GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2555 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate Pf1N1B4_1693 Cystine ABC transporter, periplasmic cystine-binding protein FliY

Query= reanno::acidovorax_3H11:Ac3H11_2555
         (249 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1693
          Length = 264

 Score =  158 bits (399), Expect = 1e-43
 Identities = 98/254 (38%), Positives = 136/254 (53%), Gaps = 12/254 (4%)

Query: 3   LRRNLLLASLAAAAFC------TTGAQAQD----NVLRVGTDATFPPMEFV-ENGKRTGF 51
           LRRNLL+ SL  A           G Q Q      V+ VG + T+PP  FV E GK +GF
Sbjct: 6   LRRNLLVGSLGLALSAGLLGQAVAGEQLQKIKDAGVINVGLEGTYPPFSFVDEAGKLSGF 65

Query: 52  DIELVEAIAKTMGKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYA 111
           ++E  EA+AK +G +V+     ++G++  L SKR D  ++ + IT+ERKK  DF+  Y  
Sbjct: 66  EVEFSEALAKELGVKVKLQPTKWEGILAALESKRLDAVINQVTITEERKKKYDFSTPYTV 125

Query: 112 GGLVVMVKADNK-AINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLV 170
            G+  +    NK  I   ADL GKKV V +GT    ++ E  PK      E +   F  +
Sbjct: 126 SGIQALTLTKNKDTIKTAADLAGKKVGVGLGTNYEQWVKENVPKADVRTYEDDPSKFQDL 185

Query: 171 DIGRADAAVTGKPAAFQYVRTRPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLK 230
            +GR DA +  + AA +Y R         E  + +E G+ALRK  PEL  AVN AI KL+
Sbjct: 186 RVGRIDAILIDRLAALEYARKAKDTAAAGEAFSRQEAGIALRKGEPELLAAVNKAIDKLR 245

Query: 231 ADGTYAAIVKKWFS 244
           ADGT   + +K+FS
Sbjct: 246 ADGTLKKLSEKYFS 259


Lambda     K      H
   0.317    0.133    0.369 

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: 157
Number of extensions: 8
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: 249
Length of database: 264
Length adjustment: 24
Effective length of query: 225
Effective length of database: 240
Effective search space:    54000
Effective search space used:    54000
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: 47 (22.7 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