GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Marinicella litoralis KMM 3900

Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_099019486.1 CCS90_RS10290 methylcrotonoyl-CoA carboxylase

Query= BRENDA::Q9I297
         (535 letters)



>NCBI__GCF_002591915.1:WP_099019486.1
          Length = 535

 Score =  710 bits (1832), Expect = 0.0
 Identities = 346/535 (64%), Positives = 421/535 (78%)

Query: 1   MAILHTQINPRSAEFAANAATMLEQVNALRTLLGRIHEGGGSAAQARHSARGKLLVRERI 60
           M I+ TQI+  S +F  N   M + V+ L   L +   GG   ++ +H+ RGKLLVR+RI
Sbjct: 1   MKIIKTQIDASSTQFDENRHFMGQLVDDLNLKLTQTSLGGSERSRIKHTDRGKLLVRDRI 60

Query: 61  NRLLDPGSPFLELSALAAHEVYGEEVAAAGIVAGIGRVEGVECMIVGNDATVKGGTYYPL 120
           N LLDPGSPFLE++ +AA  +Y     AAG+V GIG V G + ++V NDATVKGGTY+P+
Sbjct: 61  NLLLDPGSPFLEIAPMAAEGMYQNAAPAAGVVVGIGLVHGQQVVVVANDATVKGGTYFPM 120

Query: 121 TVKKHLRAQAIALENRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSARGIPQ 180
           TVKKHLRAQ +ALEN LPC+YLVDSGGA LP QDEVFPD+EHFGRIF+NQAN+SA+ IPQ
Sbjct: 121 TVKKHLRAQEVALENHLPCVYLVDSGGAFLPLQDEVFPDKEHFGRIFYNQANLSAQNIPQ 180

Query: 181 IAVVMGSCTAGGAYVPAMSDETVMVREQATIFLAGPPLVKAATGEVVSAEELGGADVHCK 240
           IAVVMGSCTAGGAYVPAM DE ++V+EQ TIFL GPPLVKAATGEVV AE LGGA+VH  
Sbjct: 181 IAVVMGSCTAGGAYVPAMCDEAIIVKEQGTIFLGGPPLVKAATGEVVDAESLGGAEVHSS 240

Query: 241 VSGVADHYAEDDDHALAIARRCVANLNWRKQGQLQCRAPRAPLYPAEELYGVIPADSKQP 300
            SGV DH+AE+D HAL +AR  +  LN  K   L+ + PR PLYPA ELYG+IP  ++ P
Sbjct: 241 QSGVTDHFAENDQHALQMARNSLQFLNRPKHNWLERKTPRKPLYPAHELYGIIPQSTRTP 300

Query: 301 YDVREVIARLVDGSEFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360
           Y+V+E+IAR+VDGSEF EFKA +GTTL+CGFAH++GYP+ I+ANNGILFAE+A KGAHF+
Sbjct: 301 YEVKEIIARIVDGSEFQEFKAKYGTTLICGFAHINGYPVGIVANNGILFAESALKGAHFV 360

Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACARVPKFTVLIGGSFGAG 420
           EL  QR IPL+FLQNITGFMVGQKYE  GIAK GAK+VTAVACA+VPKFTV+IGGSFGAG
Sbjct: 361 ELCNQRKIPLVFLQNITGFMVGQKYENAGIAKDGAKMVTAVACAQVPKFTVVIGGSFGAG 420

Query: 421 NYGMCGRAYDPRFLWMWPNARIGVMGGEQAAGVLAQVKREQAERAGQQLGVEEEAKIKAP 480
           NY M GRAY  RFLWMWPNARI VMGG+QAA VL  +K++  +++ Q+   EE+      
Sbjct: 421 NYAMNGRAYQARFLWMWPNARISVMGGDQAASVLTTIKQDGFDQSDQKWDSEEKESFYQN 480

Query: 481 ILEQYEHQGHPYYSSARLWDDGVIDPAQTREVLALALSAALNAPIEPTAFGVFRM 535
           I  QY+ QGHPYYS+ARLWDDGVIDPA TR++L+LA+ A+  A ++   +GVFRM
Sbjct: 481 IKNQYDQQGHPYYSTARLWDDGVIDPADTRQILSLAIEASTCADVKKVQYGVFRM 535


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: 852
Number of extensions: 28
Number of successful extensions: 1
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: 535
Length adjustment: 35
Effective length of query: 500
Effective length of database: 500
Effective search space:   250000
Effective search space used:   250000
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 24 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