GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Dyadobacter tibetensis Y620-1

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_025762799.1 X939_RS0108310 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_000566685.1:WP_025762799.1
          Length = 448

 Score =  446 bits (1148), Expect = e-130
 Identities = 224/442 (50%), Positives = 312/442 (70%), Gaps = 3/442 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           MF K+L+ANRGEIA+RV+R C E+G++TVAVYS AD+   HVR+ADEA  IGP  +  SY
Sbjct: 1   MFKKILIANRGEIALRVIRTCREMGIKTVAVYSTADRDSLHVRFADEAVCIGPPMSKLSY 60

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L+ +++I AA    ADAIHPGYGFL+ENAEF++   D    ++G +A  +  +G+K  A+
Sbjct: 61  LNIQNIISAAEVTGADAIHPGYGFLSENAEFSQICADYGIKFIGATAAQINGMGDKATAK 120

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
           + M  A VPVVPG+    +S E  K +A+  GYPV +KA  GGGGRG+++++  ++ +  
Sbjct: 121 ATMIKAGVPVVPGSEGLLESVEQGKRLAEGIGYPVIVKATAGGGGRGMRIINKPEDFEKA 180

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
           +  A+ E  A F N  +Y+EK++E PRHIE+QI+ D+ G V HL ERDCS+QRRHQK++E
Sbjct: 181 WTDARTESAAAFGNDGLYLEKFVEEPRHIEIQIVGDQFGTVCHLSERDCSIQRRHQKLVE 240

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVT 299
           E PSP ++ +LRE++G AA +G +A  Y  AGTVEFLV+  G+FYFME+NTRIQVEH +T
Sbjct: 241 ETPSPIITPELREKMGAAAIKGAQAIGYEGAGTVEFLVDKHGDFYFMEMNTRIQVEHPIT 300

Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359
           EEVT  D++K Q++VAAGE +  S  +   + ++ME RINAE P   F P+ G ++    
Sbjct: 301 EEVTNFDLIKEQIKVAAGEPI--SGVNYIPQLYAMECRINAEDPGNGFRPSPGKITNLHF 358

Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419
           PGG G+R+D  V  G  I  +YDSMIAK+IV+G  REEV+ R +RAL EF +EG++T IP
Sbjct: 359 PGGHGVRIDSHVYSGYTIPPNYDSMIAKVIVSGQSREEVITRMKRALQEFVLEGIKTTIP 418

Query: 420 FHRLMLTDEAFREGSHTTKYLD 441
           FH  ++ D  F+ G+ TTKYL+
Sbjct: 419 FHIKLMDDPGFKSGNFTTKYLE 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: 617
Number of extensions: 23
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: 448
Length adjustment: 35
Effective length of query: 566
Effective length of database: 413
Effective search space:   233758
Effective search space used:   233758
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 24 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