GapMind for catabolism of small carbon sources

 

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

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Pf6N2E2_2409 Methylcrotonyl-CoA carboxylase carboxyl transferase subunit (EC 6.4.1.4)

Query= BRENDA::Q9I297
         (535 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2409
          Length = 538

 Score =  471 bits (1211), Expect = e-137
 Identities = 252/541 (46%), Positives = 342/541 (63%), Gaps = 11/541 (2%)

Query: 1   MAILHTQINPRSAEFAANAATMLEQVNALRTLLGRIHEGGGSAAQARHSARGKLLVRERI 60
           M ++ + ++P  A+F  N A ML  V  LR L   + E    A Q +   RG+L+ R+R+
Sbjct: 1   MPVIESHLDPHCADFTRNHAAMLAGVEQLRQLEQAVLEKAAQA-QGKFDQRGQLMPRQRL 59

Query: 61  NRLLDPGSPFLELSALAAHEVYGEE---VAAAGIVAGIGRVEGVECMIVGNDATVKGGTY 117
           N LLDPG+PFLEL++LA ++++ ++    A  G++AGIG V GV  ++V N++ +KGGT 
Sbjct: 60  NLLLDPGAPFLELASLAGYKLHDDKDGSQAGGGLIAGIGYVSGVRVLVVANNSAIKGGTI 119

Query: 118 YPLTVKKHLRAQAIALENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSARG 177
            P  + K LR Q IA+EN+LP I L +SGGANL    ++F +     R F NQA MSA G
Sbjct: 120 SPSGLYKTLRLQQIAMENKLPVITLAESGGANLNYAAQIFVEG---ARCFANQARMSAMG 176

Query: 178 IPQIAVVMGSCTAGGAYVPAMSDETVMVREQATIFLAGPPLVKAATGEVVSAEELGGADV 237
           +PQI VV GS TAGGAY P +SD  V+VR++A +FLAGPPL+KAATGEV S EELGGA +
Sbjct: 177 LPQITVVHGSATAGGAYQPGLSDYVVVVRDKARLFLAGPPLLKAATGEVASEEELGGAQM 236

Query: 238 HCKVSGVADHYAEDDDHALAIARRCVANLNWRKQGQLQC-RAPRAPLYPAEELYGVIPAD 296
           H +V+G A++ AE+D   + +AR  ++ L W  Q   Q  R+   PLYPA+EL G++P D
Sbjct: 237 HAQVAGTAEYLAENDADGVRLAREILSLLPWNAQLPPQPERSWTEPLYPADELLGLVPDD 296

Query: 297 SKQPYDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKG 356
            K PYDV+E+IAR+ DGS F  FK+ F    +CG  H+ G+   ++ NNG +  + A K 
Sbjct: 297 PKTPYDVQEIIARIADGSNFLAFKSEFDAQTICGHLHIRGHACGLIGNNGPITPQGASKA 356

Query: 357 AHFIELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACARVPKFTVLIGGS 416
           A FI+L  Q   PLLFL N TGFMVG + E  G+ KHGAK++ AVA ARVPK TV++GGS
Sbjct: 357 AQFIQLCDQSRTPLLFLHNTTGFMVGTESERQGVIKHGAKMIQAVANARVPKLTVVVGGS 416

Query: 417 FGAGNYGMCGRAYDPRFLWMWPNARIGVMGGEQAAGVLAQVKREQAERAGQQLGVEEEAK 476
           +GAGNY MCGR  DPRF++ WPN+   VMGG QA  VL  V      + G     +    
Sbjct: 417 YGAGNYAMCGRGLDPRFIFAWPNSHTAVMGGAQAGKVLRMVTEATQIKNGLTPDPKVLDL 476

Query: 477 IKAPILEQYEHQGHPYYSSARLWDDGVIDPAQTREVLALALSAALNA---PIEPTAFGVF 533
           ++    ++ + Q    Y SA LWDDG+IDP  TR +L   L     A   P++  +FGV 
Sbjct: 477 LEQTTAQKLDSQSTALYGSASLWDDGLIDPRDTRTLLGYLLDICHEAEQRPLQANSFGVA 536

Query: 534 R 534
           R
Sbjct: 537 R 537


Lambda     K      H
   0.321    0.137    0.409 

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: 788
Number of extensions: 44
Number of successful extensions: 5
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: 535
Length of database: 538
Length adjustment: 35
Effective length of query: 500
Effective length of database: 503
Effective search space:   251500
Effective search space used:   251500
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 (21.9 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