GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1693 Cystine ABC
           transporter, periplasmic cystine-binding protein FliY
          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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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