GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutX in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for L-Histidine, periplasmic substrate-binding component (characterized)
to candidate AO356_23245 AO356_23245 ABC transporter substrate-binding protein

Query= reanno::pseudo5_N2C3_1:AO356_09620
         (322 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23245
          Length = 336

 Score =  319 bits (817), Expect = 7e-92
 Identities = 152/308 (49%), Positives = 206/308 (66%), Gaps = 19/308 (6%)

Query: 34  PVKFAGLNWESGMLLTDVLQVVLEKGYDCKTDSLPGNSITMENALSSNDIQVFAEEWVGR 93
           P+ FA LNWESG L+TD+L+V++EKGY  +TD+LPG +IT+E AL++NDIQV  EEW GR
Sbjct: 29  PIHFADLNWESGSLITDILRVIVEKGYGLQTDTLPGTTITLETALANNDIQVIGEEWAGR 88

Query: 94  SEVWNKAEKAGKVVGVGAPVVGAIEGWYVPRYVVEGDAKRKLEAKAPGLKNIADLGQYAA 153
           S VW KAE  GKVV +G  V GA EGW+VP YV++GD  + ++  AP L+++ DL +Y  
Sbjct: 89  SPVWVKAEAEGKVVALGDTVKGATEGWWVPEYVIKGDPAKGIKPLAPDLRSVEDLARYKH 148

Query: 154 VFKDPEEPSKGRFYNCPAGWTCELDNSEMLKSYGLEKTYTNFRPGTGPALDAAVLSSYKR 213
           VFKDPE P KGRF N P GWT E+ N + LK+YGL  +Y NFR G+G ALDA + S+ +R
Sbjct: 149 VFKDPESPDKGRFLNSPIGWTSEVVNKQKLKAYGLSDSYVNFRSGSGAALDAEISSTIRR 208

Query: 214 GEPILFYYWSPTPLMGQVDLVKLEE-------------------KPGVDKSVSIKVGLSK 254
           G+PILFYYWSPTPL+G+  LV+L+E                   KP    +  + +G+S 
Sbjct: 209 GKPILFYYWSPTPLLGRFKLVQLQEPPFDAEAWKTLTDADNPNPKPTRSLASKLSIGVSA 268

Query: 255 TFHDEAPELVAVLEKVNLPIDILNQNLGRMAKERIESPKLAKIFLKEHPEVWHAWVSEDA 314
            F  + PE+     KV+LPI+ LN+ L  M+++R    + A+ FLK HPEVW AW+ ++ 
Sbjct: 269 PFQKQYPEIAEFFSKVDLPIEPLNKTLADMSEKRTPPREAAEAFLKAHPEVWQAWLPKEV 328

Query: 315 AKKIDAAL 322
           A K+ A L
Sbjct: 329 ADKVSAGL 336


Lambda     K      H
   0.314    0.133    0.398 

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: 325
Number of extensions: 10
Number of successful extensions: 2
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: 322
Length of database: 336
Length adjustment: 28
Effective length of query: 294
Effective length of database: 308
Effective search space:    90552
Effective search space used:    90552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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