAGVPTIPGSEGLLDSIEQGIKIANEMGYPVILKATAGGGGRGMRIVREEKEFKKA 180

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
           ++ A++E  A F N  +Y+EK++E PRHIE+Q++ D  G   HL ERDCS+QRRHQK++E
Sbjct: 181 WDDARQESGAAFGNDGLYLEKFVEEPRHIEIQVVGDNTGKACHLSERDCSIQRRHQKLVE 240

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299
           E PSP ++++LR+ +G+AA +G  A  Y  AGT+EFLV+    FYFME+NTRIQVEH +T
Sbjct: 241 ETPSPFITDELRDAMGKAAIKGAEAIGYEGAGTIEFLVDKHRNFYFMEMNTRIQVEHPIT 300

Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359
           EEVT  D++K Q++VAAG  +  S  +   + ++ME RINAE P   F P+ G ++    
Sbjct: 301 EEVTDYDLIKEQIKVAAG--IPISGQNYYPKLYAMECRINAEDPANGFRPSPGKINNLHL 358

Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419
           PGG G+R+D  V  G  I  +YDSMIAKLIV+G  REEV+VR +RAL EF I+G++T IP
Sbjct: 359 PGGRGVRVDSHVYAGYIIPPNYDSMIAKLIVSGQSREEVIVRMKRALEEFVIDGIKTTIP 418

Query: 420 FHRLMLTDEAFREGSHTTKYLD 441
           FH  +L DE F+ G+ TTK+L+
Sbjct: 419 FHIALLEDEQFKAGNFTTKFLE 440


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: 612
Number of extensions: 21
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:

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