GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Pseudomonas fluorescens FW300-N2E2

Align propionyl-CoA carboxylase (subunit 1/2) (EC 6.4.1.3) (characterized)
to candidate Pf6N2E2_2194 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

Query= BRENDA::P05165
         (728 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2194
          Length = 649

 Score =  498 bits (1281), Expect = e-145
 Identities = 284/668 (42%), Positives = 402/668 (60%), Gaps = 33/668 (4%)

Query: 66  ILVANRGEIACRVIRTCKKMGIKTVAIHSDVDASSVHVKMADEAVCVGPAPTSKSYLNMD 125
           +LVANRGEIACRV+RT K MG+ TVA+HS  D  + H + AD  V +G +  + SYL +D
Sbjct: 9   LLVANRGEIACRVMRTAKAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68

Query: 126 AIMEAIKKTRAQAVHPGYGFLSENKEFARCLAAEDVVFIGPDTHAIQAMGDKIESKLLAK 185
            ++ A K + AQA+HPGYGFLSEN  FAR +    ++F+GP   AI AMG K  +K L +
Sbjct: 69  KLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAAKALME 128

Query: 186 KAEVNTIPGFDGVVKDAEEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGFRLS 245
            A V  +PG+ G  +D E     A  IGYPV++KA+AGGGGKGM++  D  +  +    +
Sbjct: 129 TAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188

Query: 246 SQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHGNALWLNERECSIQRRNQKVVEEAPS 305
            +EA SSFGD R+L+EK++  PRH+EIQV  D+HGN L+LNER+CSIQRR+QKVVEEAP+
Sbjct: 189 QREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248

Query: 306 IFLDAETRRAMGEQAVALARAVKYSSAGTVEFLVDSKKNFYFLEMNTRLQVEHPVTECIT 365
             L A+ R+AMGE AV  A+A+ Y  AGTVEFL+D++  F+F+EMNTRLQVEHPVTE IT
Sbjct: 249 PGLTAQLRQAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 308

Query: 366 GLDLVQEMIRVAKGYPLRHKQADIRINGWAVECRVYAEDPYKSFGLPSIGRLSQYQEPLH 425
           GLDLV   IRVA+G PL   QA + + G A+E R+YAEDP   F LP+ GRL+ Y+E   
Sbjct: 309 GLDLVAWQIRVAQGEPLPITQAQVPLLGHAIEVRLYAEDPVNDF-LPATGRLALYRESAK 367

Query: 426 LPGVRVDSGIQPGSDISIYYDPMISKLITYGSDRTEALKRMADALDNYVIRGVTHNIALL 485
            PG RVDSG++ G +IS +YDPM+ KLI +G +R +A  R+   LD + I G+  NI  L
Sbjct: 368 GPGRRVDSGVEEGDEISPFYDPMLGKLIAWGENREQARLRLLSMLDEFAIGGLKTNIGFL 427

Query: 486 REVIINSRFVKGDISTKFLSDVYPDGFKGHMLTKSEKNQLLAIASSLFVAFQLRAQHFQE 545
           R ++ +  F   ++ T F+                 + QLL     L  AF L A     
Sbjct: 428 RRIVAHPAFAAAELDTGFI--------------PRYQAQLLPEPGELDDAFWLAAAQGFA 473

Query: 546 NSRMPVIKPDIAN--WELSVKLH---DKVHTVVASNNGSVFSVEVDGSKLNVTSTWNLAS 600
            S  P I+ D A   W  +  +     +  T+  S  G   ++ +D +         L  
Sbjct: 474 LSLAPHIRGDDAGSPWASTTGMRLGLSRETTLHLSCEGQDRALTLDVT----AHCAELKG 529

Query: 601 PLLSVSVDGTQRTVQCLSREAGGNMSIQFLGTVYKVNILTRLAAELNKFMLEKVTEDTSS 660
             L++   G +R+ + + +  G ++ + + G ++++++   LAA        + +     
Sbjct: 530 ERLTIEHHGVRRSHRAIRQ--GDSLYLHWAGDLHRIDLYDPLAA-------AEASHSHQG 580

Query: 661 VLRSPMPGVVVAVSVKPGDAVAEGQEICVIEAMKMQNSMTAGKTGTVKSVHCQAGDTVGE 720
            L +PM G +V V V  G  V  G ++ V+EAMKM++S+ A K G +K+++CQ G+ V E
Sbjct: 581 GLAAPMNGSIVRVLVSVGQPVDAGAQLVVLEAMKMEHSIRAPKAGVIKALYCQEGEMVSE 640

Query: 721 GDLLVELE 728
           G  LV  E
Sbjct: 641 GSALVAFE 648


Lambda     K      H
   0.318    0.134    0.385 

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: 1039
Number of extensions: 35
Number of successful extensions: 4
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: 728
Length of database: 649
Length adjustment: 39
Effective length of query: 689
Effective length of database: 610
Effective search space:   420290
Effective search space used:   420290
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 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