GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fahA in Sinorhizobium meliloti 1021

Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate SMc03207 SMc03207 aromatic amino acid degradation protein

Query= reanno::psRCH2:GFF3447
         (327 letters)



>FitnessBrowser__Smeli:SMc03207
          Length = 338

 Score =  417 bits (1072), Expect = e-121
 Identities = 220/339 (64%), Positives = 255/339 (75%), Gaps = 18/339 (5%)

Query: 1   MKLATLNQG-RDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGL 59
           MKLATL    RDG LVVVS+DL +  +V  IA TLQAALDDW +  P+LE    R+ +G+
Sbjct: 1   MKLATLKDSTRDGKLVVVSKDLTRCSEVGHIARTLQAALDDWAHAGPRLE----RVAEGI 56

Query: 60  EEGA---FAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGG 116
           E GA     F +    SPLPRA+ WADGSAYVNHVELVRKAR AEMP SFW DPL+YQGG
Sbjct: 57  ETGAQPTMRFHEHDAASPLPRAFQWADGSAYVNHVELVRKARNAEMPASFWTDPLIYQGG 116

Query: 117 ADAFIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNL 176
           +D+F+ P  PI +AD+AWGID+EGE AVI DDVPMGAT  EA + I+L+MLVNDVSLR L
Sbjct: 117 SDSFLGPRDPILMADDAWGIDMEGEAAVIVDDVPMGATLDEAKAAIRLVMLVNDVSLRGL 176

Query: 177 IPGELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTD 236
           IPGELAKGFGFYQSKPSS+FSPVAVTP+ELGE W  GK+H PL   +NGE FG+ +AG D
Sbjct: 177 IPGELAKGFGFYQSKPSSAFSPVAVTPEELGEAWDGGKLHLPLHVDLNGEPFGRANAGID 236

Query: 237 MTFNFPTLVAHAARTRPLGAGTIIGSGTVSN----------YDRSAGSSCLAEKRMLEVV 286
           MTF+FP L+ HAARTRPL AGTIIGSGTVSN           +  AG SC+AE RM+E +
Sbjct: 237 MTFDFPQLIVHAARTRPLSAGTIIGSGTVSNKLEGGPGRPVSEGGAGYSCIAELRMIETI 296

Query: 287 EHGEAKTPFLKFGDRVRIEMFDAAGQSIFGAIDQQVERY 325
           E G  KT FLKFGD VRIEM D  G SIFGAI+Q+V +Y
Sbjct: 297 EGGAPKTQFLKFGDVVRIEMKDRTGHSIFGAIEQKVGKY 335


Lambda     K      H
   0.318    0.135    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: 413
Number of extensions: 21
Number of successful extensions: 3
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: 327
Length of database: 338
Length adjustment: 28
Effective length of query: 299
Effective length of database: 310
Effective search space:    92690
Effective search space used:    92690
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 (21.7 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