GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Rhizobium leguminosarum bv. trifolii WSM1325

Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_012760746.1 RLEG_RS35160 isovaleryl-CoA dehydrogenase

Query= reanno::Smeli:SM_b21121
         (387 letters)



>NCBI__GCF_000023185.1:WP_012760746.1
          Length = 381

 Score =  543 bits (1400), Expect = e-159
 Identities = 267/378 (70%), Positives = 311/378 (82%)

Query: 7   NFALGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHGG 66
           +F+LGE  DA+R +  RFA++ IAPLA + D SN FP  LW EMG LGL GIT +E  GG
Sbjct: 3   DFSLGETADAIRETTARFAADHIAPLAVEIDESNTFPRQLWPEMGALGLHGITVEEEFGG 62

Query: 67  AGLGYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHVG 126
           AGLGYL H VAMEE+SRASASVGLSYGAHSNLCVNQI R   P QK RYLPKLISGEHVG
Sbjct: 63  AGLGYLDHVVAMEEVSRASASVGLSYGAHSNLCVNQIRRWASPEQKRRYLPKLISGEHVG 122

Query: 127 ALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRGI 186
           +LAMSE GAGSDVVSM+L+A+K+GDRYVLNG+K WITN P ADVLVVYAKTDPAAGP+GI
Sbjct: 123 SLAMSEVGAGSDVVSMRLRAEKKGDRYVLNGTKFWITNAPHADVLVVYAKTDPAAGPKGI 182

Query: 187 TAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLDY 246
           +A ++EK  PGF   +KL KLGMRGS+T+EL+F DC VP E ++G  GEGVK+LMSGLDY
Sbjct: 183 SALIIEKGLPGFGVSKKLSKLGMRGSDTAELVFEDCAVPAEALMGREGEGVKILMSGLDY 242

Query: 247 ERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVYA 306
           ER VL+ GPLGIM ACLDVV+PY+ +RKQFG+ IG+FQLMQGK+ADMYV +N+ARAYVY+
Sbjct: 243 ERAVLAGGPLGIMQACLDVVLPYVRDRKQFGKAIGDFQLMQGKIADMYVALNSARAYVYS 302

Query: 307 VAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLYEI 366
           VA ACD G   R DAA  IL+A+E A  ++LEAIQALGG GYT ++P  R LRDAKLY+I
Sbjct: 303 VARACDAGRATRTDAAAAILFASENAVKVSLEAIQALGGAGYTKEWPVERFLRDAKLYDI 362

Query: 367 GAGTSEIRRMLIGRELFA 384
           GAGT+EIRR LIGREL A
Sbjct: 363 GAGTNEIRRYLIGRELIA 380


Lambda     K      H
   0.318    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: 425
Number of extensions: 14
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: 387
Length of database: 381
Length adjustment: 30
Effective length of query: 357
Effective length of database: 351
Effective search space:   125307
Effective search space used:   125307
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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