GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Herbaspirillum seropedicae SmR1

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate HSERO_RS01420 HSERO_RS01420 serine/threonine dehydratase

Query= BRENDA::Q74FW6
         (402 letters)



>FitnessBrowser__HerbieS:HSERO_RS01420
          Length = 326

 Score =  226 bits (577), Expect = 6e-64
 Identities = 127/301 (42%), Positives = 177/301 (58%), Gaps = 4/301 (1%)

Query: 10  ADDRLRKRVRRTELIHSHHFSEKLGIPIYFKCENLQRTGAFKIRGALNFMTSQPREALAK 69
           A +R++    RT ++ S     +LG  ++FKCEN QR GAFK RGA+N +T         
Sbjct: 19  AAERIKPWAHRTPVLRSRTADTELGAQLFFKCENFQRMGAFKFRGAMNALTQFDATQRKH 78

Query: 70  GVITASAGNHAQGVAFSADLLGVPSTVFMPESTPPQKVFATRDYGAEVVLTGRNFDEAYA 129
           GVIT S+GNHAQG A +A LLG+P+ + MP+  P  KV ATR YGAEVV   R  ++  A
Sbjct: 79  GVITFSSGNHAQGTALAAQLLGIPAVIVMPQDAPAAKVAATRGYGAEVVTYDRYTEDREA 138

Query: 130 AAVQAQEERGALFVHPFDDPLVMAGQGTIGLEVLQELPDVANILVPIGGGGLIAGIATAI 189
              +   ER    + P+D P VMAGQGT  LE+LQE   +  + V +GGGGL++G A A 
Sbjct: 139 IGARLAAERKMTLIPPYDHPHVMAGQGTATLELLQETGPLDALFVCLGGGGLLSGAALAA 198

Query: 190 RETHPHVRIIGVETAAAPSAHYSLQKGKIVQVPVTVTLADGIAVKKPGVNTFPIIRDLVD 249
           R   P  +I GVE  A      SL+ G++V +    T+ADG   +  G  TF +IR+LVD
Sbjct: 199 RALSPACKIYGVEPQAGNDGQQSLRAGQVVHIDTPKTIADGAQTQHLGKYTFGVIRELVD 258

Query: 250 EVVLVEEEEIALAIVALLERTKLLVEGAGAVPLAALLNRRVTD-LSGKTV-CVLSGGNID 307
           ++  V +EE+   +    ER K++VE  G +  AA   R++ D L GK V  ++SGGN+D
Sbjct: 259 DIHTVSDEELVAGMRFFAERMKMVVEPTGCLGFAAA--RKLKDQLQGKRVGVIISGGNVD 316

Query: 308 V 308
           +
Sbjct: 317 L 317


Lambda     K      H
   0.319    0.137    0.383 

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: 277
Number of extensions: 12
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: 402
Length of database: 326
Length adjustment: 29
Effective length of query: 373
Effective length of database: 297
Effective search space:   110781
Effective search space used:   110781
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: 49 (23.5 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