GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Marinobacter adhaerens HP15

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 GFF3280 HP15_3222 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__Marino:GFF3280
          Length = 448

 Score =  442 bits (1138), Expect = e-128
 Identities = 223/445 (50%), Positives = 308/445 (69%), Gaps = 2/445 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           M  KVL+ANRGEIA+R++RAC+ELG++TVAV+S+ D+   HVR ADE+  IGP  A DSY
Sbjct: 3   MLEKVLIANRGEIALRILRACKELGIKTVAVHSQVDRDLMHVRLADESVCIGPNSATDSY 62

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L+  ++I AA   D+  IHPGYGFLAENA+FA +VE S F ++GP A+ +  +G K  A 
Sbjct: 63  LNIPTIISAAEVTDSVGIHPGYGFLAENADFAEQVEKSGFRFIGPKAETIRLMGNKVSAI 122

Query: 121 SLMQDADVPVVPGTTEPADSAED-VKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179
           + M  A VP VPG+  P D  E+    +A + GYPV IKA  GGGGRG++VVHSE  +  
Sbjct: 123 NAMIKAGVPTVPGSDGPLDDDEERTLRIAKEIGYPVMIKAASGGGGRGMQVVHSEAALLK 182

Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239
             +  + E +  F + +VY+EK+LEAPRH+EVQ+LAD HGN  HLG+RDCS+QRR+QKVI
Sbjct: 183 GVQITQSEAKNAFGDPTVYLEKFLEAPRHVEVQVLADMHGNCIHLGDRDCSMQRRNQKVI 242

Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVT 299
           EEAP+P ++ + RER  +A     +   Y  AGT EFL +DGEFYF+E+NTR+QVEH V+
Sbjct: 243 EEAPAPNINPESRERTLKACTDACKEIGYVGAGTFEFLYQDGEFYFIEMNTRVQVEHPVS 302

Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359
           E VTG+D+V+ QLR+A+G  L ++QDD+ I GH+ME RINAE P K F P+ G +  +  
Sbjct: 303 EMVTGVDIVREQLRIASGLPLQYTQDDIRISGHAMECRINAEDP-KTFIPSPGKVKHFHA 361

Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419
           PGG G+R+D  +  G  +   YDS++AKLI  G DR+    R + AL+E  +EG++T  P
Sbjct: 362 PGGNGVRVDSHLYSGYTVPPYYDSLVAKLITWGDDRDIARRRMKNALDELVVEGIKTNQP 421

Query: 420 FHRLMLTDEAFREGSHTTKYLDEVL 444
            HR ++ D  F++   T  YL++++
Sbjct: 422 LHRKLVRDGGFKQVDFTIHYLEKLM 446


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: 639
Number of extensions: 19
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 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