GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Cupriavidus basilensis 4G11

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate RR42_RS01335 RR42_RS01335 methylmalonyl-CoA carboxyltransferase

Query= reanno::pseudo6_N2E2:Pf6N2E2_2192
         (535 letters)



>FitnessBrowser__Cup4G11:RR42_RS01335
          Length = 515

 Score =  181 bits (458), Expect = 8e-50
 Identities = 157/522 (30%), Positives = 255/522 (48%), Gaps = 54/522 (10%)

Query: 38  QGGGPKAQERHTSRGKLLPRERINRLLDPGSPFLEISPLAAHEVYGED-----VPAAGVI 92
           Q GGP   +RH   GKL  RERI+ + D GS F E+  L     Y  +     +  A ++
Sbjct: 19  QLGGPDKVKRHKDAGKLTVRERIDAIADAGS-FREVGALTGSGQYDSNGRLVGLTPANLV 77

Query: 93  AGIGRVEGVECMIVANDATVKGGSYYPLTVKKHLRAQTIAQQNRLPCIYLVD-SGGANLP 151
            G  +V+G   ++V +D TV+GG+      +K + A+ +A   RLP + LVD +GG    
Sbjct: 78  MGRAKVDGRPVVLVGDDFTVRGGANDGAVGEKLIHAEKMAHDLRLPMVRLVDGTGGGGSV 137

Query: 152 RQDEV-----FPDREHFGRIFFNQANMSAQGIPQIAVVMGSCTAGGAYVPAMADEAIMVR 206
           R  E       P  + +  +     NMS   +P +++ +GS    GA   A +  ++MV+
Sbjct: 138 RNIENKGYTNIPTMKVWQHVV---ENMSL--VPVVSLALGSVAGMGAARVAASHYSVMVK 192

Query: 207 QQATIFLAGPPLVKAATGEVVSAEDLGGADVHCKISGVADHYADSDEHALALARRSVANL 266
             A +F AGPP+V A  G+V+   +LGG+ +H + +GV D    S+E A A ARR ++ L
Sbjct: 193 GTAQLFNAGPPVV-ARIGQVLEKNELGGSQIHTR-NGVVDDEVASEEEAFARARRFLSYL 250

Query: 267 NWRKQGELQHRLPIA------PLYSGEELYGVVSADAKQPFDVREVIARLVDGSVFDEFK 320
                G + H LP        P    E L   +  D++  + VR ++  LVD   F E  
Sbjct: 251 ----PGSV-HELPPRVEPTDDPARRDEWLLSAIPRDSRSVYKVRPIVETLVDQGSFFEMG 305

Query: 321 ALFGTTLVCGFAHLHGYPIAILANNGILFA-----EAAQKGAHFIELACQRGIPLLFLQN 375
             +G  +V G A + G+P+A++A++   +        A+K   F++LA    +P++ + +
Sbjct: 306 RHWGRAIVTGLARVDGWPVAVVASDPYHYGGGWDGPTAEKFIRFVDLAEAFHLPVINMVD 365

Query: 376 ITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFG--AGNYGMCGRAYDPRF 433
           I GF +G + E  G  ++G + + AV  A  P  +VI+  ++G  A  +   GR     F
Sbjct: 366 IAGFQIGLEAEKAGTMRYGVRALAAVYQATTPWCSVILRRAYGVAAAGHQHMGRF---NF 422

Query: 434 LWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQPILDQYEEQGHPYY 493
            + WP+   G +  E   G+ V  K   AE  G     ++ AEI+Q +         P+ 
Sbjct: 423 RYAWPSGNWGSLPIE--GGLEVAYK---AEIEGADDPVQKRAEIEQRV----RSLTSPFR 473

Query: 494 SSARLWDDGVIDPAQTRDVLGLALSASLNAPI-EPS--RFGV 532
           S+     + +IDP  TR +  L   A+L AP+ EP   +FG+
Sbjct: 474 SAEAFVVEDIIDPRDTRSL--LCEFANLAAPLREPGVRKFGI 513


Lambda     K      H
   0.321    0.137    0.411 

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: 722
Number of extensions: 39
Number of successful extensions: 8
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: 515
Length adjustment: 35
Effective length of query: 500
Effective length of database: 480
Effective search space:   240000
Effective search space used:   240000
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 (21.8 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