GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_3374 N515DRAFT_3374 acetyl-CoA carboxylase, biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3374
          Length = 458

 Score =  442 bits (1138), Expect = e-128
 Identities = 223/452 (49%), Positives = 310/452 (68%), Gaps = 2/452 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           +  KV++ANRGEIA+RV+RAC  LG++TVAV+S AD++  HV  ADE+  IGPA + DSY
Sbjct: 3   LLEKVVIANRGEIALRVLRACHSLGIKTVAVHSTADRNLKHVGLADESICIGPAPSVDSY 62

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L+   +I AA   DA AIHPGYGFL+E A+FA +VE S F ++GP+AD +  +G+K +A 
Sbjct: 63  LNIPRIIAAAEITDAQAIHPGYGFLSERADFAEQVEQSGFIFIGPTADVIRLMGDKVEAI 122

Query: 121 SLMQDADVPVVPGTTEP-ADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179
             M+ A VP VPG+  P  D  ++   +A + GYPV IKA GGGGGRG++VV +E  +  
Sbjct: 123 RAMKAAGVPCVPGSGGPLGDEVDENIRIAREIGYPVIIKAAGGGGGRGMRVVRTEAHLGN 182

Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239
                K+E +A F N  VY+EK+LE PRH+E+Q+LAD  G+  HLGERDCS+QRRHQKV+
Sbjct: 183 AITMTKQEAKAAFGNDQVYMEKFLENPRHVEIQVLADGQGHAIHLGERDCSMQRRHQKVV 242

Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVT 299
           EEAP+P ++ +LRE+IG+          Y  AGT EFL E+G FYF+E+NTRIQVEH VT
Sbjct: 243 EEAPAPGITPELREQIGKVCVDACLRIGYRGAGTFEFLFENGRFYFIEMNTRIQVEHPVT 302

Query: 300 EEVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDP 359
           E +TG+D+V+ QL +A GE+L   Q+D++I GH++E RINAE P+  F P+ GT+  ++ 
Sbjct: 303 ELITGIDLVREQLLIAGGEKLSIRQEDIKIHGHAIECRINAEDPD-SFLPSPGTVKRFEA 361

Query: 360 PGGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIP 419
           PGG G+R+D  +  G +I  +YDSMI KLIV G DRE  + R   AL E  IEG++  IP
Sbjct: 362 PGGPGVRVDTHLYDGYKIPPNYDSMIGKLIVHGPDRETAIARMRLALAETVIEGVKCNIP 421

Query: 420 FHRLMLTDEAFREGSHTTKYLDEVLDPERIEA 451
             + ++ D  F+ G     YL++ +  ++ +A
Sbjct: 422 LQQRIMADVGFQHGGQNIHYLEKRMAEQKEQA 453


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: 679
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: 458
Length adjustment: 35
Effective length of query: 566
Effective length of database: 423
Effective search space:   239418
Effective search space used:   239418
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