GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Halioglobus japonicus S1-36

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_084201014.1 C0029_RS15355 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>NCBI__GCF_002869505.1:WP_084201014.1
          Length = 446

 Score =  448 bits (1153), Expect = e-130
 Identities = 230/446 (51%), Positives = 302/446 (67%), Gaps = 2/446 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           M  KVL+ANRGEIA+RV+RAC+EL ++TVAV+S AD    HVR ADE+  IGPA + +SY
Sbjct: 1   MLDKVLIANRGEIALRVLRACKELDIKTVAVHSVADAELMHVRLADESVCIGPAPSKESY 60

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L+  ++I AA   DA AIHPGYGFL+ENA+FA +VE S FT+VGP A+ +  +G+K  A 
Sbjct: 61  LNVPALISAAEVTDATAIHPGYGFLSENADFADQVEKSGFTFVGPRAETIRLMGDKVSAI 120

Query: 121 SLMQDADVPVVPGTTEP-ADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179
             M+ A VP VPG+  P  D  +  + +A   GYPV IKA  GGGGRG++VVH+E+ +  
Sbjct: 121 EAMKRAGVPTVPGSDGPLTDDHDRTREIAQRVGYPVIIKAAAGGGGRGMRVVHNEEVLIS 180

Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239
             E  K E  A F +  VY+EK+L+ PRH+EVQ+LAD  G+  HLG+RDCSLQRRHQKVI
Sbjct: 181 SIEVTKSEAAAAFGSDVVYLEKFLQKPRHVEVQVLADGQGDAIHLGDRDCSLQRRHQKVI 240

Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVT 299
           EEAP+P + EDLR ++ EA         Y  AGT EFL EDG FYF+E+NTR+QVEH VT
Sbjct: 241 EEAPAPGIPEDLRNQVYEACVNACIEIGYRGAGTFEFLYEDGGFYFIEMNTRVQVEHPVT 300

Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359
           E VT  D+VK QLR+AAG  L  +QD++   GHS E RINAE P+  F P+ G ++T+  
Sbjct: 301 EMVTSFDIVKEQLRIAAGMPLSVTQDEISFNGHSFECRINAEDPQ-NFLPSPGKVNTFHA 359

Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419
           PGG+G+R D  +  G  +   YDS+IAK+I  G  R+  L R  +AL+E  +EG+RT  P
Sbjct: 360 PGGLGVRCDSHLYDGYTVPPFYDSLIAKIITFGESRDVALARMRQALDELVVEGIRTNTP 419

Query: 420 FHRLMLTDEAFREGSHTTKYLDEVLD 445
            HR +  D AF+ G  +  YL+  L+
Sbjct: 420 LHRELCRDSAFQAGGVSIHYLESKLE 445


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: 655
Number of extensions: 30
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: 446
Length adjustment: 35
Effective length of query: 566
Effective length of database: 411
Effective search space:   232626
Effective search space used:   232626
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