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

GapMind for catabolism of small carbon sources

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

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate Pf6N2E2_2411 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

Query= reanno::PS:Dsui_0516
         (663 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2411
          Length = 656

 Score =  481 bits (1239), Expect = e-140
 Identities = 296/676 (43%), Positives = 400/676 (59%), Gaps = 40/676 (5%)

Query: 2   FKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61
           F KILIANRGEIACR+ +TA+ +G +TVAV+SEAD DAL V MADEAV IGPAA+++SYL
Sbjct: 4   FSKILIANRGEIACRIQRTAQALGYRTVAVFSEADADALHVRMADEAVLIGPAAAQQSYL 63

Query: 62  VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121
               I+ A ++ GA+A+HPGYGFLSENA F++  E   I FIGP   +I  MG K  +K 
Sbjct: 64  NPSAILDAARRCGADAIHPGYGFLSENAGFAKACEAADIVFIGPSPEAIDLMGSKRRAKI 123

Query: 122 LAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGF 181
             IEA V  I GY  A    D     A +IGYP+MIKASAGGGG+G+R+     +  E  
Sbjct: 124 AMIEAGVPCIAGYQGAAQDDDTLQREAGRIGYPLMIKASAGGGGRGMRLVQRAEDLLEQL 183

Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241
               +EA + FG D + +E+ +++PRH+E+Q+ GD HG  ++L ERDCSIQRRHQKVIEE
Sbjct: 184 RGARSEALHGFGSDELILEQALIDPRHVEVQIFGDHHGQLIHLGERDCSIQRRHQKVIEE 243

Query: 242 APSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVT 301
           AP P +  ++R+AMG+ A+  ARAVNY  AGTVEF+++ A   FYFLEMNTRLQVEHPVT
Sbjct: 244 APCPVMTTDLRRAMGDAALKAARAVNYVGAGTVEFLLA-ADGRFYFLEMNTRLQVEHPVT 302

Query: 302 ELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQP 361
           ELITGLDLV   + VA G  LPL Q  V ++G AM+ R+ AEDP   FLP TGRL+ ++P
Sbjct: 303 ELITGLDLVAWQLDVAAGRSLPLRQEQVTLSGHAMQVRLYAEDPAADFLPQTGRLIGWEP 362

Query: 362 PAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSN 421
           P++ DG VR+D G+ +G  I+ +YDSM+ KLIVHGA+RE+A  ++  A+   V+ G+ SN
Sbjct: 363 PSQ-DG-VRIDHGLLEGQAITPFYDSMLGKLIVHGATREEARRKLLRAVEDCVLLGVQSN 420

Query: 422 IPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPA--LLIGVAAFVHRRYIDR 479
                 L+ H RF  G F  GFI + +     A++ P +  A  L I  AAF    Y   
Sbjct: 421 QRLLTGLLAHPRFIDGDFGNGFIGQHFAD--HAALRPLEPSAEQLAIATAAF----YQAS 474

Query: 480 AAQVSGQLPGHERKVGDEWVVIRN----GERHPVVAKPIE--GGYLVTYNGEKYELLSDW 533
            A+ +  L G    +G   VV+      GE    ++   E  G + +   G   EL    
Sbjct: 475 QARHAQGLGGWRNSIG---VVLHYRIGVGEHDWTLSLVAEADGTFNIRSAGRLIEL---- 527

Query: 534 RQGQSLFNGTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDL 593
                L +   +G    +   R R  ++L       D+ + +      L L     AP  
Sbjct: 528 ----RLLDAAPHGATLVIDGIRRRHAWRL----DGNDLWLFTCPGG--LHLQDRTLAPIA 577

Query: 594 SK------FLLSPMPGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISV 647
           +K       L +PM G + E+ V  G  V  G+ L V+EAMKME+ LKA  D  V  + V
Sbjct: 578 AKTSASDGTLKAPMDGAIVELRVREGSTVHQGQLLMVLEAMKMEHPLKAGVDGVVTHLQV 637

Query: 648 TAGSSLSVDEIIIEFE 663
             G  +   ++++  E
Sbjct: 638 ARGDQVKKRQVLLRVE 653


Lambda     K      H
   0.319    0.135    0.391 

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: 1025
Number of extensions: 44
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 663
Length of database: 656
Length adjustment: 38
Effective length of query: 625
Effective length of database: 618
Effective search space:   386250
Effective search space used:   386250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources